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Articles in press have been peer-reviewed and accepted, which are not yet assigned to volumes/issues, but are citable by Digital Object Identifier (DOI).
On the Calculation of TCID50 for Quantitation of Virus Infectivity
Chengfeng Lei, Jian Yang, Jia Hu, Xiulian Sun
doi: 10.1007/s12250-020-00230-5
Received: 10 March 2020 Published: 26 May 2020
Abstract PDF Springerlink ESM
The most important property of a virus is its infectivity. To measure infectivity, one can assay viral replication in cells to obtain a titer for a given virus stock. A titer is defined as a given number of infectious viral units per unit volume, and an infectious unit is the smallest amount of virus that produces recognizable effects [e.g., cytopathic effect (CPE), dot blot immunoreactivity]. The median tissue culture infectious dose (TCID50) is defined as the dilution of a virus required to infect 50% of a given cell culture.
First Fatal Infection and Phylodynamic Analysis of Severe Fever with Thrombocytopenia Syndrome Virus in Jilin Province, Northeastern China
Xu Zhang, Nina Wang, Zedong Wang, Lihe Che, Chen Chen, Wen-Zhong Zhao, Quan Liu
doi: 10.1007/s12250-020-00228-z
Received: 30 October 2019 Published: 26 May 2020
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Severe fever with thrombocytopenia syndrome (SFTS), caused by SFTS virus (SFTSV) in the genus Banyangvirus of the family Phenuiviridae, is an emerging tick-borne viral zoonosis (Liu et al. 2014). Typical clinical symptoms of SFTS include fever, headache, thrombocytopenia, and leukocytopenia (Yu et al. 2011). Since SFTSV was identified in 2009, it has been found in more than 20 provinces in China and is closely related to strains from Japan and South Korea (Kim et al. 2013; Takahashi et al. 2014). In Northeastern China, the disease was discovered in Liaoning Province in 2010 (Wang et al. 2016), and the virus was detected in Haemaphysalis longicornis in Jilin Province in 2013 (Liu et al. 2016). Here we describe the first fatal case of SFTS in Jilin Province and conduct phylodynamic analysis of SFTSV.
Construction and Characterization of a Novel Recombinant Attenuated and Replication-Deficient Candidate Human Adenovirus Type 3 Vaccine: “Adenovirus Vaccine Within an Adenovirus Vector”
Yuqian Yan, Shuping Jing, Liqiang Feng, Jing Zhang, Zhiwei Zeng, Min Li, Shan Zhao, Junxian Ou, Wendong Lan, Wenyi Guan, Xiaowei Wu, Jianguo Wu, Donald Seto, Qiwei Zhang
doi: 10.1007/s12250-020-00234-1
Received: 22 February 2020 Published: 26 May 2020
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Human adenoviruses (HAdVs) are highly contagious and result in large number of acute respiratory disease (ARD) cases with severe morbidity and mortality. Human adenovirus type 3 (HAdV-3) is the most common type that causes ARD outbreaks in Asia, Europe, andtheAmericas.However, there is currently no vaccine approvedfor its general use.The hexon protein contains themain neutralizing epitopes, provoking strong and lasting immunogenicity. In this study, a novel recombinant and attenuated adenovirus vaccine candidate against HAdV-3 was constructed based on a commercially-available replication-defective HAdV-5 gene therapy and vaccine vector. The entire HAdV-3 hexon gene was integrated into the E1 region of the vector by homologous recombination using a bacterial system. Theresultantrecombinants expressing the HAdV-3 hexon protein were rescued in AD293 cells, identified and characterized by RT-PCR, Western blots, indirect immunofluorescence, and electron microscopy. This potential vaccine candidate had a similar replicative efficacy as the wild-type HAdV-3 strain. However, and importantly, the vaccine strain had been rendered replication-defective and was incapable of replication in A549 cells after more than twenty-generation passages in AD293 cells. This represents a significant safety feature. The mice immunized both intranasally and intramuscularly by this vaccine candidate raised significant neutralizing antibodies against HAdV-3. Therefore, this recombinant, attenuated, and safe adenovirus vaccine is a promising HAdV-3 vaccine candidate. The strategy of using a clinically approved and replication-defective HAdV-5 vector provides a novel approach to develop universal adenovirus vaccine candidates against all the other types of adenoviruses causing ARDs and perhaps other adenovirus-associated diseases.
Establishment of Murine Infection Models with Biological Clones of Dengue Viruses Derived from a Single Clinical Viral Isolate
Zhihang Zheng, Min Li, Zhihua Liu, Xia Jin, Jin Sun
doi: 10.1007/s12250-020-00229-y
Received: 09 November 2019 Published: 25 May 2020
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Dengue virus (DENV) is a single-stranded RNA virus transmitted by mosquitoes in tropical and subtropical regions. It causes dengue fever, dengue hemorrhagic fever and dengue shock syndrome in patients. Each year, 390 million people are estimated to be infected by four serotypes of dengue virus, creating a great burden on global public health and local economy. So far, no antiviral drug is available for dengue disease, and the newly licensed vaccine is far from satisfactory. One large obstacle for dengue vaccine and drug development is the lack of suitable small animal models. Although some DENV infection models have been developed, only a small number of viral strains can infect immunodeficient mice. In this study, with biologically cloned viruses from a single clinical isolate, we have established two mouse models of DENV infection, one is severe lethal infection in immunocompromised mice, and the other resembles self-limited disease manifestations in Balb/c mice with transient blockage of type I IFN responses. This study not only offers new small animal models of dengue viral infection, but also provides new viral variants for further investigations on dengue viral pathogenesis.
Recombination of T4-like Phages and Its Activity against Pathogenic Escherichia coli in Planktonic and Biofilm Forms
Min Li, Donglin Shi, Yanxiu Li, Yuyi Xiao, Mianmian Chen, Liang Chen, Hong Du, Wei Zhang
doi: 10.1007/s12250-020-00233-2
Received: 09 October 2019 Published: 25 May 2020
Abstract PDF Springerlink ESM
The increasing emergence of multi-drug resistant Escherichia coli (E. coli) has become a global concern, primarily due to the limitation of antimicrobial treatment options. Phage therapy has been considered as a promising alternative for treating infections caused by multi-drug resistant E. coli. However, the application of phages as a promising antimicrobial agent is limited by their narrow host range and specificity. In this research, a recombinant T4-like phage, named WGqlae, has been obtained by changing the receptor specificity determinant region of gene 37, using a homologous recombination platform of T4-like phages established by our laboratory previously. The engineered phage WGqlae can lyse four additional hosts, comparing to its parental phages WG01 and QL01. WGqlae showed similar characteristics, including thermo and pH stability, optimal multiplicity of infection and one-step growth curve, to the donor phage QL01. In addition, sequencing results showed that gene 37 of recombinant phage WGqlae had genetically stable even after 20 generations. In planktonic test, phage WGqlae had significant antimicrobial effects on E. coli DE192 and DE205B. The optical density at 600 nm (OD600) of E. coli in phage WGqlae treating group was significantly lower than that of the control group (P < 0.01). Besides, phage WGqlae demonstrated an obvious inhibitory effect on the biofilm formation and the clearance of mature biofilms. Our study suggested that engineered phages may be promising candidates for future phage therapy applications against pathogenic E. coli in planktonic and biofilm forms.
A DNA Aptamer Based Method for Detection of SARS-CoV-2 Nucleocapsid Protein
Zhiqiang Chen, Qihan Wu, Jing Chen, Xiaohua Ni, Jianfeng Dai
doi: 10.1007/s12250-020-00236-z
Received: 16 April 2020 Published: 25 May 2020
Abstract PDF Springerlink ESM
Since December 2019, the outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induced human disease, the coronavirus disease 2019 (COVID-19), has been reported in more than 200 countries and areas around the world (Wu et al. 2020). By May 13, there are 4,098,018 confirmed cases with 283,271 deaths according to the World Health Organization (WHO) report, and the numbers are keeping growing fast. Rapid and accurate diagnosis of suspected cases, effective isolation of infected patients and active treatments are the most important procedures for epidemic prevention and control.
Depletion but Activation of CD56dimCD16+ NK Cells in Acute Infection with Severe Fever with Thrombocytopenia Syndrome Virus
Mengmeng Li, Yan Xiong, Mingyue Li, Wenjing Zhang, Jia Liu, Yanfang Zhang, Shue Xiong, Congcong Zou, Boyun Liang, Mengji Lu, Dongliang Yang, Cheng Peng, Xin Zheng
doi: 10.1007/s12250-020-00224-3
Received: 11 August 2019 Published: 19 May 2020
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Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease with high mortality (12%–30%). The mechanism by which the SFTS bunyavirus (SFTSV) causes severe illness remains unclear. To evaluate the phenotypic and functional characteristics of the NK cell subsets in SFTS patients, twenty-nine SFTS patients were sequentially sampled from admission until recovery. Phenotypic and functional characteristics of NK cell subsets in circulating blood were analysed via flow cytometry. Then, correlations between NK cell subset frequencies and the SFTS index (SFTSI) were evaluated in all SFTS patients (15 mild, 14 severe) upon admission. The frequencies of CD56dimCD16+ NK cells were greatly decreased in early SFTSV infection and were negatively correlated with disease severity. Additionally, higher Ki-67 and granzyme B expression and relatively lower NKG2A expression in CD56dimCD16+ NK cells were observed in acute infection. Moreover, the effector function of CD56dim NK cells was increased in the acute phase compared with the recovery phase in nine severe SFTS patients. Additionally, interleukin (IL)-15, interferon (IFN)-α, IL-18 and IFN-γ secretion was markedly increased during early infection. Collectively, despite depletion of CD56dimCD16+ NK cells, activation and functional enhancement of CD56dimCD16+ NK cells were still observed, suggesting their involvement in defence against early SFTSV infection.
Myristoylation of EV71 VP4 is Essential for Infectivity and Interaction with Membrane Structure
Jiaming Cao, Meng Qu, Hongtao Liu, Xuan Wan, Fang Li, Ali Hou, Yan Zhou, Bo Sun, Linjun Cai, Weiheng Su, Chunlai Jiang
doi: 10.1007/s12250-020-00226-1
Received: 12 December 2019 Published: 12 May 2020
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The Enterovirus 71 (EV71) VP4 is co-translationally linked to myristic acid at its amino-terminal glycine residue. However, the role of this myristoylation in the EV71 life cycle remains largely unknown. To investigate this issue, we developed a myristoylation-deficient virus and reporter (luciferase) pseudovirus with a Gly-to-Ala mutation (G2A) on EV71 VP4. When transfecting the EV71-G2A genome encoding plasmid in cells, the loss of myristoylation on VP4 did not affect the expression of viral proteins and the virus morphology, however, it did significantly influence viral infectivity. Further, in myristoylation-deficient reporter pseudovirus-infected cells, the luciferase activity and viral genome RNA decreased significantly as compared to that of wild type virus; however, cytopathic effect and viral capsid proteins were not detected in myristoylation-deficient virus-infected cells. Also, although myristoylation-deficient viral RNA and proteins were detected in the second blind passage of infection, they were much fewer in number compared to that of the wild type virus. The replication of genomic RNA and negative-strand viral RNA were both blocked in myristoylation-deficient viruses, suggesting that myristoylation affects viral genome RNA release from capsid to cytoplasm. Besides, loss of myristoylation on VP4 altered the distribution of VP4-green fluorescent protein protein, which disappeared from the membrane structure fraction. Finally, a liposome leakage assay showed that EV71 myristoylation mediates the permeability of the model membrane. Hence, the amino-terminal myristoylation of VP4 is pivotal to EV71 infection and capsidmembrane structure interaction. This study provides novel molecular mechanisms regarding EV71 infection and potential molecular targets for antiviral drug design.
Molecular Epidemiology and Vaccine Compatibility Analysis of Seasonal Influenza Viruses in Wuhan, 2016–2019
Liang-Jun Chen, Jing-Jing Guo, Wei-Wei Guo, E-Xiang Shen, Xin Wang, Kai-Ji Li, Jie Yan, Mang Shi, Yi-Rong Li, Wei Hou
doi: 10.1007/s12250-020-00225-2
Received: 15 December 2019 Published: 11 May 2020
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Influenza viruses (FLUV) cause high morbidity and mortality annually in the world and pose a serious threat to the public health. Wuhan, as an important transportation hub in China, has a dense population and suitable climate, which also lays a major hidden danger for the outbreak of influenza. To survey and characterize the seasonal FLUV in Wuhan during 2016–2019, we collected 44,738 throat swabs, among which 15.5% were influenza A (FLUAV) positive, 6.1% influenza B (FLUBV) and 0.3% co-infection. By monitoring FLUV in each month from June 2016 to May 2019, different with the previously seasonality pattern, only a single influenza peak was appeared in winter of 2017–2018 and 2018–2019, respectively. These data indicated that the complex circulation pattern of seasonal influenza in Wuhan. In addition, we found the age group was skewed towards 5–14 years group whose activity were mostly school based, which suggested school may be an important place for influenza outbreaks. Meanwhile, phylogenic analysis revealed that two subtypes (subclade 3C.2a2 and 3C.2a1b) of A(H3N2) were circulating in Wuhan and there was an obvious transition in 2018 because the two subclades were detected simultaneously. Furthermore, by estimating the vaccine effectiveness, we found that the vaccine strain of FLUAV didn’t seem to match very well the current epidemic strain, especially A(H3N2). Hence, more accurate prediction of seasonal outbreak is essential for vaccine design. Taken together, our results provided the current information about seasonal FLUV in Wuhan which form the basis for vaccine updating.
Phylogeography of Highly Pathogenic H5 Avian Influenza Viruses in China
Xiaowen Li, Xueying Li, Bing Xu
doi: 10.1007/s12250-020-00193-7
Received: 26 May 2019 Published: 08 May 2020
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The spread of H5 highly pathogenic avian influenza viruses poses serious threats to the poultry industry, wild bird ecology and human health. Circulation of H5 viruses between poultry and wild birds is a significant public health threat in China. Thus, viral migration networks in this region need to be urgently studied. Here, we conducted molecular genetic analyses of the hemagglutinin genes of H5 highly pathogenic avian influenza viruses in multiple hosts from 2000 to 2018 in China. Our aim was to clarify the roles of different hosts in the evolution of H5 viruses. We used a flexible Bayesian statistical framework to simulate viral space diffusion and continuous-time Markov chains to infer the dynamic evolutionary process of spatiotemporal dissemination. Bayesian phylogeographic analysis of H5 viruses showed for the first time that H5 viruses in poultry and wild birds were present in Guangdong Province. Furthermore, Guangdong, Jiangsu, Shanghai and Hunan acted as the epicenters for the spread of various H5 subtypes viruses in poultry, and Henan, Shanghai, Hong Kong and Inner Mongolia acted as epicenters for the spread of various H5 subtypes viruses in wild birds. Thus, H5 viruses exhibited distinct evolutionary dynamics in poultry and wild birds. Our findings extend our understanding of the transmission and spread of highly pathogenic H5 avian influenza viruses in China.
A Comprehensive Review on Human Aichi Virus
Enrique Rivadulla, Jesús L. Romalde
doi: 10.1007/s12250-020-00222-5
Received: 21 September 2019 Published: 27 April 2020
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Although norovirus, rotavirus, adenovirus and Astrovirus are considered the most important viral agents transmitted by food and water, in recent years other viruses, such as Aichi virus (AiV), have emerged as responsible for gastroenteritis outbreaks associated with different foods. AiV belongs to the genus Kobuvirus of the family Picornaviridae. It is a virus with icosahedral morphology that presents a single stranded RNA genome with positive sense (8280 nucleotides) and a poly (A) chain. AiV was first detected from clinical samples and in recent years has been involved in acute gastroenteritis outbreaks from different world regions. Furthermore, several studies conducted in Japan, Germany, France, Tunisia and Spain showed a high prevalence of AiV antibodies in adults (between 80% and 99%), which is indicative of a large exposure to this virus. The aim of this review is to bring together all the discovered information about the emerging pathogen human Aichi virus (AiV), discussing the possibles routes of transmission, new detection techniques and future research. Although AiV is responsible for a low percentage of gastroenteritis outbreaks, the high seroprevalence shown by human populations indicates an evident role as an enteric agent. The low percentage of AiV detection could be explained by the fact that the pathogen is more associated to subclinical infections. Further studies will be needed to clarify the real impact of AiV in human health and its importance as a causative gastroenteritis agent worldwide.
IP10, KC and M-CSF is Remarkably Increased in the Brains from the Various Strains of Experimental Mice Infected with Different Scrapie Agents
Jia Chen, Cao Chen, Chao Hu, Lian Liu, Ying Xia, Lin Wang, Wei Yang, Hai-Yan Wu, Wei Zhou, Kang Xiao, Qi Shi, Yuezhang Wu, Zhi-Bao Chen, Xiao-Ping Dong
doi: 10.1007/s12250-020-00216-3
Received: 17 September 2019 Published: 20 April 2020
Abstract PDF Springerlink ESM
Activation of inflammatory cells and upregulations of a number of cytokines in the central nervous system (CNS) of patients with prion diseases are frequently observed. To evaluate the potential changes of some brain cytokines that were rarely addressed during prion infection, the levels of 17 different cytokines in the brain homogenates of mice infected with different scrapie mouse-adapted agents were firstly screened with Luminex assay. Significant upregulations of interferon gamma-induced protein 10 (IP10), keratinocyte chemoattractant (KC) and macrophage colony stimulating factor (M-CSF) were frequently detected in the brain lysates of many strains of scrapie infected mice. The upregulations of those three cytokines in the brains of scrapie infected mice were further validated by the individual specific ELISA and immunohistochemical assay. Increased specific mRNAs of IP10, M-CSF and KC in the brains of scrapie infected mice were also detected by the individual specific qRT-PCRs and IP10-specific digital PCR. Dynamic analyses of the brain samples collected at different time points post infection revealed the time-dependent increases of those three cytokines, particularly IP10 during the incubation period of scrapie infection. In addition, we also found that the levels of IP10 in cerebral spinal fluid (CSF) of 45 sporadic Creutzfeldt–Jakob disease (sCJD) patients were slightly but significantly higher than those of the cases who were excluded the diagnosis of prion diseases. These data give us a better understanding of inflammatory reaction during prion infection and progression of prion disease.
Cutaneous Dengue Virus Inoculation Triggers Strong B Cell Reactions but Contrastingly Poor T Cell Responses
Edith Marcial-Juárez, Julio García-Cordero, Raúl Antonio Maqueda-Alfaro, Rafael Eduardo Saucedo-López, Luvia Enid Sánchez-Torres, Leticia Cedillo-Barrón, Leopoldo Flores-Romo
doi: 10.1007/s12250-020-00213-6
Received: 16 October 2019 Published: 20 April 2020
Abstract PDF Springerlink
Dengue is a global health problem without current specific treatment nor safe vaccines available. While severe dengue is related to pre-existing non-neutralizing dengue virus (DENV) antibodies, the role of T cells in protection or pathology is unclear. Using cutaneous DENV infection in immunocompetent mice we previously showed the generation of PNA+ germinal centers (GCs), now we assessed the activation and proliferation of B and T cells in draining lymph nodes (DLNs). We found a drastic remodelling of DLN compartments from 7 to 14 days post-infection (dpi) with greatly enlarged B cell follicles, occupying almost half of the DLN area compared to ~24% in naïve conditions. Enormous clusters of proliferating (Ki-67+) cells inside B follicles were found 14 dpi, representing ~33% of B cells in DLNs but only ~2% in noninfected mice. Inside GCs, we noticed an important recruitment of tingle body macrophages removing apoptotic cells. In contrast, the percentage of paracortex area and total T cells decreased by 14–16 dpi, compared to controls. Scattered randomly distributed Ki-67+ T cells were found, similar to non-infected mice. CD69 expression by CD4+ and CD8+ T cells was minor, while it was remarkable in B cells, representing 1764.7% of change from basal levels 3 dpi. The apparent lack of T cell responses cannot be attributed to apoptosis since no significant differences were observed compared to noninfected mice. This study shows massive B cell activation and proliferation in DLNs upon DENV infection. In contrast, we found very poor, almost absent CD4+ and CD8+ T cell responses.
Clinical Manifestation and Laboratory Characteristics of SARS-CoV-2 Infection in Pregnant Women
Chunchen Wu, Wenzhong Yang, Xiaoxue Wu, Tianzhu Zhang, Yaoyao Zhao, Wei Ren, Jianbo Xia
doi: 10.1007/s12250-020-00227-0
Received: 06 March 2020 Published: 20 April 2020
Abstract PDF Springerlink ESM
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) epidemic has become a major challenge to public health in China and other countries, considering its pathogenicity across all age groups. Pregnancy is a unique physiological condition, and is characterized by altered immunity and elevated hormone levels to actively tolerate the semiallogeneic fetus, which undergoes a sudden and substantial fluctuation during the immediate postpartum period. Changes in clinical features, laboratory characteristics, and imaging features of pregnant women during the pre-partum and postpartum periods require further elucidation. Here, we retrospectively analyzed the clinical features, laboratory characteristics, and imaging features of eight pregnant cases of SARS-CoV-2 infection during the pre-partum and post-partum periods. Our results showed that four of the eight pregnant women were asymptomatic before delivery but became symptomatic post-partum. Correspondingly, white blood cell (WBC) counts increased and lymphocyte (LYMPH) counts decreased. C-reactive protein (CRP) levels in the serum also increased to a higher level than those in general pregnancy. Therefore, it is imperative to closely monitor laboratory parameters including the WBC count, LYMPH count, and CRP, along with other imaging features in chest CT scans, to promptly prevent, diagnose, and treat a SARS-CoV-2 infection during pregnancy.
Effect of Peroxisome Proliferator-Activated Receptor-γ Coactivator-1 Alpha Variants on Spontaneous Clearance and Fibrosis Progression during Hepatitis C Virus Infection in Moroccan Patients
Raouia ElFihry, Mohcine Elmessaoudi-Idrissi, Fatima-Zahra Jadid, Imane Zaidane, Hajar Chihab, Mohamed Tahiri, Mostafa Kabine, Wafaa Badre, Isabelle Chemin, Agnes Marchio, Pascal Pineau, Sayeh Ezzikouri, Soumaya Benjelloun
doi: 10.1007/s12250-020-00220-7
Received: 04 October 2019 Published: 15 April 2020
Abstract PDF Springerlink
Hepatitis C virus (HCV) is still one of the main causes of liver disease worldwide. Metabolic disorders, including nonalcoholic fatty liver disease (NAFLD), induced by HCV have been shown to accelerate the progression of fibrosis to cirrhosis and to increase the risk of hepatocellular carcinoma. An optimal peroxisome proliferator-activated receptor gamma coactivator 1-alpha (PPARGC1A) activity is crucial to prevent NAFLD installation. The present study aims to investigate the associations between two common PPARGC1A polymorphisms (rs8192678 and rs12640088) and the outcomes of HCV infection in a North African context. A series of 592 consecutive Moroccan subjects, including 292 patients with chronic hepatitis C (CHC), 100 resolvers and 200 healthy controls were genotyped using a TaqMan allelic discrimination assay. PPARGC1A variations at rs8192678 and rs12640088 were not associated with spontaneous clearance of HCV infection (adjusted ORs = 0.76 and 0.79 respectively, P >0.05, for both). Furthermore, multivariable logistic regression analysis showed that both SNPs were not associated with fibrosis progression (OR = 0.71; 95% CI 0.20–2.49; P = 0.739; OR = 1.28; 95% CI 0.25–6.54; P = 0.512, respectively). We conclude that, in the genetic context of South Mediterranean patients, rs8192678 and rs12640088 polymorphisms of PPARGC1A are neither associated with spontaneous clearance nor with disease progression in individuals infected with HCV.
Computational Identification of Small Interfering RNA Targets in SARS-CoV-2
Wei Chen, Pengmian Feng, Kewei Liu, Meng Wu, Hao Lin
doi: 10.1007/s12250-020-00221-6
Received: 06 March 2020 Published: 15 April 2020
Abstract PDF Springerlink
At the end of 2019,a new virus,called Severe Acute Respiratory Syndrome Coronavirus 2(SARS-CoV-2) was reported (Benvenuto et al.2020;Zhu et al.2020).The sequences of SARS-CoV-2 reported by different research groups demonstrated that it is a positive strand RNA virus. The sequence of SARS-CoV-2 is approximately 30 kb long,and could encodes spike,envelope,membrane, nucleocapsid proteins,etc.(Phan 2020).These proteins are responsible for replicating the viral genome as well as generating nested transcripts that are used in the synthesis of the viral proteins.
New Gene Variants Associated with the Risk of Chronic HBV Infection
Mengjie Fan, Jing Wang, Sa Wang, Tengyan Li, Hong Pan, Hankui Liu, Huifang Xu, Daria V. Zhernakova, Stephen J. O'Brien, Zhenru Feng, Le Chang, Erhei Dai, Jianhua Lu, Hongli Xi, Yanyan Yu, Jianguo Zhang, Binbin Wang, Zheng Zeng
doi: 10.1007/s12250-020-00200-x
Received: 05 March 2019 Published: 15 April 2020
Abstract PDF Springerlink ESM
Some patients with chronic hepatitis B virus (HBV) infection failed to clear HBV, even persistently continue to produce antibodies to HBV. Here we performed a two stage genome wide association study in a cohort of Chinese patients designed to discover single nucleotide variants that associate with HBV infection and clearance of HBV. The first stage involved genome wide exome sequencing of 101 cases (HBsAg plus anti-HBs positive) compared with 102 control patients (antiHBs positive, HBsAg negative). Over 80% of individual sequences displayed 20×sequence coverage. Adapters, uncertain bases >10% or low-quality base calls (>50%) were filtered and compared to the human reference genome hg19. In the second stage, 579 chronic HBV infected cases and 439 HBV clearance controls were sequenced with selected genes from the first stage. Although there were no significant associated gene variants in the first stage, two significant gene associations were discovered when the two stages were assessed in a combined analysis. One association showed rs506121-"T" allele [within the dedicator of cytokinesis 8 (DOCK8) gene] was higher in chronic HBV infection group than that in clearance group (P = 0.002, OR = 0.77, 95% CI [0.65, 0.91]). The second association involved rs2071676—A allele within the Carbonic anhydrase (CA9) gene that was significantly elevated in chronic HBV infection group compared to the clearance group (P = 0.0003, OR = 1.35, 95% CI [1.15, 1.58]). Upon replication these gene associations would suggest the influence of DOCK8 and CA9 as potential risk genetic factors in the persistence of HBV infection.
Chimeric Newcastle Disease Virus-like Particles Containing DC-Binding Peptide-Fused Haemagglutinin Protect Chickens from Virulent Newcastle Disease Virus and H9N2 Avian Influenza Virus Challenge
Xiaohong Xu, Jing Qian, Lingsong Qin, Jindou Li, Cong Xue, Jiaxin Ding, Weiqi Wang, Wei Ding, Renfu Yin, Ningyi Jin, Zhuang Ding
doi: 10.1007/s12250-020-00199-1
Received: 03 February 2019 Published: 09 April 2020
Abstract PDF Springerlink
Newcastle disease virus (NDV) and H9N2 subtype Avian influenza virus (AIV) are two notorious avian respiratory pathogens that cause great losses in the poultry industry. Current inactivated commercial vaccines against NDV and AIV have the disadvantages of inadequate mucosal responses, while an attenuated live vaccine bears the risk of mutation. Dendritic cell (DC) targeting strategies are attractive for their potent mucosal and adaptive immune-stimulating ability against respiratory pathogens. In this study, DC-binding peptide (DCpep)-decorated chimeric virus-like particles (cVLPs), containing NDV haemagglutinin–neuraminidase (HN) and AIV haemagglutinin (HA), were developed as a DC-targeting mucosal vaccine candidate. DCpep-decorated cVLPs activated DCs in vitro, and induced potent immune stimulation in chickens, with enhanced secretory immunoglobulin A (sIgA) secretion and splenic T cell differentiation. 40 μg cVLPs can provide full protection against the challenge with homologous, heterologous NDV strains, and AIV H9N2. In addition, DCpep-decorated cVLPs could induce a better immune response when administered intranasally than intramuscularly, as indicated by robust sIgA secretion and a reduced virus shedding period. Taken together, this chimeric VLPs are a promising vaccine candidate to control NDV and AIV H9N2 and a useful platform bearing multivalent antigens.
Potential m6A and m5C Methylations within the Genome of A Chinese African Swine Fever Virus Strain
Lijia Jia, Jianjun Chen, Haizhou Liu, Wenhui Fan, Depeng Wang, Jing Li, Di Liu
doi: 10.1007/s12250-020-00217-2
Received: 05 January 2020 Published: 08 April 2020
Abstract PDF Springerlink ESM
It has been more than 1 year since China reported the first case of African swine fever (ASF) infection in August 2018, and the epidemic situation remains severe (China News Service 2019). According to reports from the Ministry of Agriculture and Rural Affairs, China has reported 160 cases of ASF, which resulted in nearly 1.2 million pigs being killed, as of November 21, 2019 (China News Service 2019). ASF is an acute febrile, hemorrhagic and fulminating infectious disease, and would reach 100% case fatality rate to pigs (Gallardo et al. 2015). The causative pathogen, African swine fever virus (ASFV), is a doublestranded DNA virus with a genome of 170–193 kb belonging to the Asfarviridae family (Galindo and Alonso 2017; Gallardo et al. 2015). A recent study has revealed that ASFV maintains a core genome of 102 ORFs and has 168 dispensable genes (Wang et al. 2019). Thus, the complexed genomic features of ASFV require more attentions. By using the next generation sequencing (NGS) and the single molecule real-time sequencing (SMRT-seq), a couple of Chinese ASFV genomes have been uncovered (Bao et al. 2019; Wen et al. 2019; Jia et al. 2019). Compared to NGS, SMRT-seq has the advantage of long read length and can generate sequencing data containing the original single base modification information, which can be identified through the state-of-art bioinformatic procedures (Senol Cali et al. 2019; Simpson et al. 2017). DNA methylation is a chemical modification common in animal and plant genomes. It refers to the catalytic transfer of methyl groups on active methyl compounds (such as s-adenosine methionine) to other compounds under the catalysis of DNA methyltransferase (DNMT), mainly forming 5-methylcytosine (5-mC), 6-methyladenine (6-mA), 5-hydroxymethylcytosine (5-hmC), etc. DNA methylation, which triggers the epigenetic regulatory mechanism, has been proved to play important roles in gene expression and regulation, embryonic development, and disease-related aspects (Gouil and Keniry 2019). Whether ASFV genome has DNA methylation and epigenetic regulation is to be discerned.
Development of an MCA-Based Real Time RT-qPCR Assay for the Simultaneous Detection and Differentiation of Duck Hepatitis A Virus Types 1 and 3
Chunchun Meng, Yunxiu Huang, Zaib Ur Rehman, Wen Hu, Chuanfeng Li, Ruiying Liang, Zongyan Chen, Kaijie Song, Tianchao Wei, Guangqing Liu
doi: 10.1007/s12250-020-00211-8
Received: 16 October 2019 Published: 08 April 2020
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Duck virus hepatitis (DVH) is a significant concern in the duck industry as the disease causes a highly contagious infection in young ducklings that is often associated with liver necrosis, hemorrhage, and high mortality (Yugo et al. 2016). Duck hepatitis virus (DHV) was first described in 1949 on Long Island in the United States. Subsequent, outbreaks have been reported in England, Canada, Germany, Japan and elsewhere (Toth 1969). DHV is associated with at least two RNA viruses, duck hepatitis A virus (DHAV) and duck astrovirus (DAstV); however, no antigenic relationships have been identified between these two viruses (Yugo et al. 2016). DHAV is the primary causative agent of DVH. As the only member of the genus Avihepatovirus, in the Picornaviridae family, DHAV has a linear, single-stranded positive-sense RNA genome. The genomic organization of DHAV is analogous to that of other picornaviruses with one large open reading frame (ORF) that encodes a polyprotein precursor, that is preceded by a 50-untranslated-terminal-region (UTR) and followed by 30- UTR (Tseng et al. 2007). Based on systematic phylogenetic analyses and neutralization assays, DHAVs have been classified into three serotypes: the classical serotype 1 (DHAV-1) (Kim et al. 2006; Ding and Zhang 2007; Tseng et al. 2007), the second serotype that has only been reported in Taiwan Province of China (DHAV-2) (Tseng and Tsai 2007), and the third serotype that was first reported in South Korea (DHAV-3) (Kim et al. 2007). DHAV-3 also accounts for an increasing proportion of DHV pathogens in China (Liu et al. 2011; Zhang et al. 2017; Wen et al. 2018), South Korea (Cha et al. 2013; Soliman et al. 2015) and Vietnam (Doan et al. 2016).
Development of a Novel Reverse Transcription Loop-Mediated Isothermal Amplification Method for Rapid Detection of SARS-CoV-2
Renfei Lu, Xiuming Wu, Zhenzhou Wan, Yingxue Li, Lulu Zuo, Jianru Qin, Xia Jin, Chiyu Zhang
doi: 10.1007/s12250-020-00218-1
Received: 19 February 2020 Published: 01 April 2020
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Since early December 2019, a large outbreak of pneumonia caused by a novel coronavirus (COVID-19) had emerged in Wuhan, China (Wu et al. 2020a, b; Zhou et al. 2020; Zhu et al. 2020; Jiang and Shi 2020). Similar to severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV), the new coronavirus also belongs to Betacoronavirus, and shares highest sequence identity to three SARS-like CoVs of bat origin (bat_CoV_RaTG13: 96.0%, bat-SLCoVZC45: 88.0% and bat-SL-CoVZXC21: 87.2%) (Zhou et al. 2020). Although only sharing about 79.5% genomic sequence identity to SARS-CoV, the new virus was demonstrate to use the same receptor angiotensin converting enzyme II (ACE2) for human infection as SARSCoV (Lu et al. 2020; Wu 2020; Zhou et al. 2020) and is officially named as SARS-CoV-2 (also known as 2019-nCoV) (Gorbalenya et al. 2020). Epidemically data showed that the virus has strong human-to-human transmission ability, and it is spread by droplets produced by coughing and sneezing, infecting susceptible subjects through direct contacts and other possible transmission routes (e.g. fecal-mouth transmission) (Guan et al. 2020; Li et al. 2020).
The Rapid Assessment and Early Warning Models for COVID-19
Zhihua Bai, Yue Gong, Xiaodong Tian, Ying Cao, Wenjun Liu, Jing Li
doi: 10.1007/s12250-020-00219-0
Received: 08 March 2020 Published: 01 April 2020
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Human beings have experienced a serious public health event as the new pneumonia (COVID-19), caused by the severe acute respiratory syndrome coronavirus has killed more than 3000 people in China, most of them elderly or people with underlying chronic diseases or immunosuppressed states. Rapid assessment and early warning are essential for outbreak analysis in response to serious public health events. This paper reviews the current model analysis methods and conclusions from both micro and macro perspectives. The establishment of a comprehensive assessment model, and the use of model analysis prediction, is very efficient for the early warning of infectious diseases. This would significantly improve global surveillance capacity, particularly in developing regions, and improve basic training in infectious diseases and molecular epidemiology.
Characterization of the First Genome of Porcine mastadenovirus B (HNU1 Strain) and Implications on Its Lymphoid and Special Origin
Shu-Jing Liu, Qiong Wang, Ting-Ting Li, Si-Hua Zhang, Jin-Yan Li, Li-Jun Wu, Ye Qiu, Xing-Yi Ge
doi: 10.1007/s12250-020-00210-9
Received: 05 December 2019 Published: 31 March 2020
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Porcine adenoviruses (PAdVs) are classified into three species, PAdV-A, PAdV-B, and PAdV-C. The genomes of PAdV-A and PAdV-C have been well characterized. However, the genome of PAdV-B has never been completely sequenced, and the epidemiology of PAdV-B remains unclear. In our study, we have identified a novel strain of PAdV-B, named PAdV-BHNU1, in porcine samples collected in China by viral metagenomic assay and general PCR. The genome of PAdV-BHNU1 is 31,743 bp in length and highly similar to that of California sea lion adenovirus 1 (C. sea lion AdV-1), which contains typical mastadenoviral structures and some unique regions at the carboxy-terminal end. Especially, PAdV-BHNU1 harbors a dUTPase coding region not clustering with other mastadenoviruses except for C. sea lion AdV-1 and a fiber coding region homologous with galectin 4 and 9 of animals. However, the variance of GC contents between PAdV-BHNU1 (55%) and C. sea lion AdV-1 (36%) indicates their differential evolutionary paths. Further epidemiologic study revealed a high positive rate (51.7%) of PAdV-B-HNU1 in porcine lymph samples, but low positive rates of 10.2% and 16.1% in oral swabs and rectal swabs, respectively. In conclusion, this study characterized a novel representative genome of a lymphotropic PAdV-B with unique evolutionary origin, which contributes to the taxonomical and pathogenic studies of PAdVs.
Prion Protein Expression is Correlated with Glioma Grades
Qiaoli Luo, Yisong Wang, Dongying Fan, Shijie Wang, Peigang Wang, Jing An
doi: 10.1007/s12250-020-00209-2
Received: 08 October 2019 Published: 31 March 2020
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Glioma is the most common primary central nervous system (CNS) tumors in human. Gliomas are classified into low-grade glioma (LGG, grades I–II) and high-grade glioma (HGG, grades III–IV) according to the World Health Organization classification guidelines (Louis et al. 2007). Comparing to the LGG, the HGG becomes more aggressive and has a poorer median overall survival. At present, glioma is mainly treated by radiotherapy, chemotherapy and surgical resection, but the effect is not ideal, especially for the glioblastoma (GBM), which is the most malignant type of gliomas and is resistant to current therapy protocols. There are several theories about the pathogenesis of glioma, such as radiation (Ohgaki and Kleihues 2005), genetics (Farrell and Plotkin 2007; Goodenberger and Jenkins 2012) and viruses (Lawler. 2015; Xing et al. 2016), while its etiology remains obscure. Therefore, it is urgent to investigate the causes and to identify the promising molecules that target the glioma.
Inefficiency of Sera from Mice Treated with Pseudotyped SARS-CoV to Neutralize 2019-nCoV Infection
Zezhong Liu, Shuai Xia, Xinling Wang, Qiaoshuai Lan, Wei Xu, Qian Wang, Shibo Jiang, Lu Lu
doi: 10.1007/s12250-020-00214-5
Received: 22 February 2020 Published: 31 March 2020
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An outbreak of unusual pneumonia in Wuhan, China recently was caused by infection of a novel type of coronavirus. The virus and disease were denoted as 2019-nCoV and COVID-19, respectively, by the World Health Organization (WHO). Most recently, 2019-nCoV was renamed SARS-CoV-2 by Coronaviridae Study Group (CSG) of the International Committee on Taxonomy of Viruses (ICTV) (Gorbalenya et al. 2020), or HCoV-19, as a common name for the consistence with COVID-19, by a group of virologists in China (Jiang et al. 2020a, b). As of 7 March 2020, a total of 80,651 confirmed cases, including 3070 deaths, were reported in China (China CDC 2020). Global spread is undeniable with serious implications for public health, thus calling for rapid development of effective therapeutics and prophylatics (Jiang et al. 2020a, b).
Re-emergence of Highly Pathogenic Avian Influenza H5N1 in Nigeria, 2014–2016: Role of Social Network and Value Chain Forces in Interstate Transmission
Daniel Oladimeji Oluwayelu, Clement Adebajo Meseko, Adekunle Bamidele Ayinmode, Adebowale Idris Adebiyi, Mike Aneshimi Lawani, Florence Omonele Kakulu
doi: 10.1007/s12250-020-00201-w
Received: 07 August 2019 Published: 31 March 2020
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Since 2004, high pathogenic avian influenza (HPAI) due to H5N1 virus among others has caused a major veterinary health crisis, resulting in the loss of millions of poultry through death or culling in several countries in Asia, the Middle East, Europe, Africa and North America (Alexander 2007; Lee et al. 2016). The first African outbreak was reported from Nigeria in 2006 in domestic poultry (Joannis et al. 2006) and persisted till 2008 (Fusaro et al. 2010). These outbreaks negatively affected animal and public health as well as the economy, and were caused by viruses belonging to genetic clades 2.2, 2.2.1, 2.2.2 and 2.3.2.1c (Aiki-Raji et al. 2008; Fusaro et al. 2010; Monne et al. 2015).
A Unique Protease Cleavage Site Predicted in the Spike Protein of the Novel Pneumonia Coronavirus (2019-nCoV) Potentially Related to Viral Transmissibility
Qiong Wang, Ye Qiu, Jin-Yan Li, Zhi-Jian Zhou, Ce-Heng Liao, Xing-Yi Ge
doi: 10.1007/s12250-020-00212-7
Received: 15 February 2020 Published: 20 March 2020
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In December 2019, a novel human coronavirus caused an epidemic of severe pneumonia (Coronavirus Disease 2019, COVID-19) in Wuhan, Hubei, China (Wu et al. 2020; Zhu et al. 2020). So far, this virus has spread to all areas of China and even to other countries. The epidemic has caused 67,102 confirmed infections with 1526 fatal cases worldwide by February 14th, 2020. The viral infection incubation period varies from 2 to 14 days and typical clinical symptoms are fever, dry cough, dyspnea, headache, and pneumonia. Disease onset may result in progressive respiratory failure due to alveolar damage and even death (Chan et al. 2020; Chen et al. 2020; Huang et al. 2020).
Comparison of Viromes in Ticks from Different Domestic Animals in China
Tingting Zhao, Haiyan Gong, Xiaojuan Shen, Wen Zhang, Tongling Shan, Xiangqian Yu, Seong Jin Wang, Li Cui
doi: 10.1007/s12250-020-00197-3
Received: 08 May 2019 Accepted: 10 March 2020 Published: 10 March 2020
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Ticks are involved in the transmission of various arboviruses and some tick-borne viruses pose significant threats to the health of humans or livestock. This study aimed to investigate the geographical distribution of tick species and tickassociated viruses in central and eastern China. Total 573 ticks from domestic animals including dogs, sheep and cattle were collected in 2017. Two genera of ticks were identified including Rhipicephalus and Haemaphysalis. Sequencing was performed on Miseq Illumina platform to characterize the tick viromes from the four different sampling locations. Following trimming, 13,640 reads were obtained and annotated to 19 virus families. From these sequences, above 37.74% of the viral reads were related to the RNA viruses. Virome comparison study revealed that the tick viral diversity was considerably different in the two identified tick genera. The viral diversity of R. microplus was significantly different from that of other Rhipicephalus species. On the other hand, substantial overlap in viral species was observed between the same genera. In addition, we found no evidence that the natural host played a major role in shaping virus diversity based on the comparison of their viromes. Rather, the geographic location seems to significantly influence the viral families. Phylogenetic study indicated that the novel negative-sense RNA viruses identified in this study was closely related to Bole tick virus 1 and 3 viruses. In conclusion, the present study provides a baseline for comparing viruses detected in ticks, according to species, natural hosts, and geographic locations.
A Mother-to-Child Transmission Study in Nigeria: The Impact of Maternal HIV Infection and HAART on Plasma Immunoglobulins, Cytokine Profiles and Infant Outcome
Chinwe O. Ewenighi-Amankwah, Charles Chinedum Onyenekwe, Ogochukwu Udemba, Patience Muogbo, Lijun Rong
doi: 10.1007/s12250-020-00202-9
Received: 09 October 2019 Published: 10 March 2020
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Prevention of mother-to-child transmission (PMTCT) of HIV with highly active antiretroviral therapy (HARRT) allows the HIV+ pregnant mothers to have vaginal delivery and breastfeed. Here we investigated the maternal plasma immunoglobulin, cytokine secretion and the outcome of the exposed infants among the HIV+ HAART treated pregnant women in Nigeria. In this study, different plasma immunoglobulins and cytokines were measured in the HIV+ HAART treated pregnant mothers. Pooled culture supernatants of B and T lymphocytes showed lower levels of IFN-γ, IL-10 and IL-4. There were lower IFN-γ and IL-10 secretions at 1st trimester; however, IL-10 continued to be lower throughout 2nd and 3rd trimesters. TNF-α secretion significantly decreased as pregnancy progressed to term. There were high plasma IgG and low IgM in the HIV+ HAART treated pregnant women. Plasma IgG was high during 1st and 3rd trimesters. After one year of follow up, all the exposed children were seronegative for HIV-1 and HIV-2. Vaginal delivery and breastfeeding among HIV+ HAART treated mothers have shown to be safe. The use of HAART by the infected mothers and the use of septrin and niverapin by the exposed infants prevented mother to-child transmission of HIV.
The Restrictome of Flaviviruses
Lionel Berthoux
doi: 10.1007/s12250-020-00208-3
Received: 30 November 2019 Published: 09 March 2020
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Flaviviruses are a genus of mostly arthropod-borne RNA viruses that cause a range of pathologies in humans. Basic knowledge on flaviviruses is rapidly expanding, partly due to their status as frequent emerging or re-emerging pathogens. Flaviviruses include the dengue, Zika, West Nile, tick-borne encephalitis and yellow fever viruses (DENV, ZIKV, WNV, TBEV and YFV, respectively). As is the case with other families of viruses, the success of productive infection of human cells by flaviviruses depends in part on the antiviral activity of a heterogeneous group of cellular antiviral proteins called restriction factors. Restriction factors are the effector proteins of the cell-autonomous innate response against viruses, an immune pathway that also includes virus sensors as well as intracellular and extracellular signal mediators such as type I interferons (IFN-I). In this review, I summarize recent progress toward the identification and characterization of flavivirus restriction factors. In particular, I focus on IFI6, Schlafen 11, FMRP, OAS-RNase L, RyDEN, members of the TRIM family of proteins (TRIM5α, TRIM19, TRIM56, TRIM69 and TRIM79α) and a new mechanism of action proposed for viperin. Recent and future studies on this topic will lead to a more complete picture of the flavivirus restrictome, defined as the ensemble of cellular factors with demonstrated anti-flaviviral activity.
The Establishment of Infectious Clone and Single Round Infectious Particles for Coxsackievirus A10
Min Wang, Jingjing Yan, Liuyao Zhu, Meng Wang, Lizhen Liu, Rui Yu, Ming Chen, Jingna Xun, Yuling Zhang, Zhigang Yi, Shuye Zhang
doi: 10.1007/s12250-020-00198-2
Received: 27 September 2019 Published: 06 March 2020
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Coxsackievirus A10 (CVA10) is one of the major etiological agents of hand, foot, and mouth disease. There are no vaccine and antiviral drugs for controlling CVA10 infection. Reverse genetic tools for CVA10 will benefit its mechanistic study and development of vaccines and antivirals. Here, two infectious clones for the prototype and a Myc-tagged CVA10 were constructed. Viable CVA10 viruses were harvested by transfecting the viral mRNA into human rhabdomyosarcoma (RD) cells. Rescued CVA10 was further confirmed by next generation sequencing and characterized experimentally. We also constructed the vectors for CVA10 subgenomic replicon with luciferase reporter and viral capsid with EGFP reporter, respectively. Co-transfection of the viral replicon RNA and capsid expresser in human embryonic kidney 293T (HEK293T) cells led to the production of single round infectious particles (SRIPs). Based on CVA10 replicon RNA, SRIPs with either the enterovirus A71 (EVA71) capsid or the CVA10 capsid were generated. Infection by EVA71 SRIPs required SCARB2, while CVA10 SRIPs did not. Finally, we showed great improvement of the replicon activity and SRIPs production by insertion of a cis-active hammerhead ribozyme (HHRib) before the 50-untranslated region (UTR). In summary, reverse genetic tools for prototype strain of CVA10, including both the infectious clone and the SRIPs system, were successfully established. These tools will facilitate the basic and translational study of CVA10.
Conservative Evolution of Hepatitis B Virus Precore and Core Gene During Immune Tolerant Phase in Intrafamilial Transmission
Yuqian Luo, Le Zhang, Yimin Dai, Yali Hu, Biyun Xu, Yi-Hua Zhou
doi: 10.1007/s12250-020-00194-6
Received: 02 August 2019 Published: 02 March 2020
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Hepatitis B virus (HBV) is characterized with high mutations, which is attributed to the lack of proof-reading of the viral reverse transcriptase and host immune pressure. In this study, 31 HBV chronic carriers from 14 families were enrolled to investigate the evolution of the same original HBV sources in different hosts. Sequences of pre-C and C (pre-C/C) genes were analyzed in eight pairs of HBV-infected mothers with longitudinal sera (at an interval of 6.0–7.2 years) and their children (5.5–6.7 years old), and in 15 adults (21–78 years old) from six families with known intrafamilial HBV infection. The pre-C/C sequences had almost no change in eight mothers during 6.0–7.2 years and their children who were in immune tolerant phase. The pre-C/C sequences from the 15 adults of six families, mostly in the immune-clearance phase or the low replicative phase, showed various diversified mutations between individuals from each family. Compared to a reference stain (GQ205441) isolated nearby, the pre-C/C in individuals in immune tolerant phase showed 98.56%–99.52% homology at nucleotide level and 99.5%–100% homology at amino acid level. In contrast, multiple mutations were developed in the immune-clearance phase or the low replicative phase, affecting immune epitopes in core gene and G1896 in pre-C gene. The results indicate that the evolution of new HBV variants is not mainly resulted from the spontaneous error rate of viral reverse transcription, but from the host immune pressure.
Sero-Epidemiological Survey of Crimean-Congo Hemorrhagic Fever among the Human Population of the Punjab Province in Pakistan
Muhammad Furqan Shahid, Muhammad Zubair Shabbir, Kamran Ashraf, Muzaffar Ali, Saima Yaqub, Aziz Ul-Rahman, Nageen Sardar, Nadia Mukhtar, Zarfishan Tahir, Tahir Yaqub
doi: 10.1007/s12250-020-00195-5
Received: 18 April 2019 Published: 26 February 2020
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Crimean-Congo hemorrhagic fever (CCHF), caused by the CCHF virus (CCHFV), is a tick-borne zoonotic infection characterized by myalgia, high-grade fever (> 38 ℃), headache, nausea, bleeding from the body cavities, and in 10%–50% of cases, results in death (Swanepoel et al. 1989). As CCHFV belongs to the Nairoviridae family, the virus can be transmitted to humans through the bite of infected ticks or by contact with the tissues or blood of infected animals (Bente et al. 2013).
Structure of the HRV-C 3C-Rupintrivir Complex Provides New Insights for Inhibitor Design
Shuai Yuan, Kaiyue Fan, Zhonghao Chen, Yao Sun, Hai Hou, Ling Zhu
doi: 10.1007/s12250-020-00196-4
Received: 21 August 2019 Published: 26 February 2020
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Human rhinoviruses (HRVs) are the predominant infectious agents for the common cold worldwide. The HRV-C species cause severe illnesses in children and are closely related to acute exacerbations of asthma. 3C protease, a highly conserved enzyme, cleaves the viral polyprotein during replication and assists the virus in escaping the host immune system. These key roles make 3C protease an important drug target. A few structures of 3Cs complexed with an irreversible inhibitor rupintrivir have been determined. These structures shed light on the determinants of drug specificity. Here we describe the structures of HRV-C15 3C in free and inhibitor-bound forms. The volume-decreased S1’ subsite and half-closed S2 subsite, which were thought to be unique features of enterovirus A 3C proteases, appear in the HRV-C 3C protease. Rupintrivir assumes an "intermediate" conformation in the complex, which might open up additional avenues for the design of potent antiviral inhibitors. Analysis of the features of the three-dimensional structures and the amino acid sequences of 3C proteases suggest new applications for existing drugs.
Hepatitis C Virus Infection Caused by Infrequent Exposure in China Should Be of Concern
Xin-Cheng Qin, Li-Hua Zhong, Li-Ying Zhu, Alexander Plyusnin, Yong-Zhen Zhang
doi: 10.1007/s12250-019-00191-4
Received: 26 April 2019 Published: 21 February 2020
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Hepatitis C Virus (HCV) infection is a huge public health problem globally, because it can lead to adverse long-term clinical outcomes. In China, the population has experienced a skyrocketing growth of HCV infections because of paid blood donations in the late 1980s to early 1990s (Lu et al. 2013; Yin et al. 2015). Fortunately, the prevalence of HCV infection has declined dramatically since mid-1990s and was less than 1% in recent years (Cui and Jia 2013; Fu et al. 2010). However, the huge size of population in China makes a quite enormous absolute number of people infected with HCV. Like other agents causing blood-borne diseases, HCV is mainly transmitted through exchange of bodily fluids and intravenous drug use, as well as vertical transmission (Lauer and Walker 2001). Compared to the more in-depth understanding on infection and virus transmission in high-risk groups, limited data are available concerning the HCV infection caused by infrequent exposure in general population. Herein, we documented two sisters with chronic HCV infection and our attempts to dissect the transmission routes of their infections.
Compensation of ACE2 Function for Possible Clinical Management of 2019-nCoV-Induced Acute Lung Injury
Yuntao Wu
doi: 10.1007/s12250-020-00205-6
Received: 01 February 2020 Accepted: 03 February 2020 Published: 19 February 2020
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The 2019-nCoV viral infection causes clusters of severe respiratory illness such as an acute respiratory distress syndrome (ARDS) similar to that caused by SARS-CoV (severe acute respiratory syndrome coronavirus) (Huang et al. 2020). Both 2019-nCoV and SARS-CoV use the same receptor, ACE2 (angiotensin converting enzyme 2), to infect cells (Li et al. 2003; Zhou et al. 2020). ACE2 is one of the central enzymes in the renin–angiotensin system (RAS) (Donoghue et al. 2000; Imai et al. 2010; Tipnis et al. 2000) that regulates blood pressure, fluid and electrolyte balance, and systemic vascular resistance (Paul et al. 2006; Zimmerman and Dunham 1997).
Clinical Features and Treatment of 2019-nCov Pneumonia Patients in Wuhan: Report of A Couple Cases
Zhan Zhang, Xiaochen Li, Wei Zhang, Zheng-Li Shi, Zhishui Zheng, Tao Wang
doi: 10.1007/s12250-020-00203-8
Received: 25 January 2020 Accepted: 28 January 2020 Published: 17 February 2020
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Till January 20, 2020, the 2019-new coronavirus (2019-nCoV) has caused more than one hundred cases in Wuhan (WMHC 2020). During a retrospective study of recent pneumonia patients in our department, we found two patients who are likely being infected with the 2019-nCoV. During the hospitalization, those two patients were appropriately treated, and both were discharged within two weeks. Thus, we are reporting the clinical features and treatment regiment, and hope the information and experience can be shared.
Old Weapon for New Enemy: Drug Repurposing for Treatment of Newly Emerging Viral Diseases
Deyin Guo
doi: 10.1007/s12250-020-00204-7
Received: 29 January 2020 Accepted: 31 January 2020 Published: 17 February 2020
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Emerging and re-emerging viral diseases are a public health concern for the whole world and pose a major threat to human health and life. In last decades, numerous major outbreaks of emerging and re-emerging viral diseases with gross public concern were recorded in different regions, including Ebola in western Africa, Zika in South America, H7N9 in China and many Asian countries, and H1N1 influenza worldwide. In particular, coronaviruses were once regarded as the ones that just cause mild symptoms like common cold, but three new types of coronaviruses, which emerged in the 21st century, can cause severe diseases with high fatality and morbidity. Severe acute respiratory syndrome (SARS) coronavirus (SARS-CoV) emerged in November 2002 in Guangdong, China and caused globally 8098 human infections with 774 deaths (9.6%), and the Middle East respiratory syndrome (MERS) coronavirus (MERS-CoV) emerged in 2012 in Saudi Arabia and caused 2494 infections with 858 associated deaths (34.4%) as of November 2019 (WHO 2020a, b).
Understanding SARS-CoV-2-Mediated Inflammatory Responses: From Mechanisms to Potential Therapeutic Tools
Yajing Fu, Yuanxiong Cheng, Yuntao Wu
doi: 10.1007/s12250-020-00207-4
Received: 14 February 2020 Accepted: 16 February 2020 Published: 16 February 2020
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Currently there is no effective antiviral therapy for SARS-CoV-2 infection, which frequently leads to fatal inflammatory responses and acute lung injury. Here, we discuss the various mechanisms of SARS-CoV-mediated inflammation. We also assume that SARS-CoV-2 likely shares similar inflammatory responses. Potential therapeutic tools to reduce SARS-CoV-2-induced inflammatory responses include various methods to block FcR activation. In the absence of a proven clinical FcR blocker, the use of intravenous immunoglobulin to block FcR activation may be a viable option for the urgent treatment of pulmonary inflammation to prevent severe lung injury. Such treatment may also be combined with systemic anti-inflammatory drugs or corticosteroids. However, these strategies, as proposed here, remain to be clinically tested for effectiveness.
The First Disease X is Caused by a Highly Transmissible Acute Respiratory Syndrome Coronavirus
Shibo Jiang, Zheng-Li Shi
doi: 10.1007/s12250-020-00206-5
Received: 06 February 2020 Accepted: 09 February 2020 Published: 09 February 2020
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Based on the announcement of the World Health Organization (WHO) in 2018, the Wuhan pneumonia caused by an unknown etiology should be recognized as the first Disease X. Later, the pathogen was identified to be a novel coronavirus denoted 2019-nCoV, which has 79.5% and 96% whole genome sequence identify to SARS-CoV and bat SARS-related coronavirus (SARSr-CoV-RaTG13), respectively, suggesting its potential bat origin. With high human-to-human transmission rate (R0), 2019-nCoV has quickly spread in China and other countries, resulting in 34,953 confirmed cases and 725 deaths as of 8 February 2020, thus calling for urgent development of therapeutics and prophylactics. Here we suggest renaming 2019-nCoV as “transmissible acute respiratory syndrome coronavirus (TARS-CoV)” and briefly review the advancement of research and development of neutralizing antibodies and vaccines targeting the receptor-binding domain (RBD) and viral fusion inhibitors targeting the heptad repeat 1 (HR1) domain in spike protein of 2019-nCoV.
The Limitation of Rapid Tests for DENV2 Infection in Host with Unique Immune Status: Low NS1 Antigenemia and Deficient Antibody Responses
Lei Yu, Yingfen Wen, Mengrong Xiang, Wenxin Hong, Lingzhai Zhao, Fuchun Zhang
doi: 10.1007/s12250-019-00183-4
Received: 25 April 2019 Published: 14 January 2020
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Dengue infections are caused by all four serotypes of dengue virus (DENV1–4). In recent years it has been confirmed that DENV-1 and DENV-2 are co-circulated in Guangzhou, Guangdong, China (Lai et al. 2015; Luo et al. 2017). DENV-2 strains were imported from Thailand and Indonesia (Luo et al. 2017; Zhao et al. 2014, 2016), and had become the second local circulated serotype in Guangzhou.
Visualizing the Transport of Porcine Reproductive and Respiratory Syndrome Virus in Live Cells by Quantum Dots-Based Single Virus Tracking
Zhenpu Liang, Pengjuan Li, Caiping Wang, Deepali Singh, Xiaoxia Zhang
doi: 10.1007/s12250-019-00187-0
Received: 20 August 2019 Published: 23 December 2019
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Quantum dots (QDs)-based single particle analysis technique enables real-time tracking of the viral infection in live cells with great sensitivity over a long period of time. The porcine reproductive and respiratory syndrome virus (PRRSV) is a small virus with the virion size of 40–60 nm which causes great economic losses to the swine industry worldwide. A clear understanding of the viral infection mechanism is essential for the development of effective antiviral strategies. In this study, we labeled the PRRSV with QDs using the streptavidin–biotin labeling system and monitored the viral infection process in live cells. Our results indicated that the labeling method had negligible effect on viral infectivity. We also observed that prior to the entry, PRRSV vibrated on the plasma membrane, and entered the cells via endosome mediated cell entry pathway. Viruses moved in a slow–fast–slow oscillatory movement pattern and finally accumulated in a perinuclear region of the cell. Our results also showed that once inside the cell, PRRSV moved along the microtubule, microfilament and vimentin cytoskeletal elements. During the transport process, virus particles also made contacts with non-muscle myosin heavy chain II-A (NMHC II-A), visualized as small spheres in cytoplasm. This study can facilitate the application of QDs in virus infection imaging, especially the smaller-sized viruses and provide some novel and important insights into PRRSV infection mechanism.
The Establishment of an In Vivo HIV-1 Infection Model in Humanized B-NSG Mice
Tian-Jiao Fan, Li Sun, Xian-Guang Yang, Xia Jin, Wei-Wei Sun, Jian-Hua Wang
doi: 10.1007/s12250-019-00181-6
Received: 12 July 2019 Published: 21 December 2019
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Suitable animal models for human immunodeficiency virus type 1 (HIV-1) infection are important for elucidating viral pathogenesis and evaluating antiviral strategies in vivo. The B-NSG (NOD-PrkdcscidIl2rgtm1/Bcge) mice that have severe immune defect phenotype are examined for the suitability of such a model in this study. Human peripheral blood mononuclear cells (PBMCs) were engrafted into B-NSG mice via mouse tail vein injection, and the repopulated human T-lymphocytes were observed at as early as 3-weeks post-transplantation in mouse peripheral blood and several tissues. The humanized mice could be infected by HIV-1, and the infection recapitulated features of T-lymphocyte dynamic observed in HIV-1 infected humans, meanwhile the administration of combination antiretroviral therapy (cART) suppressed viral replication and restored T lymphocyte abnormalities. The establishment of HIV-1 infected humanized B-NSG mice not only provides a model to study virus and T cell interplays, but also can be a useful tool to evaluate antiviral strategies.
Pan-Genomic Analysis of African Swine Fever Virus
Ziming Wang, Lijia Jia, Jing Li, Haizhou Liu, Di Liu
doi: 10.1007/s12250-019-00173-6
Received: 10 September 2019 Published: 11 December 2019
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African swine fever (ASF) is a severe haemorrhagic fever in domestic pigs and wild boar with extremely high mortality rate. It is cataloged as a notifiable disease by the World Organization for Animal Health (OIE). The etiological agent that causes the highly lethal disease is the African swine fever virus (ASFV) (Sanchez-Vizcaino et al. 2015). ASFV is the only known member of the genus Asfivirus and family Asfarviridae. The family Asfarviridae belongs to the member of nucleocytoplasmic large DNA viruses (NCLDV) superfamily (Iyer et al. 2006; Costard et al. 2009). Overall, the ASFV virion presents an icosahedral morphology with a multilayered structure (Wang et al. 2019). The genome of ASFV is a large doublestranded DNA (dsDNA) molecule that varies in length from about 170 to 193 kilobase pairs and encodes between 150 and 167 open reading frames (ORFs) depending on the isolate (Dixon et al. 2013). In addition, ASFV also infects African wild suids, including warthogs (Phacochoerus africanus) and bushpigs (Potamochoerus larvatus), which act as asymptomatic carriers. Soft ticks of the Ornithodoros moubata complex also serve as a natural reservoir and transmit the disease to suids. In East Africa, ASFV is maintained in an ancient sylvatic cycle involving warthogs and soft ticks (Ornithodoros genus) that inhabit their burrows (Jori et al. 2013).
Isolation and Characterization of A Novel Fowl Adenovirus Serotype 8a Strain from China
Li Chen, Lijuan Yin, Peng Peng, Qingfeng Zhou, Yunping Du, Yun Zhang, Chunyi Xue, Yongchang Cao
doi: 10.1007/s12250-019-00172-7
Received: 04 June 2019 Published: 02 December 2019
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Since 2012, the clinical cases of inclusion body hepatitis showed an increasing trend in China, causing considerable economic losses to the poultry industry. In this study, a fowl adenovirus strain CH/GDLZ/201801 was isolated from a chicken flock experiencing inclusion body hepatitis and analyzed by complete genome sequencing. The pathogenicity of the new virus strain was examined by experimental infection of specific pathogen free chickens. The isolate was identified by immunofluorescence and the virions presented typical icosahedral particles under transmission electron microscopy. The full genome of the isolate was 44,329 nucleotides in length with 58% G+C content. Phylogenetic analysis, based on the whole genome, revealed that the new isolate was closest to serotype 8a from the species Fowl aviadenovirus E (FAdVE). Recombination analysis and phylogenetic analysis showed that the new isolate is a recombinant strain between FAdV- 8a and FAdV-8b. In infection experiments, three infected chickens showed clinical signs and one chicken died on day 7 post infection, corresponding to 5% mortality. Macroscopic and microscopic lesions in the liver were observed, and viral antigen could be detected in the livers by immunohistochemical staining and TEM. Taken together, our study describes the genomic characteristics and pathogenicity of a FAdV-8a strain in China. It would lay a solid foundation for further study of the pathogenic mechanism and vaccine development of the virus.
Hepatitis C Virus NS2 Protein Suppresses RNA Interference in Cells
Hui Zhou, Qi Qian, Ting Shu, Jiuyue Xu, Jing Kong, Jingfang Mu, Yang Qiu, Xi Zhou
doi: 10.1007/s12250-019-00182-5
Received: 12 October 2019 Published: 27 November 2019
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RNAi interference (RNAi) is an evolutionarily conserved post-transcriptional gene silencing mechanism and has been well recognized as an important antiviral immunity in eukaryotes. Numerous viruses have been shown to encode viral suppressors of RNAi (VSRs) to antagonize antiviral RNAi. Hepatitis C virus (HCV) is a medically important human pathogen that causes acute and chronic hepatitis. In this study, we screened all the nonstructural proteins of HCV and found that HCV NS2 could suppress RNAi induced either by small hairpin RNAs (shRNAs) or small interfering RNAs (siRNAs) in mammalian cells. Moreover, we demonstrated that NS2 could suppress RNAi via its direct interaction with double-stranded RNAs (dsRNAs) and siRNAs, and further identified that the cysteine 184 of NS2 is required for the RNAi suppression activity through a serial of point mutation analyses. Together, our findings uncovered that HCV NS2 can act as a VSR in vitro, thereby providing novel insights into the life cycle and virus-host interactions of HCV.

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Review
Bacteriophages and Lysins in Biofilm Control
Marzanna Łusiak-Szelachowska, Beata Weber-Dąbrowska, Andrzej Górski
2020, 35(2): 125-133.  doi: 10.1007/s12250-019-00192-3
Received: 30 May 2019 Accepted: 17 December 2019 Published: 01 April 2020
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To formulate the optimal strategy of combatting bacterial biofilms, in this review we update current knowledge on the growing problem of biofilm formation and its resistance to antibiotics which has spurred the search for new strategies to deal with this complication. Based on recent findings, the role of bacteriophages in the prevention and elimination of biofilm-related infections has been emphasized. In vitro, ex vivo and in vivo biofilm treatment models with single bacteriophages or phage cocktails have been compared. A combined use of bacteriophages with antibiotics in vitro or in vivo confirms earlier reports of the synergistic effect of these agents in improving biofilm removal. Furthermore, studies on the application of phage-derived lysins in vitro, ex vivo or in vivo against biofilm-related infections are encouraging. The strategy of combined use of phage and antibiotics seems to be different from using lysins and antibiotics. These findings suggest that phages and lysins alone or in combination with antibiotics may be an efficient weapon against biofilm formation in vivo and ex vivo, which could be useful in formulating novel strategies to combat bacterial infections. Those findings proved to be relevant in the prevention and destruction of biofilms occurring during urinary tract infections, orthopedic implant-related infections, periodontal and peri-implant infections. In conclusion, it appears that most efficient strategy of eliminating biofilms involves phages or lysins in combination with antibiotics, but the optimal scheme of their administration requires further studies.
Research Article
Genome Analysis of Dasineura jujubifolia Toursvirus 2, A Novel Ascovirus
Jun Wang, Minglu Yang, Haibing Xiao, Guo-Hua Huang, Fei Deng, Zhihong Hu
2020, 35(2): 134-142.  doi: 10.1007/s12250-019-00177-2
Received: 28 May 2019 Accepted: 09 September 2019 Published: 01 April 2020
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So far, ascoviruses have only been identified from Lepidoptera host insects and their transmission vectors—endoparasitic wasps. Here, we reported the first finding of a complete novel ascovirus genome from a Diptera insect, Dasineura jujubifolia. Initially, sequence fragments with homology to ascoviruses were incidentally identified during metagenomic sequencing of the mitochondria of D. jujubifolia (Cecidomyiidae, Diptera) which is a major pest on Ziziphus jujuba. Then a full circular viral genome was assembled from the metagenomic data, which has an A+T percentage of 74% and contains 142, 600 bp with 141 open reading frames (ORFs). Among the 141 ORFs, 37 were conserved in all sequenced ascoviruses (core genes) including proteins predicted to participate in DNA replication, gene transcription, protein modification, virus assembly, lipid metabolism and apoptosis. Multi-gene families including those encode for baculovirus repeated open reading frames (BROs), myristylated membrane proteins, RING/U-box E3 ubiquitin ligases, and ATP-binding cassette (ABC) transporters were found in the virus genome. Phylogenetic analysis showed that the newly identified virus belongs to genus Toursvirus of Ascoviridae, and is therefore named as Dasineura jujubifolia toursvirus 2 (DjTV-2a). The virus becomes the second reported species of the genus after Diadromus pulchellus toursvirus 1 (DpTV-1a). The genome arrangement of DjTV-2a is quite different from that of DpTV-1a, suggesting these two viruses separated in an early time of evolution. The results suggest that the ascoviruses may infect a much broader range of hosts than our previous knowledge, and shed lights on the evolution of ascoviruses and particularly on that of the toursviruses.
Proteomic Profiling of Purified Rabies Virus Particles
Yan Zhang, Yuyang Wang, Ye Feng, Zhongzhong Tu, Zhiyong Lou, Changchun Tu
2020, 35(2): 143-155.  doi: 10.1007/s12250-019-00157-6
Received: 11 May 2019 Accepted: 31 July 2019 Published: 01 April 2020
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While host proteins incorporated into virions during viral budding from infected cell are known to play essential roles in multiple process of the life cycle of progeny virus, these characteristics have been largely neglected in studies on rabies virus (RABV). Here, we purified the RABV virions with good purity and integrity, and analyzed their proteome by nano LC-MS/MS, followed by the confirmation with immunoblot and immuno-electronic microscopy. In addition to the 5 viral proteins, 49 cellular proteins were reproducibly identified to be incorporated into matured RABV virions. Function annotation suggested that 24 of them were likely involved in virus replication. Furthermore, cryo-EM was employed to observe the purified RABV virions, generating high-resolution pictures of the bullet-shaped virion structure of RABV. This study has provided new insights into the host proteins composition in RABV virion and shed the light for further investigation on molecular mechanisms of RABV infection, as well as the discovery of new anti-RABV therapeutics.
Structural Basis of Glycan Recognition in Globally Predominant Human P[8] Rotavirus
Xiaoman Sun, Lei Dang, Dandi Li, Jianxun Qi, Mengxuan Wang, Wengang Chai, Qing Zhang, Hong Wang, Ruixia Bai, Ming Tan, Zhaojun Duan
2020, 35(2): 156-170.  doi: 10.1007/s12250-019-00164-7
Received: 25 July 2019 Accepted: 21 August 2019 Published: 01 April 2020
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Rotavirus (RV) causes acute gastroenteritis in infants and children worldwide. Recent studies showed that glycans such as histo-blood group antigens (HBGAs) function as cell attachment factors affecting RV host susceptibility and prevalence. P[8] is the predominant RV genotype in humans, but the structural basis of how P[8] RVs interact with glycan ligands remains elusive. In this study, we characterized the interactions between P[8] VP8*s and glycans which showed that VP8*, the RV glycan binding domain, recognized both mucin core 2 and H type 1 antigens according to the ELISA-based oligosaccharide binding assays. Importantly, we determined the structural basis of P[8] RV-glycans interaction from the crystal structures of a Rotateq P[8] VP8* in complex with core 2 and H type 1 glycans at 1.8? and 2.3?, respectively, revealing a common binding pocket and similar binding mode. Structural and sequence analysis demonstrated that the glycan binding site is conserved among RVs in the P[II] genogroup, while genotype-specific amino acid variations determined different glycan binding preference. Our data elucidated the detailed structural basis of the interactions between human P[8] RVs and different host glycan factors, shedding light on RV infection, epidemiology, and development of anti-viral agents.
Analysis of Expression Profiles of Long Noncoding RNAs and mRNAs in A549 Cells Infected with H3N2 Swine Influenza Virus by RNA Sequencing
Yina Zhang, Tianqi Yu, Yingnan Ding, Yahui Li, Jing Lei, Boli Hu, Jiyong Zhou
2020, 35(2): 171-180.  doi: 10.1007/s12250-019-00170-9
Received: 23 May 2019 Accepted: 27 August 2019 Published: 01 April 2020
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Long noncoding RNAs (lncRNAs) participate in regulating many biological processes. However, their roles in influenza A virus (IAV) pathogenicity are largely unknown. Here, we analyzed the expression profiles of lncRNAs and mRNAs in H3N2-infected cells and mock-infected cells by high-throughput sequencing. The results showed that 6129 lncRNAs and 50, 031 mRNA transcripts in A549 cells displayed differential expression after H3N2 infection compared with mock infection. Among the differentially expressed lncRNAs, 4963 were upregulated, and 1166 were downregulated. Functional annotation and enrichment analysis using gene ontology and Kyoto Encyclopedia of Genes and Genomes databases (KEGG) suggested that target genes of the differentially expressed lncRNAs were enriched in some biological processes, such as cellular metabolism and autophagy. The up- or downregulated lncRNAs were selected and further verified by quantitative real-time polymerase chain reaction (RT-qPCR) and reverse transcription PCR (RT-PCR). To the best of our knowledge, this is the first report of a comparative expression analysis of lncRNAs in A549 cells infected with H3N2. Our results support the need for further analyses of the functions of differentially expressed lncRNAs during H3N2 infection.
Premature Stop Codon at Residue 101 within HIV-1 Rev Does Not Influence Viral Replication of Clade BC but Severely Reduces Viral Fitness of Clade B
Zheng Wang, Xiaolin Ji, Yanling Hao, Kunxue Hong, Liying Ma, Dan Li, Yiming Shao
2020, 35(2): 181-190.  doi: 10.1007/s12250-019-00179-0
Received: 02 March 2019 Accepted: 17 October 2019 Published: 01 April 2020
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HIV-1 Rev is an accessory protein that plays a key role in nuclear exportation, stabilization, and translation of the viral mRNAs. Rev of HIV-1 clade BC often shows a truncation of 16 AAs due to a premature stop codon at residue 101. This stop codon presents the highest frequency in clade BC and the lowest frequency in clade B. In order to discover the potential biological effect of this truncation on Rev activity and virus replication of clade BC, we constructed Rev expression vectors of clade BC with or without 16 AAs within C-terminal separately, and replaced the stop codon by Q in a CRF07_BC infectious clone. We found that 16 AAs truncation had no effect on expression and activity of Rev in clade BC. Also, the mutation from the stop codon to Q had no effect on virus replication of clade BC. Next, to investigate the effect of this truncation on Rev activity and replication capacity of clade B, Rev expression vectors of clade B carrying or lacking 16 AAs in C-terminal were constructed respectively, and residue Q at position 101 within Rev was substituted by the stop codon in a clade B infectious clone. It was found that 16 AAs truncation significantly down-regulated Rev expression and impaired clade B Rev activity. Furthermore, a Q-to-stop codon substitution within Rev significantly reduced viral replication fitness of clade B. These results indicate that the premature stop codon at residue 101 within Rev exerts diverse impact on viral replication among different HIV-1 clades.
Highly Efficient Base Editing in Viral Genome Based on Bacterial Artificial Chromosome Using a Cas9-Cytidine Deaminase Fused Protein
Ke Zheng, Fang-Fang Jiang, Le Su, Xin Wang, Yu-Xin Chen, Huan-Chun Chen, Zheng-Fei Liu
2020, 35(2): 191-199.  doi: 10.1007/s12250-019-00175-4
Received: 12 April 2019 Accepted: 09 September 2019 Published: 01 April 2020
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Viruses evolve rapidly and continuously threaten animal health and economy, posing a great demand for rapid and efficient genome editing technologies to study virulence mechanism and develop effective vaccine. We present a highly efficient viral genome manipulation method using CRISPR-guided cytidine deaminase. We cloned pseudorabies virus genome into bacterial artificial chromosome, and used CRISPR-guided cytidine deaminase to directly convert cytidine (C) to uridine (U) to induce premature stop mutagenesis in viral genes. The editing efficiencies were 100%. Comprehensive bioinformatic analysis revealed that a large number of editable sites exist in pseudorabies virus (PRV) genomes. Notably, in our study viral genome exists as a plasmid in E. coli, suggesting that this method is virus species-independent. This application of base-editing provided an alternative approach to generate mutant virus and might accelerate study on virulence and vaccine development.
Endosomes and Microtubles are Required for Productive Infection in Aquareovirus
Fuxian Zhang, Hong Guo, Qingxiu Chen, Zheng Ruan, Qin Fang
2020, 35(2): 200-211.  doi: 10.1007/s12250-019-00178-1
Received: 16 April 2019 Accepted: 18 September 2019 Published: 01 April 2020
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Grass carp reovirus (GCRV), the genus Aquareovirus in family Reoviridae, is viewed as the most pathogenic aquareovirus. To understand the molecular mechanism of how aquareovirus initiates productive infection, the roles of endosome and microtubule in cell entry of GCRV are investigated by using quantum dots (QDs)-tracking in combination with biochemical approaches. We found that GCRV infection and viral protein synthesis were significantly inhibited by pretreating host cells with endosome acidification inhibitors NH4Cl, chloroquine and bafilomycin A1 (Bafi). Confocal images indicated that GCRV particles could colocalize with Rab5, Rab7 and lysosomes in host cells. Further ultrastructural examination validated that viral particle was found in late endosomes. Moreover, disruption of microtubules with nocodazole clearly blocked GCRV entry, while no inhibitory effects were observed with cytochalasin D treated cells in viral infection, hinting that intracellular transportation of endocytic uptake in GCRV infected cells is via microtubules but not actin filament. Notably, viral particles were observed to transport along microtubules by using QD-labeled GCRV. Altogether, our results suggest that GCRV can use endosomes and microtubules to initiate productive infection.
A Deleted Deletion Site in a New Vector Strain and Exceptional Genomic Stability of Plaque-Purified Modified Vaccinia Ankara (MVA)
Ingo Jordan, Deborah Horn, Kristin Thiele, Lars Haag, Katharina Fiddeke, Volker Sandig
2020, 35(2): 212-226.  doi: 10.1007/s12250-019-00176-3
Received: 06 June 2019 Accepted: 18 September 2019 Published: 01 April 2020
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Vectored vaccines based on highly attenuated modified vaccinia Ankara (MVA) are reported to be immunogenic, tolerant to pre-existing immunity, and able to accommodate and stably maintain very large transgenes. MVA is usually produced on primary chicken embryo fibroblasts, but production processes based on continuous cell lines emerge as increasingly robust and cost-effective alternatives. An isolate of a hitherto undescribed genotype was recovered by passage of a non-plaque-purified preparation of MVA in a continuous anatine suspension cell line (CR.pIX) in chemically defined medium. The novel isolate (MVA-CR19) replicated to higher infectious titers in the extracellular volume of suspension cultures and induced fewer syncytia in adherent cultures. We now extend previous studies with the investigation of the point mutations in structural genes of MVA-CR19 and describe an additional point mutation in a regulatory gene. We furthermore map and discuss an extensive rearrangement of the left telomer of MVA-CR19 that appears to have occurred by duplication of the right telomer. This event caused deletions and duplications of genes that may modulate immunologic properties of MVA-CR19 as a vaccine vector. Our characterizations also highlight the exceptional genetic stability of plaque-purified MVA: although the phenotype of MVA-CR19 appears to be advantageous for replication, we found that all genetic markers that differentiate wildtype and MVA-CR19 are stably maintained in passages of recombinant viruses based on either wildtype or MVA-CR.
Monoclonal Antibody-Based Serological Detection of Rice Stripe Mosaic Virus Infection in Rice Plants or Leafhoppers
Liqian Guo, Jiayu Wu, Rui Chen, Jian Hong, Xueping Zhou, Jianxiang Wu
2020, 35(2): 227-234.  doi: 10.1007/s12250-019-00186-1
Received: 17 August 2019 Accepted: 21 October 2019 Published: 01 April 2020
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Rice stripe mosaic virus (RSMV) is a rhabdovirus recently found in southern part of China and can cause severe reduction in rice production. To establish serological methods for RSMV epidemiological studies and to establish a control strategy for this virus, we first purified RSMV virions from infected rice plants and then used them as an immunogen to produce four RSMV-specific monoclonal antibodies (MAbs) (i.e., 1D4, 4A8, 8E4 and 11F11). With these MAbs, we have developed a highly specific and sensitive antigen-coated plate enzyme-linked immunosorbent assay (ACP-ELISA), a Dot-ELISA and a Tissue print-ELISA for rapid detections of RSMV infection in rice plants or in leafhoppers. Our results showed that RSMV can be readily detected in RSMV-infected rice plant tissue crude extracts diluted at 1:20, 971, 520 (w/v, g/mL) through ACP-ELISA or diluted at 1:327, 680 (w/v, g/mL) through Dot-ELISA. Both ACP-ELISA and Dot-ELISA can also be used to detect RSMV infection in individual RSMV viruliferous leafhopper (Recilia dorsalis) homogenate diluted at 1:307, 200 and 1:163, 840 (individual leafhopper/μL), respectively. Detection of RSMV infection in field-collected rice samples or in RSMV viruliferous leafhoppers indicated that the three serological methods can produce same results with that produced by RT-PCR (19 of the 33 rice samples and 5 of the 16 leafhoppers were RSMV-positive). We consider that the four MAbs produced in this study are very specific and sensitive, and the three new serological methods are very useful for detections of RSMV infection in rice plants or in leafhoppers and the establishment of the disease control strategies.
Letter
Screening and Identification of Marburg Virus Entry Inhibitors Using Approved Drugs
Li Zhang, Shan Lei, Hui Xie, Qianqian Li, Shuo Liu, Qiang Liu, Weijin Huang, Xinyue Xiao, Youchun Wang
2020, 35(2): 235-239.  doi: 10.1007/s12250-019-00184-3
Received: 03 June 2019 Accepted: 21 October 2019 Published: 01 April 2020
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Meta-Transcriptome Profiling of Novel Invasive Pest Spodoptera frugiperda in Yunnan, China
Junming Shi, Weiwei Li, Yunyu Wang, Quanyan Chen, Fei Deng
2020, 35(2): 240-244.  doi: 10.1007/s12250-019-00188-z
Received: 23 July 2019 Accepted: 01 November 2019 Published: 01 April 2020
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Identification and Characterization of the First Equine Parainfluenza Virus 5
Jinxin Xie, Panpan Tong, Aoyuntuya Zhang, Lei Zhang, Xiaozhen Song, Ling Kuang
2020, 35(2): 245-247.  doi: 10.1007/s12250-019-00185-2
Received: 02 August 2019 Accepted: 18 November 2019 Published: 01 April 2020
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Meeting Report
WSV 2019: The First Committee Meeting of the World Society for Virology
Ahmed S. Abdel-Moneim, Matthew D. Moore, Mahmoud M. Naguib, Jesus L. Romalde, Maria Söderlund-Venermo
2020, 35(2): 248-252.  doi: 10.1007/s12250-019-00189-y
Received: 26 November 2019 Accepted: 28 November 2019 Published: 01 April 2020
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The World Society for Virology (WSV) was founded and incorporated as a nonprofit organization in the United States in 2017. WSV seeks to strengthen and support both virological research and virologists who conduct research of viruses that affect humans, other animals, plants, and other organisms. One of the objectives of WSV is to connect virologists worldwide and support collaboration. Fulfilling this objective, virologists from fourteen countries in North America, Europe, Africa, Asia, and the Middle East met on 25–27th August 2019 in Stockholm, Sweden at the Karolinska University Hospital for the first Committee Meeting of WSV. This meeting included compelling keynote and honorary speeches and a series of 18 scientific talks were given encompassing a diverse array of subjects within virology. Followed by the scientific session, a business session was held where multiple aspects and next steps of the society were discussed and charted out.