For best viewing of the website please use Mozilla Firefox or Google Chrome.
Citation: Chunge Zhang, Yongchun Yang, Tao Hu, Hong Zhou, Cheng Zhang, Jian Cao, Juan Li, Peihan Wang, Gary Wong, Xiaodu Wang, Houhui Song, George F. Gao, Weifeng Shi, Yuhai Bi. Three Novel Avastroviruses Identified in Dead Wild Crows [J].VIROLOGICA SINICA.  http://dx.doi.org/10.1007/s12250-021-00416-5

Three Novel Avastroviruses Identified in Dead Wild Crows

  • Corresponding author: Weifeng Shi, shiwf@ioz.ac.cn, ORCID: http://orcid.org/0000-0002-8717-2942
    Yuhai Bi, beeyh@im.ac.cn, ORCID: http://orcid.org/0000-0002-5595-363X
  • Supplementary Information The online version contains supplementary material available at https://doi.org/10.1007/s12250-021-00416-5.
  • Received Date: 22 February 2021
    Accepted Date: 27 April 2021
    Published Date: 30 August 2021

  • 加载中
  • s12250-021-00416-5_ESM.pdf
    1. Atkins A, Wellehan JF Jr, Childress AL, Archer LL, Fraser WA, Citino SB (2009) Characterization of an outbreak of astroviral diarrhea in a group of cheetahs (Acinonyx jubatus). Vet Microbiol 136: 160–165
        doi: 10.1016/j.vetmic.2008.10.035

    2. Cattoli G, De Battisti C, Toffan A, Salviato A, Lavazza A, Cerioli M, Capua I (2007) Co-circulation of distinct genetic lineages of astroviruses in turkeys and guinea fowl. Arch Virol 152: 595–602
        doi: 10.1007/s00705-006-0862-4

    3. Chu DK, Chin AW, Smith GJ, Chan KH, Guan Y, Peiris JS, Poon LL (2010) Detection of novel astroviruses in urban brown rats and previously known astroviruses in humans. J Gen Virol 91: 2457–2462
        doi: 10.1099/vir.0.022764-0

    4. Chu DK, Poon LL, Guan Y, Peiris JS (2008) Novel astroviruses in insectivorous bats. J Virol 82: 9107–9114
        doi: 10.1128/JVI.00857-08

    5. De Benedictis P, Schultz-Cherry S, Burnham A, Cattoli G (2011) Astrovirus infections in humans and animals - molecular biology, genetic diversity, and interspecies transmissions. Infect Genet Evol 11: 1529–1544
        doi: 10.1016/j.meegid.2011.07.024

    6. Guix S, Bosch A, Pintó RM (2013) Astrovirus taxonomy. In: Astrovirus research, pp. 97–110

    7. Kang KI, Icard AH, Linnemann E, Sellers HS, Mundt E (2012) Determination of the full length sequence of a chicken astrovirus suggests a different replication mechanism. Virus Genes 44: 45–50
        doi: 10.1007/s11262-011-0663-z

    8. Li JY, Hu WQ, Liu TN, Zhang HH, Opriessnig T, Xiao CT (2021) Isolation and evolutionary analyses of gout-associated goose astrovirus causing disease in experimentally infected chickens. Poult Sci 100: 543–552
        doi: 10.1016/j.psj.2020.11.003

    9. Madeley CR, Cosgrove BP (1975) Letter: 28 nm particles in faeces in infantile gastroenteritis. Lancet 2: 451–452
        doi: 10.1016/S0140-6736(75)90020-3

    10. Pantin-Jackwood MJ, Spackman E, Woolcock PR (2006) Molecular characterization and typing of chicken and turkey astroviruses circulating in the United States: implications for diagnostics. Avian Dis 50: 397–404
        doi: 10.1637/7512-020606R.1

    11. Reuter G, Nemes C, Boros A, Kapusinszky B, Delwart E, Pankovics P (2012a) Astrovirus in wild boars (Sus scrofa) in Hungary. Arch Virol 157: 1143–1147
        doi: 10.1007/s00705-012-1272-4

    12. Reuter G, Pankovics P, Delwart E, Boros A (2012b) Identification of a novel astrovirus in domestic sheep in Hungary. Arch Virol 157: 323–327
        doi: 10.1007/s00705-011-1151-4

    13. Rivera R, Nollens HH, Venn-Watson S, Gulland FM, Wellehan JF Jr (2010) Characterization of phylogenetically diverse astroviruses of marine mammals. J Gen Virol 91: 166–173
        doi: 10.1099/vir.0.015222-0

    14. Toffan A, Jonassen CM, De Battisti C, Schiavon E, Kofstad T, Capua I, Cattoli G (2009) Genetic characterization of a new astrovirus detected in dogs suffering from diarrhoea. Vet Microbiol 139: 147–152
        doi: 10.1016/j.vetmic.2009.04.031

    15. Tzipori S, Menzies JD, Gray EW (1981) Detection of astrovirus in the faeces of red deer. Vet Rec 108: 286
        doi: 10.1136/vr.108.13.286

  • 加载中

Figures(1) / Tables(1)

Article Metrics

Article views(2801) PDF downloads(10) Cited by()

Related
Proportional views
    通讯作者: 陈斌, bchen63@163.com
    • 1. 

      沈阳化工大学材料科学与工程学院 沈阳 110142

    1. 本站搜索
    2. 百度学术搜索
    3. 万方数据库搜索
    4. CNKI搜索

    Three Novel Avastroviruses Identified in Dead Wild Crows

      Corresponding author: Weifeng Shi, shiwf@ioz.ac.cn
      Corresponding author: Yuhai Bi, beeyh@im.ac.cn
    • 1. Key Laboratory of Applied Technology on Green-EcoHealthy Animal Husbandry of Zhejiang Province, College of Animal Science and Technology and College of Veterinary Medicine of Zhejiang, A & F University, Lin'an 311300, China
    • 2. CAS Key Laboratory of Pathogenic Microbiology and Immunology, Institute of Microbiology, Center for Influenza Research and Early-Warning (CASCIRE), CAS-TWAS Center of Excellence for Emerging Infectious Diseases (CEEID), Chinese Academy of Sciences, Beijing 100101, China
    • 3. Key Laboratory of Etiology and Epidemiology of Emerging Infectious Diseases in Universities of Shandong, School of Public Health, Shandong First Medical University and Shandong Academy of Medical Sciences, Taian 271016, China
    • 4. Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai 200031, China
    • 5. Département de microbiologie-infectiologie et d'immunologie, Université Laval, Québec City G1V 0A6, Canada
    • 6. University of Chinese Academy of Sciences, Beijing 100049, China

    Abstract: 

    • Dear Editor,

      Astroviruses (AstVs) are non-enveloped, single-stranded RNA viruses with a diameter of approximately 35 nm (Madeley and Cosgrove 1975). The genomes of AstVs range in size from 6.8 to 7.9 kb (De Benedictis et al. 2011), consisting of a 5'-untranslated region (UTR), three open reading frames (ORFs), a 3'-UTR, and a poly-adenylated (polyA) tail (Pantin-Jackwood et al. 2006). In 1975, AstVs were first discovered in faeces of infants (Madeley and Cosgrove 1975). Until now, a variety of animal species, including cows, sheep, pigs, dogs, deer, rats, bats, chickens, ducks, turkeys, sea lions and seals have been reported to be infected with AstVs (Tzipori et al. 1981; Cattoli et al. 2007; Chu et al. 2008, 2010; Atkins et al. 2009; Toffan et al. 2009; Rivera et al. 2010; Guix et al. 2013; Kang et al. 2012; Reuter et al. 2012a, 2012b; Li et al. 2021). Currently, AstVs comprise two genera, Mamastrovirus (MAstV) and Avastrovirus (AAstV). Herein, we describe three novel AAstVs identified from dead crow tissues. To our knowledge, this is the first report for identification of AstVs in crows.

      Over 300 crows were found dead in Henan Province in late December 2017. 35 samples, including the heart (n = 5), liver (n = 5), spleen (n = 5), lung (n = 5), kidney (n = 5), intestine (n = 5), and brain (n = 5) tissues were collected from five dead crows for processing. Total RNA was extracted using the QIAamp RNA Viral Kit following manufacturer's instructions. Samples were tested for West Nile virus, Newcastle disease virus, influenza A virus, Japanese encephalitis virus (Mabsky Biotech Co., Ltd., SKY-8624), and Russian spring-summer encephalitis virus (Mabsky Biotech Co., Ltd., SKY-8630) by RT-PCR or qRT-PCR using specific primers (Supplementary Table S1) or commercial kits (Mabsky Biotech Co., Ltd., SKY-8624 and SKY-8630). However, all samples tested negative for these pathogens. The lungs of the first four crows were mixed and named as sample 1; their brains, kidneys, livers and spleens were mixed and named as sample 2; in which RNAs were extracted from the two samples for next generation sequencing (NGS).

      After removing low quality reads, we obtained 133, 747, 472 and 127, 631, 716 reads from the two libraries, respectively. The remaining high quality reads were assembled de novo using CLC Genomic Workbench (version 10.0). Six contigs were obtained and annotated using multiple BLAST searches. Three genomes were found to be related to AstVs. The NGS results were confirmed by Sanger sequencing with the designed primers (Supplementary Fig. S2 and Table S2). These three genome sequences of AstV from crows have been deposited at the National Microbiology Data Center (accession no. NMDC60014580, NMDC60014581, and NMDC60014582) and GenBank (accession no. MW385412, MW385413, and MW385414).

      The near complete genomes of these three AstVs comprised 6152 nt (Astrovirus/crow/Henan/JZ1228CAS001/2017, AstV-CAS001), 6652 nt (Astrovirus/crow/Henan/JZ1228-CAS002/2017, AstV-CAS002), and 6645 nt (Astrovirus/crow/Henan/JZ1228-CAS003/2017, AstV-CAS003), respectively, excluding the polyA tail. These poly-adenylated genomes possessed an astrovirus-like organization, consisting of three sequential open reading frames (ORFs): ORF1a, ORF1b and ORF2. For AstV-CAS001, ORF1a comprised 2625 nt encoding a protein of 874 amino acids (aa) in length. The ORF1b was 1419 nt encoding the RNA dependent RNA polymerase (RdRp) of 472 aa in length. The ORF2 was 2052 nt encoding a capsid protein of 683 aa in length. There was a space of 77 nt between the ORF1a stop codon and the ORF1b start codon, and an overlap of 29 nt between ORF1b and ORF2. The 5' and 3' ends comprised UTRs, with 7 nt and 1 nt sequenced, respectively.

      Regarding AstV-CAS002, the length of ORF1a was the same as that of AstV-CAS001, while the ORF1b of AstVCAS002 was 1299 nt, encoding the RdRp of 432 aa. ORF2 was 2370 nt in length, encoding a capsid protein of 789 aa. There was a space of 203 nt between the ORF1a stop codon and the ORF1b start codon, and a space of 3 nt between ORF1b and ORF2. The lengths of 5' UTR and 3' UTR were 4 nt and 148 nt, respectively. The genome organization of AstV-CAS003 was highly similar to that of AstV-CAS002, with the only difference in the ORF2, which was 2349 nt in length and encoded a capsid protein of 782 aa. In addition, 1 nt of 5' UTR and 165 nt of 3' UTR were obtained for AstV-CAS003. Interestingly, the lengths of the ORF1a, ORF1b or ORF2 were not completely identical among these three strains. However, enough reads were obtained from NGS, and the results have been confirmed by Sanger sequencing. Therefore, the results should be credible, although the full UTRs of these three strains were not obtained in the present study.

      Phylogenetic analyses of these three AstVs were performed using the Maximum-Likelihood (ML) method. As shown in the phylogenetic trees, astroviruses were clustered into the Mamastrovirus (MAstV) and Avastrovirus (AAstV) lineages (Fig. 1A-1C). The AAstVs were further clustered into AAstV-1 (identified in turkey), AAstV-2 (identified in chicken), AAstV-3 (identified in turkey and duck), AAstV-4 (identified in chicken), AAstV-5 (identified in chicken and pigeon), AAstV-6 (identified in pigeon), AAstV-7 (identified in pigeon), GoAstV-1 and GoAstV-2 (identified in goose) sublineages. These three new AstVs grouped within the AAstVs lineage and formed a separate cluster (Fig. 1A) in the tree of whole genomes, which was also found in the phylogenetic trees of the nucleotide and amino acid sequences of ORF1b (Fig. 1B, 1C), ORF1a (Supplementary Fig. S1A-S1B), and ORF2 (Supplementary Fig. S1C-S1D). Therefore, we suggest that these three novel AstVs should be named as crow astrovirus (CrAstV).

      Figure 1.  Phylogenetic analysis of astroviruses. A Nucleotide sequence of whole genome. B Nucleotide sequence of ORF1b gene. C Amino acid sequence of ORF1b gene. The red points highlighted in the phylogenetic tree represent the viruses identified in the present study. The labels on the right represent different genotypes of Astrovirus.

      These three CrAstVs shared 47.8%-52.3%, 46.1%-51%, and 45.7%-50.5% nucleotide identities to known AAstVs at the scale of whole genome, respectively; and shared 39.3%-44.0%, 53.4%-61.1%, and 52.5%-60.6% nucleotide identities in the ORF1a, ORF1b, and ORF2 genes, respectively, and the identities of the corresponding amino acid sequence were 22.0%-28.7% (ORF1a), 44.0%-67.2% (ORF1b), and 46.8%-57.1% (ORF2) (Table 1). In summary, the results from phylogenetic analysis and sequence identities showed that these three novel CrAstVs strains had a distant relationship with known AAstVs, both at the scale of whole genome and single genes.

      Strain Accession no. CrAstV-CAS001 CrAstV-CAS002
      Nucleotide and amino acid identity (%) Nucleotide and amino acid identity (%)
      ORF 1a ORF 1b ORF 2 Genome ORF 1a ORF 1b ORF 2 Genome
      aa nt aa nt aa nt nt aa nt aa nt aa nt nt
      AAstV-1_TAstV-1 Y15936 26.1 41.5 57.2 56.8 57.1 59.6 52.3 25 41.9 55.8 59.2 52.6 56.3 50.3
      AAstV-1_TAstV-1 NC_002470 26.1 41.5 57.2 56.8 57.1 59.6 52.3 25 41.9 55.8 59.2 52.6 56.3 50.3
      AAstV-2_ANV-1 AB033998 22.9 40.4 54.6 56.6 54.6 57.7 51.3 23.9 41.1 51.8 55.3 50.9 53.9 49.8
      AAstV-3_DAstV-1_C-NGB NC012437 26.9 42.6 58.6 59.4 51.6 56.6 48.7 26.2 43.2 66.6 60.8 47.6 54.5 48.1
      AAstV-3_DAstV-1_DA06 FJ919225 26.6 42.6 58.8 59 51.9 56.7 48.8 26 43.2 66.6 60.6 47.4 54.6 48
      AAstV-3_DAstV-1_DA07 FJ919226 26.7 42.7 58.9 58.9 51.9 56.7 48.7 26.1 43.1 66.6 60.6 47.3 54.5 47.9
      AAstV-3_DAstV-1_DA08 FJ919227 27.3 42.9 58.8 59 51.8 56.7 49 26.3 43.2 66.6 60.4 47.4 54.6 48
      AAstV-3_TAstV-2_AK-98 EU143843 26.5 42.4 58.2 59.3 52.4 56.2 51.4 28.1 43.9 67.1 59.5 46.8 54.4 50.6
      AAstV-3_TAstV-2_CA00 EU143844 26.3 43.2 58.9 59 52.5 56.3 51.5 27.5 42.9 67.2 58.4 47.5 54.3 50.5
      AAstV-3_TAstV-2_CO-01 EU143845 26.5 43.2 58.4 58.8 52.4 56.2 51.7 27.4 43.1 66.7 58 47.3 54.2 50.4
      AAstV-3_TAstV-2_MN-01 EU143847 26.2 42.5 60.5 59.2 52 56.3 51.4 27.6 43.1 64.6 58.3 47.2 54.9 50.5
      AAstV-4_CAstV_GA2006 JF832365 26.6 41.6 47.3 57.7 53.1 58.6 50.2 26.4 43.2 44 58 49.4 54.3 48.7
      AAstV-4_CAstV_GA2011 JF414802 26.2 41.3 51.3 58.5 50.5 58.1 48.8 26.3 43 48.7 58 48.3 54.9 47.2
      AAstV-5_ANV1 HM029238 22.4 39.3 47.5 56.9 54.2 57.8 51.4 23.7 41.5 53 56.6 49.7 53.3 49.6
      AAstV-5_Pigeon_ANV1 HQ889774 22 41 47.8 56.1 54 57.9 51.3 23.7 41.3 53.6 57.1 49.6 53.4 49.3
      AAstV-6_Wood-pigeon FR727149 - - 47.7 56.3 52.1 57 48.2 - - 54.2 56.6 49.6 53.5 46.5
      AAstV-7_Feral-pigeon FR727147 - - 45.1 53.4 53 57 47.8 - - 51.8 56.8 49.7 53.2 46.1
      AAstV-7_Feral-pigeon FR727148 - - 45.4 55.9 53.7 57.4 48 - - 52.3 56.7 51.1 54.6 46.2
      AAstV-7_pigeon MF768270 22.6 40.1 50.1 55.9 53.3 57.1 52.1 22.8 40.6 47.7 57.2 50.3 53.4 50.3
      GoAstV-1_FLX KY271027 26.8 42.3 51.6 59.6 54.8 60.6 51.7 26.8 42.3 49.4 59.4 49.7 57.9 50.4
      GoAstV-1_AHDY MH410610 26.6 42.4 51.5 59.1 54.2 60.1 51.8 26.5 42.3 49 59.2 49.7 57.8 50.4
      GoAstV-2_CSZ2 MT934439 25.4 41.7 49.9 57 54.5 58 51.8 26.1 41.1 50.1 57.8 49.3 54.9 51
      GoAstV-2_LYG3 MT934438 25.4 41.8 49.9 57.2 54.5 58 51.9 26.1 41.3 50.1 57.9 49.3 54.9 51
      CrAstV-CAS002 MW385412 46.9 57.3 67.9 68.1 53.6 60.7 65.6 100 100 100 100 100 100 100
      CrAstV-CAS003 MW385413 47.4 57.5 68.8 68.7 54.9 59.9 65.6 - - - - - - -
      CrAstV-CAS001 MW385414 100 100 100 100 100 100 100 - - - - - - -
      Strain Accession no. CrAstV-CAS003
      Nucleotide and amino acid identity (%)
      ORF 1a ORF 1b ORF 2 Genome
      aa nt aa nt aa nt nt
      AAstV-1_TAstV-1 Y15936 25.5 42 55.3 57.9 51.9 55 49.5
      AAstV-1_TAstV-1 NC_002470 25.5 42 55.3 57.9 51.9 55 49.5
      AAstV-2_ANV-1 AB033998 24.5 40.9 51.8 55.2 50.2 52.8 49.9
      AAstV-3_DAstV-1_C-NGB NC012437 26.4 42.8 66.4 60.4 47.5 53.5 47.6
      AAstV-3_DAstV-1_DA06 FJ919225 26.1 43.1 66.4 60.8 47.4 53.5 47.9
      AAstV-3_DAstV-1_DA07 FJ919226 26.2 43.1 66.4 61.1 47.4 53.4 47.9
      AAstV-3_DAstV-1_DA08 FJ919227 26.4 43.3 66.6 61.1 47.5 53.5 48
      AAstV-3_TAstV-2_AK-98 EU143843 28.7 44 66.2 60.2 47 53 50.1
      AAstV-3_TAstV-2_CA00 EU143844 28.3 42.5 66.4 58.9 47.3 53.2 49.9
      AAstV-3_TAstV-2_CO-01 EU143845 28.2 43.2 66 59.1 47.3 52.9 50
      AAstV-3_TAstV-2_MN-01 EU143847 28.4 43.1 63.8 59.5 47.4 53.2 49.8
      AAstV-4_CAstV_GA2006 JF832365 27 43.3 44.4 59 48.6 54.1 48.8
      AAstV-4_CAstV_GA2011 JF414802 27 43.3 48.9 58.5 47 53.5 47.1
      AAstV-5_ANV1 HM029238 24.4 40.5 53 56.7 49.5 53.1 49.6
      AAstV-5_Pigeon_ANV1 HQ889774 24.2 40.9 53.6 57.8 49.4 53.2 49.6
      AAstV-6_Wood-pigeon FR727149 - - 54.6 56.5 49.4 53.1 46.2
      AAstV-7_Feral-pigeon FR727147 - - 52 57.2 48.8 52.7 45.8
      AAstV-7_Feral-pigeon FR727148 - - 52.5 56.6 49.8 53 45.7
      AAstV-7_pigeon MF768270 23.4 40 47.3 57.1 48.8 52.5 50
      GoAstV-1_FLX KY271027 26.8 42.3 49.2 58.5 50.3 55.7 49.5
      GoAstV-1_AHDY MH410610 26.5 42.4 48.9 57.4 50.3 56 49.5
      GoAstV-2_CSZ2 MT934439 26.9 42.3 49.6 58.3 49 53 50.4
      GoAstV-2_LYG3 MT934438 26.9 42.5 49.6 58.5 49 53 50.5
      CrAstV-CAS002 MW385412 96.6 87 97.1 90.4 62.8 66 82.9
      CrAstV-CAS003 MW385413 100 100 100 100 100 100 100
      CrAstV-CAS001 MW385414 - - - - - - -
      aa amino acid sequence, nt nucleotide sequence.

      Table 1.  Genetic identities among the identified astroviruses and different types of avian astroviruses

      Specific primers (Supplementary Table S3) were designed to detect the CrAstVs in different tissues of the dead crows. CrAstV-CAS001 was found in the spleen, kidney and intestine from crow 2; CrAstV-CAS002 was found in the spleen and intestine from crow 2; CrAstVCAS003 was detected in the liver, spleen, lung and intestine from crow 1. Interestingly, both CrAstV-CAS001 and CrAstV-CAS002 were found in the spleen and intestine of the same crow, crow 2 (Supplementary Table S4). The supernatants of different tissues that were RT-PCR positive for the novel CrAstVs were used for virus isolation using specific pathogen free chicken and duck embryos via the chorioallantoic membrane and allantoic cavity inoculation routes. However, no deaths and pathological changes were observed in the embryos after eight passages, and all passages were negative for live CrAstVs, suggesting that these novel astroviruses may have strong host specificity.

      In this study, we reported three novel AAstV strains from dead crows, which formed a separate lineage within Avastrovirus. However, it is not known whether these novel CrAstVs are the causative agents of death, although they were detected in different tissues. However, our study highlighted the expanded host range of astroviruses and that wild birds (e.g. crows) may play an important host in the maintenance and evolution of astroviruses, which warrant further investigations.

    • This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (CAS) (Grant No. XDB29010102), National Natural Science Foundation of China (NSFC) (Grant No. 31870163 and 32061123001), the Academic Promotion Programme of Shandong First Medical University (2019QL006). W.S. is supported by the Taishan Scholars program of Shandong Province. Y.B. is supported by the NSFC Outstanding Young Scholars (Grant No. 31822055), and Youth Innovation Promotion Association of CAS (Grant No. 2017122).

    • The authors declare no conflict of interest.

    • Samples used in this study were obtained from animal carcasses hence requiring no ethical approval.

    Figure (1)  Table (1) Reference (15) Relative (20)

    目录

    /

    DownLoad:  Full-Size Img  PowerPoint
    Return
    Return