Genomics and proteomics of Apis mellifera filamentous virus isolated from honeybees in China

Dahe Yang; Jun Wang; Xi Wang; Fei Deng; Qingyun Diao; Manli Wang; Zhihong Hu; Chunsheng Hou

doi:10.1016/j.virs.2022.02.007

August 2022

Dahe Yang, Jun Wang, Xi Wang, Fei Deng, Qingyun Diao, Manli Wang, Zhihong Hu and Chunsheng Hou. Genomics and proteomics of Apis mellifera filamentous virus isolated from honeybees in China[J]. Virologica Sinica, 2022, 37(4): 483-490. doi: 10.1016/j.virs.2022.02.007

Citation: Dahe Yang, Jun Wang, Xi Wang, Fei Deng, Qingyun Diao, Manli Wang, Zhihong Hu, Chunsheng Hou. Genomics and proteomics of Apis mellifera filamentous virus isolated from honeybees in China .VIROLOGICA SINICA, 2022, 37(4) : 483-490. http://dx.doi.org/10.1016/j.virs.2022.02.007

蜜蜂丝状病毒中国株（AmFV CN）的基因组学及蛋白质组学

杨大贺 ^a,b ,
王君 ^b ,
汪习 ^b ,
邓菲 ^b ,
刁青云 ^a ,
王曼丽 ^b ,
胡志红 ^b,, ,
侯春生 ^c,,

1. 中国农业科学院蜜蜂研究所;
2. 中国科学院武汉病毒研究所, 病毒学国家重点实验室, 国家病毒保藏中心, 生物安全大科学中心;
3. 中国农业科学院麻类研究所

通讯作者： 胡志红, huzh@wh.iov.cn; 侯春生, houchunsheng@caas.cn
收稿日期： 2021-10-22
录用日期： 2022-02-21

摘要

蜜蜂丝状病毒（Apis mellifera filamentous virus，AmFV）是在蜜蜂种群中广泛存在的一种大DNA病毒。之前，AmFV瑞士分离株（AmFV CH-C05）的基因组序列已被报道，但迄今为止对该病毒的分子研究还很少。本文从我国自然感染AmFV的蜜蜂种群中分离纯化出病毒（AmFV CN），并对其开展了基因组学和蛋白质组学研究。电镜观测发现，纯化的AmFV呈卵圆型，大小为300ー500×210ー285nm，其中包裹着一个扭转为三个“8”字环的3165×40nm大小的丝状核衣壳.。基因组测序发现，与以往已报道的AmFV CH-C05环状基因组不同，AmFV CN拥有一个大约493 kb的线性基因组。AmFV CN基因组与AmFV CH-C05基因组的核苷酸相似性为96.9%。AmFV CN基因组编码197个ORF，其中36个ORF（包括18个杆状病毒同源基因）被注释，包括新注释的口服感染因子4（PIF4）和整合酶等潜在基因。系统发育分析揭示，AmFV位于新提出的病毒纲Naldaviricetes中的一个独立分支。蛋白质组学分析揭示了47个AmFV病毒粒子相关蛋白，其中14个有超过50%的序列覆盖率，提示它们可能是主要的病毒结构蛋白。此外，蛋白质组学鉴定到所有被注释的口服感染因子（PIF 0-5），提示它们可能在AmFV的入侵过程中发挥作用。该研究为深入开展AmFV的分子生物学研究奠定了基础。
- 蜜蜂丝状病毒(AmFV)
- , 口服感染因子4 (PIF4)
- , 基因组序列
- , 蛋白质组学
- , 结构蛋白
- , Naldaviricetes

Genomics and proteomics of Apis mellifera filamentous virus isolated from honeybees in China

Dahe Yang ^a,b ,
Jun Wang ^b ,
Xi Wang ^b ,
Fei Deng ^b ,
Qingyun Diao ^a ,
Manli Wang ^b ,
Zhihong Hu ^b,, ,
Chunsheng Hou ^c,,

a Institute of Apicultural Research, Chinese Academy of Agricultural Sciences, Beijing, 100093, China;
b State Key Laboratory of Virology and National Virus Resource Center, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, 430071, China;
c Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China

Corresponding author: Zhihong Hu, huzh@wh.iov.cn Chunsheng Hou, houchunsheng@caas.cn
Received Date: 22 October 2021
Accepted Date: 21 February 2022

Abstract

Apis mellifera filamentous virus (AmFV) is a large DNA virus that is endemic in honeybee colonies. The genome sequence of the AmFV Swiss isolate (AmFV CH–C05) has been reported, but so far very few molecular studies have been conducted on this virus. In this study, we isolated and purified AmFV (AmFV CN) from Chinese honeybee (Apis mellifera) colonies and elucidated its genomics and proteomics. Electron microscopy showed ovoid purified virions with dimensions of 300–500×210–285 nm, wrapping a 3165×40 nm filamentous nucleocapsid in three figure-eight loops. Unlike AmFV CH–C05, which was reported to have a circular genome, our data suggest that AmFV CN has a linear genome of approximately 493 kb. A total of 197 ORFs were identified, among which 36 putative genes including 18 baculoviral homologs were annotated. The overall nucleotide similarity between the CN and CH–C05 isolates was 96.9%. Several ORFs were newly annotated in AmFV CN, including homologs of per os infectivity factor 4 (PIF4) and a putative integrase. Phylogenomic analysis placed AmFVs on a separate branch within the newly proposed virus class Naldaviricetes. Proteomic analysis revealed 47 AmFV virion-associated proteins, of which 14 had over 50% sequence coverage, suggesting that they are likely to be main structural proteins. In addition, all six of the annotated PIFs (PIF-0–5) were identified by proteomics, suggesting that they may function as entry factors in AmFV infection. This study provides fundamental information regarding the molecular biology of AmFV.
- Apis mellifera filamentous Virus (AmFV)
- , per os infectivity factor 4 (PIF4)
- , Genome sequence
- , Proteomics
- , Structural proteins
- , Naldaviricetes

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