Obtaining of Whole Genome Sequence of Reoviridae Viruses Through Full-length cDAN Amplification and High-throughput Sequencing Techniques
LI Zhan-Hong1,*, SONG Zi-Ang2 *, ZHU Jian-Bo1, YANG Zhen-Xing1, LI Zhuo-Ran1, LI Hua-Chun1, YANG Heng1,**
1 Yunnan Tropical and Subtropical Animal Virology Laboratory, Yunnan Veterinary and Animal Science Institute, Kunming 650224, China; 2 College of Veterinary Medicine, Yunnan Agricultural University, Kunming 650201, China
Abstract It is vital to obtain the viral genome sequence for taxonomy, diagnostic reagent development and epidemiology studies of Reoviridae viruses. In this study, the whole genome sequences of Reoviridae viruses belonging to 8 different species were acquired through full-length cDAN amplification (FLAC) and next generation sequencing (NGS) techniques, including Bluetongue virus (BTV), Epizootic haemorrhagic disease virus (EHDV), Palyam virus (PALV), Guangxi orbivirus (GXOV), Tibet orbivirus (TIBOV), Mammalian orthoreovirus (MRV), Banna virus (BAV) and Mangshi virus (MSV). The FLAC technique established by this study showed highly sensitive and could amplify the complete genomic DNA of different species of Reoviridae viruses through one RT-PCR reaction, without any sequence information or primer designing for target viruses. The genome size of the viruses sequenced in this study ranged from 18 266 to 23 605 bp with 10 or 12 genomic segments, which were obtained in a week through NGS sequencing and de novo assembling. The amount of data generated by NGS for different Reoviridae virus strains ranged from 1.6 to 1.9 GB, with the number of reads (Q>30) used for assembling virus genome ranged from 293 016 800 to 423 210 600 and the sequencing depth for each base site in the viral genome ranged from 6 000 to 20 000. The establishment of the FLAC and NGS techniques could provide technical guarantee for rapid and accurate acquisition of the whole genome sequence of Reoviridae,which would promote the studies on evolution, diagnostic reagents development and epidemiology of Reoviridae viruses.
LI Zhan-Hong,SONG Zi-Ang,ZHU Jian-Bo, et al. Obtaining of Whole Genome Sequence of Reoviridae Viruses Through Full-length cDAN Amplification and High-throughput Sequencing Techniques[J]. 农业生物技术学报, 2021, 29(1): 93-104.
[1] 扈荣良. 2014. 现代动物病毒学[M]. 北京: 中国农业出版社, pp. 910-950. (HU R L.2014. Modern Animal Virology[M]. China Agriculture Press, Beijing, China, pp. 910-950.) [2] 李占鸿, 王金萍, 杨恒, 等. 2019a. 蓝舌病病毒血清9型毒株在我国的首次分离[J]. 畜牧医学报, 50(02): 354-363. (Li Z H, Wang J P, Yang H, et al.2019a. Isolation of Bluetongue virus serotype 9 strain in China for the first time[J]. Acta Veterinaria et Zootechnica Sinica, 50(2): 354-363.) [3] 李占鸿, 肖雷, 杨振兴, 等. 2019b. 牛源流行性出血病病毒(EHDV)血清10型毒株在我国的离鉴定[J]. 病毒学报, 35(01): 118-126. (Li Z H, Xiao L, Zhang Y H, et al.2019b. Isolation and identification of the Epidemic hemorrhagic fever virus serotype 10 strain from cattle in China[J]. Chinese Journal of Virology, 35(01): 118-126.) [4] 杨恒, 李占鸿, 张怡轩, 等. 2018a. 牛血液中一株新型环状病毒的分离与全基因组序列分析[J]. 病毒学报, 34(01): 75-84. (Yang H, Li Z H, Zhang Y H, et al.2018a. Genomic characterization of a novel orbivirus strain isolated from cattle[J]. Chinese Journal of Virology, 34(1): 75-84.) [5] 杨恒, 王金萍, 李乐, 等. 2019. 我国蓝舌病病毒血清24型毒株的分离与遗传特征分析[J]. 中国兽医学报, 39(01): 31-37. (Yang H, Wang J P, Li L, et al.2019. Genetic characteristics of Bluetongue virus serotype 24 strains isolated in China[J]. Chinese Journal of Veterinary Science, 39(01): 31-37.) [6] 杨恒, 肖雷, 李占鸿, 等. 2018b. 2012-2016年中国南方地区帕利亚姆血清群病毒的分离与序列特征分析[J]. 畜牧兽医学报, 49(04): 761-770. (Yang H, Xiao L, Li Z H, et al.2018b. Sequence analysis Palyam serogroup virus isolated in south China from 2012 to 2016[J]. Acta Veterinaria et Zootechnica Sinica, 49(04): 761-770.) [7] 杨振兴, 孟锦昕, 肖雷, 等. 2019a. 流行性出血病病毒(EHDV)血清7型毒株在中国的首次离与鉴定[J]. 畜牧兽医学报, 50(03): 602-610. (Yang Z X, Meng J X, Xiao L, et al.2019a. Isolation of Epizootic haemorrhagic disease virus serotype 7 strain in China for the first time[J]. Acta Veterinaria et Zootechnica Sinica, 50(03): 602-610.) [8] 杨振兴, 朱建波, 李占鸿, 等. 2019b. 蓝舌病病毒和流行性出血病病毒双重荧光定量RT-PCR检测方法的建立及应用[J]. 中国兽医科学, 49(09): 1104-1111. (Yang Z X, Zhu J B, Li Z H, et al.2019b. Establishment and application of a duplex real-time RT-PCR assay for simultaneous detection of Bluetongue virus and Epidemic haemorrhagic disease virus[J]. Chinese Veterinary Science, 49(09): 1104-1111.) [9] Aliabadi N, Antoni S, Mwenda J M, et al.2019. Global impact of rotavirus vaccine introduction on rotavirus hospitalisations among children under 5 years of age, 2008-16: Findings from the global rotavirus surveillance network[J]. Lancet Global Health, 7(7): e893-e903. [10] Anna C F, Justin S L, Robert M K, et al.2019. Discovery and characterization of Bukakata orbivirus (Reoviridae:Orbivirus), a novel virus from a Ugandan bat[J]. Viruses, 11(3): 209. [11] Attoui H, Becnel J, Belaganahalli S, et al.2012. PartⅡ: The Viruses-the Double Stranded RNA Viruses-family Reoviridae[M]. Elsevier Academic Press, San Diego, pp. 541-637. [12] Attoui H, Billoir F, Cantaloube J F, et al.2000. Strategies for the sequence determination of viral dsRNA genomes[J]. Journal of Virological Methods, 89(1-2): 147-158. [13] Belaganahalli M N, Maan S, Maan N S, et al.2013. Full genome sequencing of Corriparta virus, identifies California mosquito pool virus as a member of the Corriparta virus species[J]. PLOS ONE, 8(8): e70779. [14] Belaganahalli M N, Maan S, Maan N S, et al.2014. Full genome characterization of the culicoides-borne marsupial orbiviruses: Wallal virus, Mudjinbarry virus and Warrego viruses[J]. PLOS ONE, 9(10): e108379. [15] Bolger A M, Lohse M, Usadel B.2014. Trimmomatic: A flexible trimmer for Illumina sequence data[J]. Bioinformatics, 30(15): 2114-2120. [16] Boyce M, Roy P.2007. Recovery of infectious Bluetongue virus from RNA[J]. Journal of Virology, 81(5): 2179-2186. [17] David H, Ryan T, Jean-Baptiste V, et al.2014. De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads[J]. Bioinformatics, 30(1): 40-49. [18] Domingo E, Sheldon J, Perales C.2012. Viral quasispecies evolution[J]. Microbiology and Molecular Biology Reviews, 76(2):159-216. [19] Ejiri H, Lim C K, Isawa H, et al.2015. Genetic and biological characterization of Muko virus, a new distinct member of the species Great Island virus (genus Orbivirus, family Reoviridae), isolated from ixodid ticks in Japan[J]. Archives of Virology, 160(12): 2965-2977. [20] Hernandez D, Francois P, Farinelli L, et al.2008. De novo bacterial genome sequencing: Millions of very short reads assembled on a desktop computer[J]. Genome Research, 18(5): 802-809. [21] Katoh K, Asimenos G, Toh H.2009. Multiple alignment of DNA sequences with MAFFT[J]. Methods in Molecular Biology, 537: 39-64. [22] Kumar K R, Cowley M J, Davis R L.2019. Next-generation sequencing and emerging technologies[J]. Seminars in Thrombosis and Hemostasis, 45(7): 661-673. [23] Kumar S, Stecher G, Li M, et al.2018. MEGA X: Molecular evolutionary genetics analysis across computing platforms[J]. Molecular Biology and Evolution, 35(6): 1547-1549. [24] Liu S, Vijayendran D, Bonning B C.2011. Next generation sequencing technologies for insect virus discovery[J]. Viruses, 3(10): 1849-1869. [25] Maclachlan N J.2011. Bluetongue: History, global epidemiology, and pathogenesis[J]. Preventive Veterinary Medicine, 102(2): 107-111. [26] Maan S, Rao S, Maan N S, et al.2007. Rapid cDNA synthesis and sequencing techniques for the genetic study of bluetongue and other dsRNA viruses[J]. Journal of Virological Methods, 143(2): 132-139. [27] Muller A, Rudel T.2001. Modification of host cell apoptosis by viral and bacterial pathogens[J]. International Journal of Medical Microbiology, 291(3): 197-207. [28] Nelson M I, Viboud C, Simonsen L, et al.2008. Multiple reassortment events in the evolutionary history of H1N1 Influenza A virus since 1918[J]. PLOS Pathogens, 4(2): e1000012. [29] Nomikou K, Hughes J, Wash R, et al.2015. Widespread reassortment shapes the evolution and epidemiology of Bluetongue virus following european invasion[J]. PLOS Pathogens, 11(8): e1005056. [30] Nunes S F, Hamers C, Ratinier M, et al.2014. A synthetic biology approach for a vaccine platform against known and newly emerging serotypes of Bluetongue virus[J]. Journal of Virology, 88(21): 12222-12232. [31] Ruby J G, Bellare P, Derisi J L.2013. PRICE: Software for the targeted assembly of components of (Meta) genomic sequence data[J]. G3 (Bethesda), 3(5): 865-880. [32] Svanella-Dumas L, Marais A, Faure C, et al.2016. Complete nucleotide sequence of a French isolate of Maize rough dwarf virus, a Fijivirus member in the family Reoviridae[J]. Genome announcement, 4(4): e00623-16. [33] Thorvaldsdottir H, Robinson J T, Mesirov J P.2013. Integrative genomics viewer (IGV): High-performance genomics data visualization and exploration[J]. Briefings in Bioinformaticsm, 14(2): 178-192. [34] Urbano P, Urbano F G.1994. The Reoviridae family[J]. Comparative Immunology Microbiology and Infectious Diseases, 17(3-4): 151-161. [35] Wang J, Li H C, He Y W, et al.2015. Isolation and genetic characterization of Mangshi virus: A newly discovered Seadorna virus of the Reoviridae family found in Yunnan Province, China[J]. PLOS ONE, 10(12): e0143601. [36] Wang J, Li H C, He Y W, et al.2017. Isolation of Tibet orbivirus from Culicoides and associated infections in livestock in Yunnan, China[J]. Virology Journal, 14(1): 105. [37] Yang H, Lv M, Sun M, et al.2015. Complete genome sequence of the first bluetongue virus serotype 7 isolate from China: Evidence for entry of African-lineage strains and reassortment between the introduced and native strains[J]. Archives of Virology, 161(1): 223-227. [38] Yang H, Xiao L, Meng J X, et al.2016. Complete genome sequence of a Chuzan virus strain isolated for the first time in mainland China[J]. Archives of Virology, 161(4): 1073-1077. [39] Yang H, Xiao L, Wang J P, et al.2017. Phylogenetic Characterization Genome Segment 2 of Bluetongue virus strains belonging to serotypes 5, 7 and 24 isolated for the first time in China during 2012 to 2014[J]. Transboundary and Emerging Diseases, 64(4): 1317-1321. [40] Zhu J B, Yang H, Li H C, et al.2013. Full-genome sequence of Bluetongue virus serotype 1 (BTV-1) strain Y863, the first BTV-1 isolate of eastern origin found in China[J]. Genome Announcement, 1(4): e00403-e00413.
