Characterisation of Human Astrovirus in a Diarrhoea Outbreak Using Nanopore and Sanger Sequencing Protocols

Overview

Journal Virol J

Publisher Biomed Central

Specialty Microbiology

Date 2023 Nov 14

PMID 37964283

Authors

Jinhui Li

Lang Yang

Kaiying Wang

Zhiyong Gao

Peihan Li

Yanfeng Lin

Leili Jia

Quanyi Wang

Hongbin Song

Peng Li

Affiliations

Soon will be listed here.

Abstract

Human astroviruses (HAstV) are etiologic agents of acute gastroenteritis that most often afflict young children and elderly adults. Most studies of HAstV have focused on epidemiology. In this study, we collected 10 stool samples from a diarrhea outbreak from a diarrhea sentinel surveillance hospital in Beijing. Samples were evaluated immediately using parallel multiplex RT-qPCR and nanopore sequencing, and were then amplified by designed primers and Sanger sequencing to obtain whole genome sequences. Six isolates were categorized as HAstV-5 and subjected to whole genome analysis to characterize their genetic variation and evolution. Full genome analysis revealed low genetic variation (99.38-100% identity) among isolates. Phylogenetic analysis showed that all isolates were closely related to domestic strains Yu/1-CHN and 2013/Fuzhou/85. The recombination breakpoint of the six isolates was located at 2741 bp in the overlap region of ORF1a and ORF1b, similar to those of Yu/1-CHN and 2013/Fuzhou/85. Overall, our study highlights the combined use of RT-qPCR and sequencing as an important tool in rapid diagnosis and acquisition of whole genome sequences of HAstV.

References

Johnson C, Hargest V, Cortez V, Meliopoulos V, Schultz-Cherry S . Astrovirus Pathogenesis. Viruses. 2017; 9(1). PMC: 5294991. DOI: 10.3390/v9010022. View

Yu J, Wang Z, Liu N, Zhang Q, Dong Y, Duan Z . Complete genome of a novel recombinant human astrovirus and its quasispecies in patients following hematopoietic stem cell transplantation. Virus Res. 2020; 288:198138. DOI: 10.1016/j.virusres.2020.198138. View

Yoon S, Ha S, Lim J, Kwon S, Chun J . A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek. 2017; 110(10):1281-1286. DOI: 10.1007/s10482-017-0844-4. View

Wu L, Teng Z, Lin Q, Liu J, Wu H, Kuang X . Epidemiology and Genetic Characterization of Classical Human Astrovirus Infection in Shanghai, 2015-2016. Front Microbiol. 2020; 11:570541. PMC: 7546348. DOI: 10.3389/fmicb.2020.570541. View

Wolfaardt M, Kiulia N, Mwenda J, Taylor M . Evidence of a recombinant wild-type human astrovirus strain from a Kenyan child with gastroenteritis. J Clin Microbiol. 2010; 49(2):728-31. PMC: 3043485. DOI: 10.1128/JCM.01093-10. View

Babkin I, Tikunov A, Zhirakovskaia E, Netesov S, Tikunova N . High evolutionary rate of human astrovirus. Infect Genet Evol. 2012; 12(2):435-42. DOI: 10.1016/j.meegid.2012.01.019. View

Glass R, Noel J, Mitchell D, Herrmann J, Blacklow N, Pickering L . The changing epidemiology of astrovirus-associated gastroenteritis: a review. Arch Virol Suppl. 1996; 12:287-300. DOI: 10.1007/978-3-7091-6553-9_31. View

Li H, Durbin R . Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25(14):1754-60. PMC: 2705234. DOI: 10.1093/bioinformatics/btp324. View

Strain E, Kelley L, Schultz-Cherry S, Muse S, Koci M . Genomic analysis of closely related astroviruses. J Virol. 2008; 82(10):5099-103. PMC: 2346738. DOI: 10.1128/JVI.01993-07. View

10.

Zhirakovskaia E, Tikunov A, Tymentsev A, Sokolov S, Sedelnikova D, Tikunova N . Changing pattern of prevalence and genetic diversity of rotavirus, norovirus, astrovirus, and bocavirus associated with childhood diarrhea in Asian Russia, 2009-2012. Infect Genet Evol. 2018; 67:167-182. DOI: 10.1016/j.meegid.2018.11.006. View

11.

Kumthip K, Khamrin P, Ushijima H, Maneekarn N . Molecular epidemiology of classic, MLB and VA astroviruses isolated from <5 year-old children with gastroenteritis in Thailand, 2011-2016. Infect Genet Evol. 2018; 65:373-379. DOI: 10.1016/j.meegid.2018.08.024. View

12.

Li D, Liu C, Luo R, Sadakane K, Lam T . MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015; 31(10):1674-6. DOI: 10.1093/bioinformatics/btv033. View

13.

Lu L, Zhong H, Xu M, Su L, Cao L, Jia R . Molecular and epidemiological characterization of human adenovirus and classic human astrovirus in children with acute diarrhea in Shanghai, 2017-2018. BMC Infect Dis. 2021; 21(1):713. PMC: 8320412. DOI: 10.1186/s12879-021-06403-1. View

14.

Guix S, Caballero S, Villena C, Bartolome R, Latorre C, Rabella N . Molecular epidemiology of astrovirus infection in Barcelona, Spain. J Clin Microbiol. 2002; 40(1):133-9. PMC: 120088. DOI: 10.1128/JCM.40.1.133-139.2002. View

15.

Martella V, Medici M, Terio V, Catella C, Bozzo G, Tummolo F . Lineage diversification and recombination in type-4 human astroviruses. Infect Genet Evol. 2013; 20:330-5. DOI: 10.1016/j.meegid.2013.09.015. View

16.

Cortez V, Freiden P, Gu Z, Adderson E, Hayden R, Schultz-Cherry S . Persistent Infections with Diverse Co-Circulating Astroviruses in Pediatric Oncology Patients, Memphis, Tennessee, USA. Emerg Infect Dis. 2017; 23(2):288-290. PMC: 5324824. DOI: 10.3201/eid2302.161436. View

17.

De Grazia S, Martella V, Chironna M, Bonura F, Tummolo F, Calderaro A . Nationwide surveillance study of human astrovirus infections in an Italian paediatric population. Epidemiol Infect. 2012; 141(3):524-8. PMC: 9151877. DOI: 10.1017/S0950268812000945. View

18.

LeBaron C, Furutan N, Lew J, Allen J, Gouvea V, Moe C . Viral agents of gastroenteritis. Public health importance and outbreak management. MMWR Recomm Rep. 1990; 39(RR-5):1-24. View

19.

Jacobsen S, Hohne M, Mas Marques A, Beslmuller K, Bock C, Niendorf S . Co-circulation of classic and novel astrovirus strains in patients with acute gastroenteritis in Germany. J Infect. 2018; 76(5):457-464. DOI: 10.1016/j.jinf.2018.02.006. View

20.

Mendez-Toss M, Griffin D, Calva J, Contreras J, Puerto F, Mota F . Prevalence and genetic diversity of human astroviruses in Mexican children with symptomatic and asymptomatic infections. J Clin Microbiol. 2004; 42(1):151-7. PMC: 321733. DOI: 10.1128/JCM.42.1.151-157.2004. View