Whole genome sequencing and genome characterization of Aichivirus isolated from Korean adults.
aichivirus
nanopore sequencing
phylogenetic analysis
sanger sequencing
whole genome sequencing
Journal
Journal of medical virology
ISSN: 1096-9071
Titre abrégé: J Med Virol
Pays: United States
ID NLM: 7705876
Informations de publication
Date de publication:
Sep 2024
Sep 2024
Historique:
revised:
14
08
2024
received:
26
04
2024
accepted:
24
08
2024
medline:
4
9
2024
pubmed:
4
9
2024
entrez:
4
9
2024
Statut:
ppublish
Résumé
The whole-genome sequence (WGS) analysis of Aichivirus (AiV) identified in Korea was performed in this study. Using Sanger and Nanopore sequencing, the 8228-nucleotide-long genomic sequence of AiV (OQ121963) was determined and confirmed to belong to genotype A. The full-length genome of OQ121963 consisted of a 7296 nt open reading frame (ORF) that encodes a single polyprotein, and 5' UTR (676 nt) and 3' UTR (256 nt) at 5' and 3' ends, respectively. The ORF consisted of leader protein (L), structural protein P1 (VP0, VP1, and VP3), and nonstructural protein P2 (2A, 2B, and 2C) and P3 (3A, 3B, 3C, and 3D). The secondary structure analysis of the 5' UTR identified only stem-loop C (SL-C) and not SL-A and SL-B. The variable region of the AiV genome was analyzed by MegAlign Pro and reconfirmed by SimPlot analysis using 16 AiV whole genomes known to date. Among the entire regions, structural protein region P1 showed the lowest amino acid identity (96.07%) with reference sequence AB040749 (originated in Japan; genotype A), while the highest amino acid identity (98.26%) was confirmed in the 3D region among nonstructural protein region P2 and P3. Moreover, phylogenetic analysis of the WGS of OQ121963 showed the highest homology (96.96%) with JX564249 (originated in Taiwan; genotype A) and lowest homology (90.14%) with DQ028632 (originated in Brazil; genotype B). Therefore, the complete genome characterization of OQ121963 and phylogenetic analysis of the AiV conducted in this study provide useful information allowing to improve diagnostic tools and epidemiological studies of AiVs.
Substances chimiques
5' Untranslated Regions
0
RNA, Viral
0
3' Untranslated Regions
0
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e29902Subventions
Organisme : National Research Foundation of Korea
ID : NRF2018R1A6A1A03025159
Informations de copyright
© 2024 The Author(s). Journal of Medical Virology published by Wiley Periodicals LLC.
Références
Yamashita T, Kobayashi S, Sakac K, et al. Isolation of cytopathic small round viruses with BS‐Cl cells from patients with gastroenteritis. J Infect Dis. 1991;164(5):954‐957.
Rivadulla E, Romalde JL. A comprehensive review on human Aichi virus. Virol Sin. 2020;35(5):501‐516.
Kebe O, Fernandez‐Garcia MD, Fall A, et al. Prevalence and genetic diversity of Aichi virus 1 from urban wastewater in Senegal. Intervirology. 2021;64(2):96‐101.
Rivadulla E, Varela MF, Romalde JL. Epidemiology of Aichi virus in fecal samples from outpatients with acute gastroenteritis in northwestern Spain. J Clin Virol. 2019;118:14‐19.
Kitajima M, Gerba C. Aichi virus 1: environmental occurrence and behavior. Pathogens. 2015;4(2):256‐268.
Taghinejad M, Ghaderi M, Mousavi‐Nasab SD. High frequency of Aichivirus in children with acute gastroenteritis in Iran. Pediatr Infect Dis. 2021;39(7):576‐579.
Nielsen ACY, Gyhrs ML, Nielsen LP, Pedersen C, Böttiger B. Gastroenteritis and the novel picornaviruses Aichi virus, cosavirus, saffold virus, and salivirus in young children. J Clin Virol. 2013;57(3):239‐242.
Yip CCY, Lo KL, Que TL, et al. Epidemiology of human parechovirus, Aichi virus and salivirus in fecal samples from hospitalized children with gastroenteritis in Hong Kong. Virol J. 2014;11:182.
Chuchaona W, Khamrin P, Yodmeeklin A, et al. Detection and characterization of Aichi virus 1 in pediatric patients with diarrhea in Thailand. J Med Virol. 2017;89(2):234‐238.
Onosi O, Upfold NS, Jukes MD, Luke GA, Knox C. The first molecular detection of Aichi virus 1 in raw sewage and mussels collected in South Africa. Food Environ Virol. 2019;11:96‐100.
Chen BC, Huang TS, Huang NY, Chen CS, Chen YS, Chang TH. Low seroprevalence of Aichi virus infection in Taiwan. Pathogens. 2021;10(5):553.
Northill JA, Simmons RJ, Genge D, Moore FA. Molecular characterization of the first reported Aichivirus A in Australia. Access Microbiol. 2020;2(4):e000099.
Räsänen S, Lappalainen S, Kaikkonen S, Hämäläinen M, Salminen M, Vesikari T. Mixed viral infections causing acute gastroenteritis in children in a waterborne outbreak. Epidemiol Infect. 2010;138(9):1227‐1234.
Rodrigues Portes S, Mello Volotao E, Rose T, et al. Aichi virus positivity in HIV‐1 seropositive children hospitalized with diarrheal disease. Curr HIV Res. 2015;13(4):325‐331.
Lukashev AN. Recombination among picornaviruses. Rev Med Virol. 2010;20(5):327‐337.
John G, Sahajpal NS, Mondal AK, et al. Next‐generation sequencing (NGS) in COVID‐19: a tool for SARS‐CoV‐2 diagnosis, monitoring new strains and phylodynamic modeling in molecular epidemiology. Curr Issues Mol Biol. 2021;43(2):845‐867.
Goodwin S, McPherson JD, McCombie WR. Coming of age: ten years of next‐generation sequencing technologies. Nat Rev Genet. 2016;17(6):333‐351.
Quick J, Grubaugh ND, Pullan ST, et al. Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples. Nat Protoc. 2017;12(6):1261‐1276.
Grädel C, Terrazos Miani MA, Baumann C, et al. Whole‐genome sequencing of human enteroviruses from clinical samples by nanopore direct RNA sequencing. Viruses. 2020;12(8):841.
Xu Y, Lewandowski K, Lumley S, et al. Detection of viral pathogens with multiplex nanopore MinION sequencing: be careful with cross‐talk. Front Microbiol. 2018;9:2225.
Laver T, Harrison J, O'neill PA, et al. Assessing the performance of the Oxford nanopore technologies minion. Biomol Detect Quantif. 2015;3:1‐8.
Kitajima M, Hata A, Yamashita T, Haramoto E, Minagawa H, Katayama H. Development of a reverse transcription‐quantitative PCR system for detection and genotyping of Aichi viruses in clinical and environmental samples. Appl Environ Microbiol. 2013;79(13):3952‐3958.
Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single‐cell sequencing. J Comput Biol. 2012;19(5):455‐477.
Langmead B, Salzberg SL. Fast gapped‐read alignment with Bowtie 2. Nat Methods. 2012;9(4):357‐359.
Schäffer AA, Hatcher EL, Yankie L, et al. VADR: validation and annotation of virus sequence submissions to GenBank. BMC Bioinformatics. 2020;21:211.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30(4):772‐780.
Nguyen LT, Schmidt HA, Von Haeseler A, Minh BQ. IQ‐TREE: a fast and effective stochastic algorithm for estimating maximum‐likelihood phylogenies. Mol Biol Evol. 2015;32(1):268‐274.
Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14(6):587‐589.
Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. RAxML‐NG: a fast, scalable and user‐friendly tool for maximum likelihood phylogenetic inference. Bioinformatics. 2019;35(21):4453‐4455.
Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics (Oxford, England). 2001;17:754‐755.
Bao Y, Bolotov P, Dernovoy D, Kiryutin B, Tatusova T. FLAN: a web server for influenza virus genome annotation. Nucleic Acids Res. 2007;35(suppl 2):W280‐W284.
Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406‐3415.
Yang Z. PAML: a program package for phylogenetic analysis by maximum likelihood. Bioinformatics. 1997;13(5):555‐556.
Yang Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol. 2007;24(8):1586‐1591.
Yang Z. Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol Biol Evol. 1998;15(5):568‐573.
Yang Z, Nielsen R. Codon‐substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol. 2002;19(6):908‐917.
Yang Z. Bayes empirical Bayes inference of amino acid sites under positive selection. Mol Biol Evol. 2005;22(4):1107‐1118.
Goldman N, Yang Z. A codon‐based model of nucleotide substitution for protein‐coding DNA sequences. Mol Biol Evol. 1994;11(5):725‐736.
Sasaki J, Kusuhara Y, Maeno Y, et al. Construction of an infectious cDNA clone of Aichi virus (a new member of the family Picornaviridae) and mutational analysis of a stem‐loop structure at the 5′ end of the genome. J Virol. 2001;75(17):8021‐8030.
Nagashima S, Sasaki J, Taniguchi K. The 5′‐terminal region of the Aichi virus genome encodes cis‐acting replication elements required for positive‐and negative‐strand RNA synthesis. J Virol. 2005;79(11):6918‐6931.
Spielman SJ, Weaver S, Shank SD, et al. Evolution of viral genomes: Interplay between selection, recombination, and other forcesIn: Anisimova M, ed. Evolutionary Genomics. Methods in Molecular Biology. Vol 1910. Humana; 2019:427‐468.
Pham NTK, Khamrin P, Nguyen TA, et al. Isolation and molecular characterization of Aichi viruses from fecal specimens collected in Japan, Bangladesh, Thailand, and Vietnam. J Clin Microbiol. 2007;45(7):2287‐2288.
Weirather JL, de Cesare M, Wang Y, et al. Comprehensive comparison of Pacific Biosciences and Oxford Nanopore Technologies and their applications to transcriptome analysis. F1000Research. 2017;6:100.
Goldberg SMD, Johnson J, Busam D, et al. A sanger/pyrosequencing hybrid approach for the generation of high‐quality draft assemblies of marine microbial genomes. Proc Natl Acad Sci USA. 2006;103(30):11240‐11245.
Dang M, Wang X, Wang Q, et al. Molecular mechanism of SCARB2‐mediated attachment and uncoating of EV71. Protein Cell. 2014;5(9):692‐703.
Ribeiro J, Lorenzetti E, Júnior JCR, da Silva Medeiros TN, Alfieri AF, Alfieri AA. Phylogenetic analysis of VP1 and RdRP genes of Brazilian aichivirus B strains involved in a diarrhea outbreak in dairy calves. Arch Virol. 2017;162(12):3691‐3696.
Baumgarte S, de Souza Luna LK, Grywna K, et al. Prevalence, types, and RNA concentrations of human parechoviruses, including a sixth parechovirus type, in stool samples from patients with acute enteritis. J Clin Microbiol. 2008;46(1):242‐248.
Lukashev AN, Drexler JF, Belalov IS, Eschbach‐Bludau M, Baumgarte S, Drosten C. Genetic variation and recombination in Aichi virus. J Gen Virol. 2012;93(6):1226‐1235.
Zhu L, Wang X, Ren J, et al. Structure of human Aichi virus and implications for receptor binding. Nat Microbiol. 2016;1(11):16150.
Sasaki J, Taniguchi K. Aichi virus 2A protein is involved in viral RNA replication. J Virol. 2008;82(19):9765‐9769.