A custom hepatitis A virus assay for whole-genome sequencing

被引：3

作者：

Cleary, Nora G. ^{[1
]}

Bryant, Patrick W. ^{[1
]}

Lamson, Daryl M. ^{[1
]}

Newman, Alexandra P. ^{[3
]}

George, Kirsten St. ^{[1
,2
]}

机构：

[1] New York State Dept Hlth, Lab Viral Dis, Wadsworth Ctr, Albany, NY 12208 USA

[2] SUNY Albany, Dept Biomed Sci, Albany, NY 12144 USA

[3] New York State Dept Hlth, Bur Communicable Dis Control, Albany, NY 12237 USA

来源：

JOURNAL OF VIROLOGICAL METHODS | 2023年 / 312卷

关键词：

Hepatitis A; AmpliSeq TM; Whole-genome sequencing; GHOST; Molecular epidemiology; MOLECULAR EPIDEMIOLOGY;

D O I：

10.1016/j.jviromet.2022.114649

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Since 2016, the United States has experienced a resurgence in the number of hepatitis A virus (HAV) cases and outbreaks. These outbreaks have been sustained by person-to-person transmission with cases occurring pre-dominantly in high-risk populations including intravenous drug users, individuals experiencing homelessness, and men who have sex with men. To investigate HAV transmission, a molecular-surveillance system consisting of real-time RT-PCR (rRT-PCR) for detection, and a conventional RT-PCR assay for genotyping of HAV, was established in New York State (NYS) in 2019. Since then, a total of 271 HAV-positive serum samples collected from cases across NYS between 2019 and 2021 were identified by rRT-PCR. To rapidly and efficiently generate HAV whole-genome sequences, a custom AmpliSeqTM panel was designed in collaboration with Thermo Fisher. To streamline the process, sample preparation was performed on an Ion Chef and sequencing on an Ion S5XL. Of the 271 HAV-positive samples, the whole-genome sequencing (WGS) assay successfully generated 134 near -complete, high-quality HAV sequences. Phylogenetic analysis of the VP1-2A region identified 216 IB, 48 IA, and 2 IIIA genotypes, while 5 were unable to be typed due to poor sequence in this key region. The HAV whole-genome sequencing approach provided a more efficient and streamlined approach for genotyping HAV compared to previous methods and resulted in phylogenetic trees with enhanced resolution compared to the HAV VP1-2A region alone.

引用

页数：6

共 20 条

[1]

Administration UFaD, HEP A VIR HAV

[2]

[Anonymous], 2020, GENEIOUS PRIME

[3] 5' UTR OF HEPATITIS-A VIRUS-RNA - MUTATIONS IN THE 5'-MOST PYRIMIDINE-RICH TRACT REDUCE ITS ABILITY TO DIRECT INTERNAL INITIATION OF TRANSLATION [J].

CARNEIRO, JS ;

EQUESTRE, M ;

PAGNOTTI, P ;

GRADI, A ;

SONENBERG, N ;

BERCOFF, RP .

JOURNAL OF GENERAL VIROLOGY, 1995, 76 :1189-1196

[4]

Comptroller OotNYS, OSC EC REG NYS

[5]

Control ECfDPa, FACTSH HEP A

[6] Increase in Hepatitis A Virus Infections - United States, 2013-2018 [J].

Foster, Monique A. ;

Hofmeister, Megan G. ;

Kupronis, Benjamin A. ;

Lin, Yulin ;

Xia, Guo-Liang ;

Yin, Shaoman ;

Teshale, Eyasu .

MMWR-MORBIDITY AND MORTALITY WEEKLY REPORT, 2019, 68 (18) :413-415

[7]

Health NYSDo, HEP A

[8] Globalization and the Changing Epidemiology of Hepatitis A Virus [J].

Jacobsen, Kathryn H. .

COLD SPRING HARBOR PERSPECTIVES IN MEDICINE, 2018, 8 (10)

[9] A conserved RNA structural motif for organizing topology within picornaviral internal ribosome entry sites [J].

Koirala, Deepak ;

Shao, Yaming ;

Koldobskaya, Yelena ;

Fuller, James R. ;

Watkins, Andrew M. ;

Shelke, Sandip A. ;

Pilipenko, Evgeny, V ;

Das, Rhiju ;

Rice, Phoebe A. ;

Piccirilli, Joseph A. .

NATURE COMMUNICATIONS, 2019, 10 (1)

[10] MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms [J].

Kumar, Sudhir ;

Stecher, Glen ;

Li, Michael ;

Knyaz, Christina ;

Tamura, Koichiro .

MOLECULAR BIOLOGY AND EVOLUTION, 2018, 35 (06) :1547-1549

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