A PCR-based NGS protocol for whole genome sequencing of West Nile virus lineage 2 directly from biological specimens

被引：15

作者：

Chaintoutis, Serafeim C. ^{[1
]}

Papadopoulou, Elpida ^{[2
]}

Melidou, Angeliki ^{[2
]}

Papa, Anna ^{[2
]}

Dovas, Chrysostomos I. ^{[1
]}

机构：

[1] Aristotle Univ Thessaloniki, Fac Hlth Sci, Sch Vet Med, Diagnost Lab, Thessaloniki, Greece

[2] Aristotle Univ Thessaloniki, Fac Hlth Sci, Dept Microbiol, Natl Reference Ctr Arboviruses,Med Sch, Thessaloniki, Greece

来源：

MOLECULAR AND CELLULAR PROBES | 2019年 / 46卷

关键词：

West Nile virus; Lineage; 2; Whole genome sequencing; PCR-Based; Next generation sequencing; INFECTION;

D O I：

10.1016/j.mcp.2019.06.002

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Lineage 2 West Nile virus (WNV) strains have been implicated in severe encephalitis outbreaks in humans and equines residing in Europe. WNV molecular characterization is important for the development of diagnostic assays, as well as for obtaining molecular information, which is necessary for epidemiological investigations of virus transmission in areas at risk. For whole genome sequencing of lineage 2 WNV strains, directly from biological specimens, a PCR-based NGS protocol was developed. The method was applied in WNV-positive specimens obtained from animal, human and mosquito hosts in Greece. The results of its application indicate that, even in cases of low virus titers, the developed PCR-based NGS approach is able to provide whole genome sequences of lineage 2 WNV strains.

引用

页数：5

共 21 条

[1] Genome Sequencing of West Nile Virus from Human Cases in Greece, 2012 [J].

Barzon, Luisa ;

Papa, Anna ;

Pacenti, Monia ;

Franchin, Elisa ;

Lavezzo, Enrico ;

Squarzon, Laura ;

Masi, Giulia ;

Martello, Thomas ;

Testa, Theodolinta ;

Cusinato, Riccardo ;

Palu, Giorgio .

VIRUSES-BASEL, 2013, 5 (09) :2311-2319

[2]

Bunning ML, 2002, EMERG INFECT DIS, V8, P380

[3]

Busch M. P., 2005, SCREENING BLOOD SUPP

[4] Detection and Early Warning of West Nile Virus Circulation in Central Macedonia, Greece, Using Sentinel Chickens and Mosquitoes [J].

Chaskopoulou, Alexandra ;

Dovas, Chrysostomos I. ;

Chaintoutis, Serafeim C. ;

Kashefi, Javid ;

Koehler, Philip ;

Papanastassopoulou, Maria .

VECTOR-BORNE AND ZOONOTIC DISEASES, 2013, 13 (10) :723-732

[5] West Nile Virus: Biology, Transmission, and Human Infection [J].

Colpitts, Tonya M. ;

Conway, Michael J. ;

Montgomery, Ruth R. ;

Fikrig, Erol .

CLINICAL MICROBIOLOGY REVIEWS, 2012, 25 (04) :635-648

[6] Next-generation sequencing shows West Nile virus quasispecies diversification after a single passage in a carrion crow (Corvus corone) in vivo infection model [J].

Dridi, M. ;

Rosseel, T. ;

Orton, R. ;

Johnson, P. ;

Lecollinet, S. ;

Muylkens, B. ;

Lambrecht, B. ;

Van Borm, S. .

JOURNAL OF GENERAL VIROLOGY, 2015, 96 :2999-3009

[7] An optimized methodology for whole genome sequencing of RNA respiratory viruses from nasopharyngeal aspirates [J].

Goya, Stephanie ;

Valinotto, Laura E. ;

Tittarelli, Estefania ;

Rojo, Gabriel L. ;

Nabaes Jodar, Mercedes S. ;

Greninger, Alexander L. ;

Zaiat, Jonathan J. ;

Marti, Marcelo A. ;

Mistchenko, Alicia S. ;

Viegas, Mariana .

PLOS ONE, 2018, 13 (06)

[8] Mosquitoes Transmit Unique West Nile Virus Populations during Each Feeding Episode [J].

Grubaugh, Nathan D. ;

Fauver, Joseph R. ;

Ruckert, Claudia ;

Weger-Lucarelli, James ;

Garcia-Luna, Selene ;

Murrieta, Reyes A. ;

Gendernalik, Alex ;

Smith, Darci R. ;

Brackney, Doug E. ;

Ebel, Gregory D. .

CELL REPORTS, 2017, 19 (04) :709-718

[9] Dynamics of West Nile virus evolution in mosquito vectors [J].

Grubaugh, Nathan D. ;

Ebel, Gregory D. .

CURRENT OPINION IN VIROLOGY, 2016, 21 :132-138

[10] Clinical and biological insights from viral genome sequencing [J].

Houldcroft, Charlotte J. ;

Beale, Mathew A. ;

Breuer, Judith .

NATURE REVIEWS MICROBIOLOGY, 2017, 15 (03) :183-192

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