The Modification of the Illumina® CovidSeq™ Workflow for RSV Genomic Surveillance: The Genetic Variability of RSV during the 2022–2023 Season in Northwest Spain

Author:

Davina-Nunez Carlos12ORCID,Perez-Castro Sonia13ORCID,Cabrera-Alvargonzalez Jorge Julio13ORCID,Montano-Barrientos Jhon3,Godoy-Diz Montse3,Regueiro Benito1ORCID

Affiliation:

1. Microbiology and Infectology Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), 36312 Vigo, Spain

2. Faculty of Biology, Universidade de Vigo, 36310 Vigo, Spain

3. Microbiology Department, Complexo Hospitalario Universitario de Vigo (CHUVI), Servizo Galego de Saúde (SERGAS), 36214 Vigo, Spain

Abstract

There is growing interest in the molecular surveillance of the Respiratory Syncytial Virus and the monitorization of emerging mutations that could impair the efficacy of antiviral prophylaxis and treatments. A simple, scalable protocol for viral nucleic acid enrichment could improve the surveillance of RSV. We developed a protocol for RSV-A and B amplification based on the Illumina CovidSeq workflow using an RSV primer panel. A total of 135 viral genomes were sequenced from nasopharyngeal samples through the optimization steps of this panel, while an additional 15 samples were used to test the final version. Full coverage of the G gene and over 95% of the coverage of the F gene, the target of the available RSV antivirals or monoclonal antibodies, were obtained. The F:K68N mutation, associated with decreased nirsevimab activity, was detected in our facility. Additionally, phylogenetic analysis showed several sublineages in the 2022–2023 influenza season in Europe. Our protocol allows for a simple and scalable simultaneous amplification of the RSV-A and B whole genome, increasing the yield of RSV sequencing and reducing costs. Its application would allow the world to be ready for the detection of arising mutations in relation to the widespread use of nirsevimab for RSV prevention.

Funder

European Centre for Disease Prevention and Control

Galician Innovation Agency

Consellería de Sanidade, Galicia, Spain

Publisher

MDPI AG

Subject

Inorganic Chemistry,Organic Chemistry,Physical and Theoretical Chemistry,Computer Science Applications,Spectroscopy,Molecular Biology,General Medicine,Catalysis

Reference39 articles.

1. Global and regional mortality from 235 causes of death for 20 age groups in 1990 and 2010: A systematic analysis for the Global Burden of Disease Study 2010;Lozano;Lancet Lond. Engl.,2012

2. Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015: A systematic review and modelling study;Shi;Lancet Lond. Engl.,2017

3. Goya, S., Rojo, G.L., Jordar, M.S.N., Valinotto, L.E., Mistchenko, A.S., and Viegas, M. (2023, November 01). Whole Genome Sequencing of Respiratory Syncytial (RSV) Virus from Clinical Samples with Low Viral Load. Available online: https://www.protocols.io/view/whole-genome-sequencing-of-respiratory-syncytial-r-e6nvwwdwvmkj/v2.

4. Novel and extendable genotyping system for human respiratory syncytial virus based on whole-genome sequence analysis;Chen;Influenza Other Respir. Viruses,2022

5. M2-2 gene as a new alternative molecular marker for phylogenetic, phylodynamic, and evolutionary studies of hRSV;Nunes;Virus Res.,2022

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3