-
Genomic characterisation of respiratory syncytial virus: a novel system for whole genome sequencing and full-length G and F gene sequences
- María Iglesias-Caballero1,* , Sara Camarero-Serrano1 , Sarai Varona2 , Vicente Mas1 , Cristina Calvo3,4 , María Luz García4,6 , Juan García-Costa7 , Sonia Vázquez-Morón1,5 , Sara Monzón2 , Albert Campoy1 , Isabel Cuesta2 , Francisco Pozo1,5 , Inmaculada Casas1,5,*
-
View Affiliations Hide AffiliationsAffiliations: 1 Laboratory of Reference and Research in Respiratory Viruses, National Centre for Microbiology, Instituto de Salud Carlos III, Majadahonda, Spain 2 Bioinformatics Unit, Unidades Centrales Científico Técnicas, Instituto de Salud Carlos III, Majadahonda, Spain 3 Paediatric Infectious and Tropical Diseases Department, Hospital Universitario La Paz, Hospital La Paz Institute for Health Research (IdiPAZ Foundation), Madrid, Spain 4 CIBER de Enfermedades Infecciosas (CIBERINFEC), ISCIII, Madrid, Spain 5 CIBER de Epidemiología y Salud Pública (CIBERESP), ISCIII, Madrid, Spain 6 Paediatric Department, Severo Ochoa University Hospital, Leganés, Biomedical Sciences Research Institute, Puerta de Hierro-Majadahonda University Hospital, Madrid, Spain 7 Santa María Nai Hospital, Ourense, Spain * These authors contributed equallyMaría Iglesias-Caballeromiglesias isciii.es
-
View Citation Hide Citation
Citation style for this article: Iglesias-Caballero María, Camarero-Serrano Sara, Varona Sarai, Mas Vicente, Calvo Cristina, García María Luz, García-Costa Juan, Vázquez-Morón Sonia, Monzón Sara, Campoy Albert, Cuesta Isabel, Pozo Francisco, Casas Inmaculada. Genomic characterisation of respiratory syncytial virus: a novel system for whole genome sequencing and full-length G and F gene sequences. Euro Surveill. 2023;28(49):pii=2300637. https://doi.org/10.2807/1560-7917.ES.2023.28.49.2300637 Received: 16 Nov 2023; Accepted: 30 Nov 2023
Abstract
To advance our understanding of respiratory syncytial virus (RSV) impact through genomic surveillance, we describe two PCR-based sequencing systems, (i) RSVAB-WGS for generic whole-genome sequencing and (ii) RSVAB-GF, which targets major viral antigens, G and F, and is used as a complement for challenging cases with low viral load. These methods monitor RSV genetic diversity to inform molecular epidemiology, vaccine effectiveness and treatment strategies, contributing also to the standardisation of surveillance in a new era of vaccines.
Article metrics loading...
Full text loading...
References
-
Venkatesan P. First RSV vaccine approvals. Lancet Microbe. 2023;4(8):e577. https://doi.org/10.1016/S2666-5247(23)00195-7 PMID: 37390835
-
Zhu Q, McLellan JS, Kallewaard NL, Ulbrandt ND, Palaszynski S, Zhang J, et al. A highly potent extended half-life antibody as a potential RSV vaccine surrogate for all infants. Sci Transl Med. 2017;9(388):eaaj1928. https://doi.org/10.1126/scitranslmed.aaj1928 PMID: 28469033
-
Hammitt LL, Dagan R, Yuan Y, Baca Cots M, Bosheva M, Madhi SA, et al. Nirsevimab for prevention of RSV in healthy late-preterm and term infants. N Engl J Med. 2022;386(9):837-46. https://doi.org/10.1056/NEJMoa2110275 PMID: 35235726
-
European Medicines Agency (EMA). Beyfortus. Amsterdam: EMA; 2022. Available from: https://www.ema.europa.eu/en/medicines/human/EPAR/beyfortus
-
RSVAB WGS and GF protocols. Majadahonda: Instituto de Salud Carlos III; 2023. dx.doi.org/10.17504/protocols.io.kqdg3xbzqg25/v1
-
Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, et al. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020;38(3):276-8. https://doi.org/10.1038/s41587-020-0439-x PMID: 32055031
-
Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490. https://doi.org/10.1371/journal.pone.0009490 PMID: 20224823
-
Garcia-Garcia ML, Calvo C, Ruiz S, Pozo F, Del Pozo V, Remedios L, et al. Role of viral coinfections in asthma development. PLoS One. 2017;12(12):e0189083. https://doi.org/10.1371/journal.pone.0189083 PMID: 29206851
-
Goya S, Galiano M, Nauwelaers I, Trento A, Openshaw PJ, Mistchenko AS, et al. Toward unified molecular surveillance of RSV: A proposal for genotype definition. Influenza Other Respir Viruses. 2020;14(3):274-85. https://doi.org/10.1111/irv.12715 PMID: 32022426
-
Ramaekers K, Rector A, Cuypers L, Lemey P, Keyaerts E, Van Ranst M. Towards a unified classification for human respiratory syncytial virus genotypes. Virus Evol. 2020;6(2):veaa052. https://doi.org/10.1093/ve/veaa052 PMID: 33072402
-
Teirlinck AC, Broberg EK, Stuwitz Berg A, Campbell H, Reeves RM, Carnahan A, et al. Recommendations for respiratory syncytial virus surveillance at the national level. Eur Respir J. 2021;58(3):2003766. https://doi.org/10.1183/13993003.03766-2020 PMID: 33888523
-
Malboeuf CM, Yang X, Charlebois P, Qu J, Berlin AM, Casali M, et al. Complete viral RNA genome sequencing of ultra-low copy samples by sequence-independent amplification. Nucleic Acids Res. 2013;41(1):e13. https://doi.org/10.1093/nar/gks794 PMID: 22962364
-
Goya S, Valinotto LE, Tittarelli E, Rojo GL, Nabaes Jodar MS, Greninger AL, et al. An optimized methodology for whole genome sequencing of RNA respiratory viruses from nasopharyngeal aspirates. PLoS One. 2018;13(6):e0199714. https://doi.org/10.1371/journal.pone.0199714 PMID: 29940028
-
Graf EH, Simmon KE, Tardif KD, Hymas W, Flygare S, Eilbeck K, et al. Unbiased detection of respiratory viruses by use of RNA Sequencing-based metagenomics: a systematic comparison to a commercial PCR panel. J Clin Microbiol. 2016;54(4):1000-7. https://doi.org/10.1128/JCM.03060-15 PMID: 26818672
-
O’Flaherty BM, Li Y, Tao Y, Paden CR, Queen K, Zhang J, et al. Comprehensive viral enrichment enables sensitive respiratory virus genomic identification and analysis by next generation sequencing. Genome Res. 2018;28(6):869-77. https://doi.org/10.1101/gr.226316.117 PMID: 29703817
-
Agoti CN, Otieno JR, Munywoki PK, Mwihuri AG, Cane PA, Nokes DJ, et al. Local evolutionary patterns of human respiratory syncytial virus derived from whole-genome sequencing. J Virol. 2015;89(7):3444-54. https://doi.org/10.1128/JVI.03391-14 PMID: 25609811
-
Beerenwinkel N, Günthard HF, Roth V, Metzner KJ. Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data. Front Microbiol. 2012;3:329. https://doi.org/10.3389/fmicb.2012.00329 PMID: 22973268
-
Holmes EC. Error thresholds and the constraints to RNA virus evolution. Trends Microbiol. 2003;11(12):543-6. https://doi.org/10.1016/j.tim.2003.10.006 PMID: 14659685
-
Agoti CN, Munywoki PK, Phan MVT, Otieno JR, Kamau E, Bett A, et al. Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis. Virus Evol. 2017;3(1):vex006. https://doi.org/10.1093/ve/vex006 PMID: 28458916
-
Di Giallonardo F, Kok J, Fernandez M, Carter I, Geoghegan JL, Dwyer DE, et al. Evolution of human respiratory syncytial virus (RSV) over multiple seasons in New South Wales, Australia. Viruses. 2018;10(9):476. https://doi.org/10.3390/v10090476 PMID: 30200580
-
Robertson M, Eden JS, Levy A, Carter I, Tulloch RL, Cutmore EJ, et al. The spatial-temporal dynamics of respiratory syncytial virus infections across the east-west coasts of Australia during 2016-17. Virus Evol. 2021;7(2):veab068. https://doi.org/10.1093/ve/veab068 PMID: 34532066
-
Díez-Fuertes F, Iglesias-Caballero M, García-Pérez J, Monzón S, Jiménez P, Varona S, et al. A Founder effect led early SARS-CoV-2 transmission in Spain. J Virol. 2021;95(3):e01583-20. https://doi.org/10.1128/JVI.01583-20 PMID: 33127745
-
Pérez-Sautu U, Wiley MR, Iglesias-Caballero M, Pozo F, Prieto K, Chitty JA, et al. Target-independent high-throughput sequencing methods provide evidence that already known human viral pathogens play a main role in respiratory infections with unexplained etiology. Emerg Microbes Infect. 2019;8(1):1054-65. https://doi.org/10.1080/22221751.2019.1640587 PMID: 31335277
Data & Media loading...
Supplementary data
-
-
Supplement
-