Genomic Characterization of Human Respiratory Syncytial Virus Circulating in Islamabad, Pakistan, During an Outbreak in 2022-2023

Overview

Journal Arch Virol

Specialty Microbiology

Date 2024 Apr 21

PMID 38644429

Authors

Syed Adnan Haider

Zunera Jamal

Faheem Tahir

Muhammad Salman

Massab Umair

Affiliations

Soon will be listed here.

Abstract

In this study, conducted at the National Institute of Health, Islamabad, during an outbreak of human respiratory syncytial virus (hRSV) from December 2022 to January 2023, the first whole-genome sequences of hRSV isolates from Islamabad, Pakistan, were determined. Out of 10 positive samples, five were sequenced, revealing the presence of two genotypes: RSV-A (GA2.3.5, ON1 strain) and RSV-B (GB5.0.5.a, BA-10 strain). A rare non-synonymous substitution (E232G) in G the protein and N276S in the F protein were found in RSV-A. In RSV-B, the unique mutations K191R, Q209R, and I206M were found in the F protein. These mutations could potentially influence vaccine efficacy and viral pathogenicity. This research underscores the importance of genomic surveillance for understanding RSV diversity and guiding public health responses in Pakistan.

Citing Articles

Landscape of respiratory syncytial virus.

Duan Y, Liu Z, Zang N, Cong B, Shi Y, Xu L Chin Med J (Engl). 2024; 137(24):2953-2978.

PMID: 39501814 PMC: 11706595. DOI: 10.1097/CM9.0000000000003354.

References

Li Z, Zhang H, Ren L, Lu Q, Ren X, Zhang C . Etiological and epidemiological features of acute respiratory infections in China. Nat Commun. 2021; 12(1):5026. PMC: 8373954. DOI: 10.1038/s41467-021-25120-6. View

Li Y, Johnson E, Shi T, Campbell H, Chaves S, Commaille-Chapus C . National burden estimates of hospitalisations for acute lower respiratory infections due to respiratory syncytial virus in young children in 2019 among 58 countries: a modelling study. Lancet Respir Med. 2020; 9(2):175-185. DOI: 10.1016/S2213-2600(20)30322-2. View

Di Giallonardo F, Kok J, Fernandez M, Carter I, Geoghegan J, Dwyer D . Evolution of Human Respiratory Syncytial Virus (RSV) over Multiple Seasons in New South Wales, Australia. Viruses. 2018; 10(9). PMC: 6164696. DOI: 10.3390/v10090476. View

MUFSON M, Orvell C, Rafnar B, Norrby E . Two distinct subtypes of human respiratory syncytial virus. J Gen Virol. 1985; 66 ( Pt 10):2111-24. DOI: 10.1099/0022-1317-66-10-2111. View

Goya S, Sereewit J, Pfalmer D, Nguyen T, Bakhash S, Sobolik E . Genomic Characterization of Respiratory Syncytial Virus during 2022-23 Outbreak, Washington, USA. Emerg Infect Dis. 2023; 29(4):865-868. PMC: 10045680. DOI: 10.3201/eid2904.221834. View

Bashir U, Nisar N, Mahmood N, Alam M, Sadia H, Zaidi S . Molecular detection and characterization of respiratory syncytial virus B genotypes circulating in Pakistani children. Infect Genet Evol. 2016; 47:125-131. DOI: 10.1016/j.meegid.2016.11.024. View

Aamir U, Salman M, Nisar N, Badar N, Alam M, Ansari J . Molecular characterization of circulating respiratory syncytial virus genotypes in Pakistani children, 2010-2013. J Infect Public Health. 2019; 13(3):438-445. DOI: 10.1016/j.jiph.2019.05.014. View

Bankevich A, Nurk S, Antipov D, Gurevich A, Dvorkin M, Kulikov A . SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012; 19(5):455-77. PMC: 3342519. DOI: 10.1089/cmb.2012.0021. View

Kearse M, Moir R, Wilson A, Stones-Havas S, Cheung M, Sturrock S . Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics. 2012; 28(12):1647-9. PMC: 3371832. DOI: 10.1093/bioinformatics/bts199. View

10.

Goya S, Galiano M, Nauwelaers I, Trento A, Openshaw P, Mistchenko A . Toward unified molecular surveillance of RSV: A proposal for genotype definition. Influenza Other Respir Viruses. 2020; 14(3):274-285. PMC: 7182609. DOI: 10.1111/irv.12715. View

11.

Nguyen L, Schmidt H, von Haeseler A, Minh B . IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2014; 32(1):268-74. PMC: 4271533. DOI: 10.1093/molbev/msu300. View

12.

McLellan J, Chen M, Kim A, Yang Y, Graham B, Kwong P . Structural basis of respiratory syncytial virus neutralization by motavizumab. Nat Struct Mol Biol. 2010; 17(2):248-50. PMC: 3050594. DOI: 10.1038/nsmb.1723. View

13.

Venter M, Madhi S, Tiemessen C, Schoub B . Genetic diversity and molecular epidemiology of respiratory syncytial virus over four consecutive seasons in South Africa: identification of new subgroup A and B genotypes. J Gen Virol. 2001; 82(Pt 9):2117-2124. DOI: 10.1099/0022-1317-82-9-2117. View

14.

Tariq W, Waqar T, Ali S, Ghani E . Winter peak of respiratory syncytial virus in Islamabad. Trop Doct. 2005; 35(1):28-9. DOI: 10.1258/0049475053001958. View

15.

Ali A, Yousafzai M, Waris R, Jafri F, Aziz F, Abbasi I . RSV associated hospitalizations in children in Karachi, Pakistan: Implications for vaccine prevention strategies. J Med Virol. 2017; 89(7):1151-1157. PMC: 5805860. DOI: 10.1002/jmv.24768. View

16.

Ali A, Khowaja A, Bashir M, Aziz F, Mustafa S, Zaidi A . Role of human metapneumovirus, influenza A virus and respiratory syncytial virus in causing WHO-defined severe pneumonia in children in a developing country. PLoS One. 2013; 8(9):e74756. PMC: 3776743. DOI: 10.1371/journal.pone.0074756. View

17.

Rana M, Usman M, Alam M, Ikram A, Salman M, Zaidi S . Impact of COVID-19 preventive measures on other infectious and non-infectious respiratory diseases in Pakistan. J Infect. 2021; 82(5):e31-e32. PMC: 7845518. DOI: 10.1016/j.jinf.2021.01.018. View

18.

Trento A, Casas I, Calderon A, Garcia-Garcia M, Calvo C, Perez-Brena P . Ten years of global evolution of the human respiratory syncytial virus BA genotype with a 60-nucleotide duplication in the G protein gene. J Virol. 2010; 84(15):7500-12. PMC: 2897623. DOI: 10.1128/JVI.00345-10. View

19.

Adams G, Moreno G, Petros B, Uddin R, Levine Z, Kotzen B . Viral Lineages in the 2022 RSV Surge in the United States. N Engl J Med. 2023; 388(14):1335-1337. PMC: 10081154. DOI: 10.1056/NEJMc2216153. View

20.

Papi A, Ison M, Langley J, Lee D, Leroux-Roels I, Martinon-Torres F . Respiratory Syncytial Virus Prefusion F Protein Vaccine in Older Adults. N Engl J Med. 2023; 388(7):595-608. DOI: 10.1056/NEJMoa2209604. View