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01-05-2024 | Respiratory Syncytial Virus Infection | Brief Report

Genomic characterization of human respiratory syncytial virus circulating in Islamabad, Pakistan, during an outbreak in 2022-2023

Authors: Syed Adnan Haider, Zunera Jamal, Faheem Tahir, Muhammad Salman, Massab Umair

Published in: Archives of Virology | Issue 5/2024

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.

Li Z-J et al (2021) Etiological and epidemiological features of acute respiratory infections in China. Nat Commun 12(1):5026CrossRefPubMedPubMedCentral

Li Y et al (2021) 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 9(2):175–185CrossRefPubMed

Di Giallonardo F et al (2018) Evolution of human respiratory syncytial virus (RSV) over multiple seasons in New South Wales, Australia. Viruses 10(9):476CrossRefPubMedPubMedCentral

Mufson MA et al (1985) Two distinct subtypes of human respiratory syncytial virus. J Gen Virol 66(10):2111–2124CrossRefPubMed

Rojo S et al (2023) Respiratory syncytial virus incidence and typing in the last six seasons in the north of Spain (Asturias). Genetic characterization during the SARS-CoV-2 pandemic. J Med Virol 96(3):e29499

Goya S et al (2023) Genomic Characterization of Respiratory Syncytial Virus during 2022–23 Outbreak, Washington, USA. Emerg Infect Dis 29(4):865CrossRefPubMedPubMedCentral

Pasha O et al (2015) Maternal and newborn outcomes in Pakistan compared to other low and middle income countries in the Global Network’s Maternal Newborn Health Registry: an active, community-based, pregnancy surveillance mechanism. Reprod Health 12:1–10CrossRef

Bashir U et al (2017) Molecular detection and characterization of respiratory syncytial virus B genotypes circulating in Pakistani children. Infect Genet Evol 47:125–131CrossRefPubMed

Aamir UB et al (2020) Molecular characterization of circulating respiratory syncytial virus genotypes in Pakistani children, 2010–2013. J Infect Public Health 13(3):438–445CrossRefPubMed

10.

Aamir UB et al (2013) Molecular characterization of circulating respiratory syncytial virus (RSV) genotypes in Gilgit Baltistan Province of Pakistan during 2011–2012 winter season. PLoS ONE 8(9):e74018CrossRefPubMedCentral

11.

Bankevich A et al (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19(5):455–477CrossRefPubMedPubMedCentral

12.

Kearse M et al (2012) Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647–1649CrossRefPubMedPubMedCentral

13.

Goya S et al (2020) Toward unified molecular surveillance of RSV: a proposal for genotype definition. Influenza Other Respir Viruses 14(3):274–285CrossRefPubMedPubMedCentral

14.

Nguyen L-T et al (2015) IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol 32(1):268–274CrossRefPubMed

15.

McLellan JS et al (2010) Structural basis of respiratory syncytial virus neutralization by motavizumab. Nat Struct Mol Biol 17(2):248–250CrossRefPubMedPubMedCentral

16.

Venter M et al (2001) 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 82(9):2117–2124CrossRefPubMed

17.

Tariq W-U-Z et al (2005) Winter peak of respiratory syncytial virus in Islamabad. Trop Doct 35(1):28–29CrossRefPubMed

18.

Ali A et al (2017) RSV associated hospitalizations in children in Karachi, Pakistan: implications for vaccine prevention strategies. J Med Virol 89(7):1151–1157CrossRefPubMedPubMedCentral

19.

Ali A et al (2013) 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 8(9):e74756CrossRefPubMedPubMedCentral

20.

Rana MS et al (2021) Impact of COVID-19 preventive measures on other infectious and non-infectious respiratory diseases in Pakistan. J Infect 82(5):e31–e32CrossRefPubMedPubMedCentral

21.

Trento A et al (2010) 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 84(15):7500–7512CrossRefPubMedPubMedCentral

22.

Rachael Zimlich R. (2023) BSN. RSV surges early in 2022, but appears to make early retreat. Available from: https://www.contemporarypediatrics.com/view/rsv-surges-early-in-2022-but-appears-to-make-early-retreat. Accessed 15 Sept 2023

23.

Adams G et al (2023) Viral lineages in the 2022 RSV surge in the United States. N Engl J Med 388(14):1335–1337CrossRefPubMedPubMedCentral

24.

Holland LA et al (2023) Genomic sequencing surveillance and antigenic site mutations of respiratory syncytial virus in arizona, USA. medRxiv pp 2023–06

25.

Papi A et al (2023) Respiratory syncytial virus prefusion F protein vaccine in older adults. N Engl J Med 388(7):595–608CrossRefPubMed

26.

Kampmann B et al (2023) Bivalent prefusion F vaccine in pregnancy to prevent RSV illness in infants. N Engl J Med 388(16):1451–1464CrossRefPubMed

27.

Gilman MS et al (2016) Rapid profiling of RSV antibody repertoires from the memory B cells of naturally infected adult donors. Sci Immunol 1(6):eaaj1879CrossRefPubMedPubMedCentral

28.

Choi S-H, Park KS, Kim Y-J (2019) Analysis of respiratory syncytial virus fusion protein from clinical isolates of Korean children in palivizumab era, 2009–2015. J Infect Chemother 25(7):514–519CrossRefPubMed

29.

Respiratory Syncytial Virus (RSV) There are FDA-approved vaccines and monoclonal antibodies for RSV now available. [09/11/2023 19 Oct 2023]; Available from: https://www.fda.gov/consumers/covid-19-flu-and-rsv/respiratory-syncytial-virus-rsv

30.

Hotard AL et al (2015) Identification of residues in the human respiratory syncytial virus fusion protein that modulate fusion activity and pathogenesis. J Virol 89(1):512–522CrossRefPubMed

31.

Ahani B et al (2023) Molecular and phenotypic characteristics of RSV infections in infants during two nirsevimab randomized clinical trials. Nat Commun 14(1):4347CrossRefPubMedPubMedCentral

32.

Tabor DE et al (2020) Global molecular epidemiology of respiratory syncytial virus from the 2017–2018 INFORM-RSV Study. J Clin Microbiol 59(1):10–1128. https://doi.org/10.1128/jcm.01828-20CrossRef

33.

McLellan JS, Ray WC, Peeples ME (2013) Structure and function of respiratory syncytial virus surface glycoproteins. Challenges and opportunities for respiratory syncytial virus vaccines 83–104

34.

Tripp RA et al (2018) Respiratory syncytial virus: targeting the G protein provides a new approach for an old problem. J Virol 92(3):10–1128. https://doi.org/10.1128/jvi.01302-17CrossRef

35.

Jung HE, Kim TH, Lee HK (2020) Contribution of dendritic cells in protective immunity against respiratory syncytial virus infection. Viruses 12(1):102CrossRefPubMedPubMedCentral

36.

Pickens JA, Tripp RA (2018) Verdinexor targeting of CRM1 is a promising therapeutic approach against RSV and influenza viruses. Viruses 10(1):48CrossRefPubMedPubMedCentral

37.

Rios Guzman E, Hultquist JF (2022) Clinical and biological consequences of respiratory syncytial virus genetic diversity. Ther Adv Infect Dis 9:20499361221128092PubMedPubMedCentral

38.

Liu C et al (2015) Adenovirus infection in children with acute lower respiratory tract infections in Beijing, China, 2007 to 2012. BMC Infect Dis 15(1):1–9CrossRef

39.

Palomino MA et al (2004) Adenovirus and respiratory syncytial virus-adenovirus mixed acute lower respiratory infections in Chilean infants. Pediatr Infect Dis J 23(4):337–341CrossRefPubMed

40.

Swets MC et al (2022) SARS-CoV-2 co-infection with influenza viruses, respiratory syncytial virus, or adenoviruses. The Lancet 399(10334):1463–1464CrossRef

Title: Genomic characterization of human respiratory syncytial virus circulating in Islamabad, Pakistan, during an outbreak in 2022-2023
Authors: Syed Adnan Haider
Zunera Jamal
Faheem Tahir
Muhammad Salman
Massab Umair
Publication date: 01-05-2024
Publisher: Springer Vienna
Keyword: Respiratory Syncytial Virus Infection
Published in: Archives of Virology / Issue 5/2024
Print ISSN: 0304-8608
Electronic ISSN: 1432-8798
DOI: https://doi.org/10.1007/s00705-024-06036-0

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