Genetic Diversity and Detection of Respiratory Viruses Excluding SARS-CoV-2 During the COVID-19 Pandemic in Gabon, 2020-2021

Overview

Journal Viruses

Publisher MDPI

Specialty Microbiology

Date 2024 May 25

PMID 38793579

Authors

Georgelin Nguema Ondo

Yuri Ushijima

Haruka Abe

Saidou Mahmoudou

Rodrigue Bikangui

Anne Marie Nkoma

Marien Juliet Veraldy Magossou Mbadinga

Ayong More

Maradona Daouda Agbanrin

Christelle M Pemba

Romuald Beh Mba

Ayola Akim Adegnika

Bertrand Lell

Jiro Yasuda

Affiliations

Soon will be listed here.

Abstract

Acute respiratory infections are a major global burden in resource-limited countries, including countries in Africa. Although COVID-19 has been well studied since the pandemic emerged in Gabon, Central Africa, less attention has been paid to other respiratory viral diseases, and very little data are available. Herein, we provide the first data on the genetic diversity and detection of 18 major respiratory viruses in Gabon during the COVID-19 pandemic. Of 582 nasopharyngeal swab specimens collected from March 2020 to July 2021, which were SARS-CoV-2 negative, 156 were positive (26%) for the following viruses: enterovirus (20.3%), human rhinovirus (HRV) (4.6%), human coronavirus OC43 (1.2%), human adenovirus (0.9%), human metapneumovirus (hMPV) (0.5%), influenza A virus (IAV) (0.3%), and human parainfluenza viruses (0.5%). To determine the genetic diversity and transmission route of the viruses, phylogenetic analyses were performed using genome sequences of the detected viruses. The IAV strain detected in this study was genetically similar to strains isolated in the USA, whereas the hMPV strain belonging to the A2b subtype formed a cluster with Kenyan strains. This study provides the first complete genomic sequences of HRV, IAV, and hMPV detected in Gabon, and provides insight into the circulation of respiratory viruses in the country.

References

Abe H, Ushijima Y, Bikangui R, Ondo G, Pemba C, Zadeh V . Genetic Diversity of Hepatitis B and C Viruses Revealed by Continuous Surveillance from 2015 to 2021 in Gabon, Central Africa. Microorganisms. 2023; 11(8). PMC: 10458803. DOI: 10.3390/microorganisms11082046. View

Dare R, Sanghavi S, Bullotta A, Keightley M, St George K, Wadowsky R . Diagnosis of human metapneumovirus infection in immunosuppressed lung transplant recipients and children evaluated for pertussis. J Clin Microbiol. 2006; 45(2):548-52. PMC: 1829004. DOI: 10.1128/JCM.01621-06. View

Lu X, Holloway B, Dare R, Kuypers J, Yagi S, Williams J . Real-time reverse transcription-PCR assay for comprehensive detection of human rhinoviruses. J Clin Microbiol. 2007; 46(2):533-9. PMC: 2238069. DOI: 10.1128/JCM.01739-07. View

Kamau E, Oketch J, de Laurent Z, Phan M, Agoti C, Nokes D . Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia. BMC Genomics. 2020; 21(1):5. PMC: 6941262. DOI: 10.1186/s12864-019-6400-z. View

Belizaire M, Ngattia A, Wassonguema B, Mbeko Simaleko M, Nakoune E, Rafai C . Circulation and seasonality of influenza viruses in different transmission zones in Africa. BMC Infect Dis. 2022; 22(1):820. PMC: 9641867. DOI: 10.1186/s12879-022-07727-2. View

Heim A, Ebnet C, Harste G, Pring-Akerblom P . Rapid and quantitative detection of human adenovirus DNA by real-time PCR. J Med Virol. 2003; 70(2):228-39. DOI: 10.1002/jmv.10382. View

Kuypers J, Wright N, Morrow R . Evaluation of quantitative and type-specific real-time RT-PCR assays for detection of respiratory syncytial virus in respiratory specimens from children. J Clin Virol. 2004; 31(2):123-9. PMC: 7128826. DOI: 10.1016/j.jcv.2004.03.018. View

Tamura K, Stecher G, Kumar S . MEGA11: Molecular Evolutionary Genetics Analysis Version 11. Mol Biol Evol. 2021; 38(7):3022-3027. PMC: 8233496. DOI: 10.1093/molbev/msab120. View

Nabakooza G, Owuor D, de Laurent Z, Galiwango R, Owor N, Kayiwa J . Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains. Sci Rep. 2023; 13(1):5516. PMC: 10072032. DOI: 10.1038/s41598-023-30667-z. View

10.

van Elden L, Nijhuis M, Schipper P, Schuurman R, van Loon A . Simultaneous detection of influenza viruses A and B using real-time quantitative PCR. J Clin Microbiol. 2001; 39(1):196-200. PMC: 87701. DOI: 10.1128/JCM.39.1.196-200.2001. View

11.

Ushijima Y, Abe H, Ondo G, Bikangui R, Massinga Loembe M, Zadeh V . Surveillance of the major pathogenic arboviruses of public health concern in Gabon, Central Africa: increased risk of West Nile virus and dengue virus infections. BMC Infect Dis. 2021; 21(1):265. PMC: 7966894. DOI: 10.1186/s12879-021-05960-9. View

12.

Oh D, Buda S, Biere B, Reiche J, Schlosser F, Duwe S . Trends in respiratory virus circulation following COVID-19-targeted nonpharmaceutical interventions in Germany, January - September 2020: Analysis of national surveillance data. Lancet Reg Health Eur. 2021; 6:100112. PMC: 8183189. DOI: 10.1016/j.lanepe.2021.100112. View

13.

Munshili Njifon H, Monamele C, Vernet M, Njankouo M, Deweerdt L, Nono R . Genetic diversity of influenza A(H3N2) viruses in Northern Cameroon during the 2014-2016 influenza seasons. J Med Virol. 2019; 91(8):1400-1407. DOI: 10.1002/jmv.25456. View

14.

Kenmoe S, Sadeuh-Mba S, Vernet M, Beng V, Vabret A, Njouom R . Molecular epidemiology of Enteroviruses and Rhinoviruses in patients with acute respiratory infections in Yaounde, Cameroon. Influenza Other Respir Viruses. 2021; 15(5):641-650. PMC: 8404047. DOI: 10.1111/irv.12851. View

15.

Teoh Z, Conrey S, McNeal M, Burrell A, Burke R, Mattison C . Burden of Respiratory Viruses in Children Less Than 2 Years Old in a Community-based Longitudinal US Birth Cohort. Clin Infect Dis. 2023; 77(6):901-909. PMC: 10838707. DOI: 10.1093/cid/ciad289. View

16.

Hummel K, Lowe L, Bellini W, Rota P . Development of quantitative gene-specific real-time RT-PCR assays for the detection of measles virus in clinical specimens. J Virol Methods. 2005; 132(1-2):166-73. DOI: 10.1016/j.jviromet.2005.10.006. View

17.

Bruning A, de Kruijf W, van Weert H, Willems W, de Jong M, Pajkrt D . Diagnostic performance and clinical feasibility of a point-of-care test for respiratory viral infections in primary health care. Fam Pract. 2017; 34(5):558-563. PMC: 7108454. DOI: 10.1093/fampra/cmx019. View

18.

Wisdom A, McWilliam Leitch E, Gaunt E, Harvala H, Simmonds P . Screening respiratory samples for detection of human rhinoviruses (HRVs) and enteroviruses: comprehensive VP4-VP2 typing reveals high incidence and genetic diversity of HRV species C. J Clin Microbiol. 2009; 47(12):3958-67. PMC: 2786677. DOI: 10.1128/JCM.00993-09. View

19.

Lekana-Douki S, Nkoghe D, Drosten C, Ngoungou E, Drexler J, Leroy E . Viral etiology and seasonality of influenza-like illness in Gabon, March 2010 to June 2011. BMC Infect Dis. 2014; 14:373. PMC: 4107952. DOI: 10.1186/1471-2334-14-373. View

20.

Kengne-Nde C, Kenmoe S, Modiyinji A, Njouom R . Prevalence of respiratory viruses using polymerase chain reaction in children with wheezing, a systematic review and meta-analysis. PLoS One. 2020; 15(12):e0243735. PMC: 7735590. DOI: 10.1371/journal.pone.0243735. View