Tracking severe acute respiratory syndrome coronavirus 2 transmission and co-infection with other acute respiratory pathogens using a sentinel surveillance system in Rift Valley, Kenya.
Humans
Child, Preschool
Influenza, Human
/ epidemiology
SARS-CoV-2
Sentinel Surveillance
Coinfection
/ epidemiology
Kenya
/ epidemiology
Cross-Sectional Studies
COVID-19
/ epidemiology
Respiratory Tract Infections
Respiratory Syncytial Virus, Human
Respiratory Syncytial Virus Infections
/ epidemiology
SARS-CoV-2
acute respiratory infections
influenza
sentinel surveillance
Journal
Influenza and other respiratory viruses
ISSN: 1750-2659
Titre abrégé: Influenza Other Respir Viruses
Pays: England
ID NLM: 101304007
Informations de publication
Date de publication:
Nov 2023
Nov 2023
Historique:
revised:
29
10
2023
received:
29
05
2023
accepted:
05
11
2023
medline:
1
12
2023
pubmed:
29
11
2023
entrez:
29
11
2023
Statut:
ppublish
Résumé
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been the most significant public health challenge in over a century. SARS-CoV-2 has infected over 765 million people worldwide, resulting in over 6.9 million deaths. This study aimed to detect community transmission of SARS-CoV-2 and monitor the co-circulation of SARS-CoV-2 with other acute respiratory pathogens in Rift Valley, Kenya. We conducted a cross-sectional active sentinel surveillance for the SARS-CoV-2 virus among patients with acute respiratory infections at four sites in Rift Valley from January 2022 to December 2022. One thousand two hundred seventy-one patients aged between 3 years and 98 years presenting with influenza-like illness (ILI) were recruited into the study. Nasopharyngeal swab specimens from all study participants were screened using a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for SARS-CoV-2, influenza A, influenza B and respiratory syncytial virus (RSV). The samples that tested positive for influenza A (n = 73) and RSV (n = 12) were subtyped, while SARS-CoV-2 (n = 177) positive samples were further screened for 12 viral and seven bacterial respiratory pathogens. We had a prevalence of 13.9% for SARS-CoV-2, 5.7% for influenza A, 2% for influenza B and 1% for RSV. Influenza A-H1pdm09 and RSV B were the most dominant circulating subtypes of influenza A and RSV, respectively. The most common co-infecting pathogens were Streptococcus pneumoniae (n = 29) and Haemophilus influenzae (n = 19), accounting for 16.4% and 10.7% of all the SARS-CoV-2 positive samples. Augmenting syndromic testing in acute respiratory infections (ARIs) surveillance is crucial to inform evidence-based clinical and public health interventions.
Sections du résumé
BACKGROUND
BACKGROUND
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been the most significant public health challenge in over a century. SARS-CoV-2 has infected over 765 million people worldwide, resulting in over 6.9 million deaths. This study aimed to detect community transmission of SARS-CoV-2 and monitor the co-circulation of SARS-CoV-2 with other acute respiratory pathogens in Rift Valley, Kenya.
METHODS
METHODS
We conducted a cross-sectional active sentinel surveillance for the SARS-CoV-2 virus among patients with acute respiratory infections at four sites in Rift Valley from January 2022 to December 2022. One thousand two hundred seventy-one patients aged between 3 years and 98 years presenting with influenza-like illness (ILI) were recruited into the study. Nasopharyngeal swab specimens from all study participants were screened using a reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for SARS-CoV-2, influenza A, influenza B and respiratory syncytial virus (RSV).
RESULTS
RESULTS
The samples that tested positive for influenza A (n = 73) and RSV (n = 12) were subtyped, while SARS-CoV-2 (n = 177) positive samples were further screened for 12 viral and seven bacterial respiratory pathogens. We had a prevalence of 13.9% for SARS-CoV-2, 5.7% for influenza A, 2% for influenza B and 1% for RSV. Influenza A-H1pdm09 and RSV B were the most dominant circulating subtypes of influenza A and RSV, respectively. The most common co-infecting pathogens were Streptococcus pneumoniae (n = 29) and Haemophilus influenzae (n = 19), accounting for 16.4% and 10.7% of all the SARS-CoV-2 positive samples.
CONCLUSIONS
CONCLUSIONS
Augmenting syndromic testing in acute respiratory infections (ARIs) surveillance is crucial to inform evidence-based clinical and public health interventions.
Identifiants
pubmed: 38019696
doi: 10.1111/irv.13227
pmc: PMC10686236
pii: IRV13227
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
e13227Subventions
Organisme : Pfizer Inc.
ID : 61773471
Informations de copyright
© 2023 The Authors. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd.
Références
Eur Respir Rev. 2016 Mar;25(139):36-40
pubmed: 26929419
Chest. 2022 May;161(5):1153-1154
pubmed: 35051424
BMC Infect Dis. 2015 Feb 25;15:95
pubmed: 25879805
J Infect. 2020 Aug;81(2):266-275
pubmed: 32473235
Virol J. 2016 Feb 01;13:18
pubmed: 26833249
Laryngoscope Investig Otolaryngol. 2020 Apr 16;5(3):354-359
pubmed: 32587887
Can J Infect Dis Med Microbiol. 2022 Apr 9;2022:1553266
pubmed: 35411212
Science. 2021 Aug 27;373(6558):
pubmed: 34446582
Nat Microbiol. 2020 Apr;5(4):536-544
pubmed: 32123347
Curr Opin Infect Dis. 2004 Jun;17(3):185-91
pubmed: 15166819
Nature. 2020 Mar;579(7798):265-269
pubmed: 32015508
BMC Infect Dis. 2021 Mar 11;21(1):257
pubmed: 33706702
J Clin Invest. 2020 May 1;130(5):2620-2629
pubmed: 32217835
Int J Environ Res Public Health. 2020 Oct 17;17(20):
pubmed: 33080869
Liver Int. 2020 May;40(5):998-1004
pubmed: 32170806
Pan Afr Med J. 2013 Apr 08;14:138
pubmed: 23785543
Int Ophthalmol. 2021 Jan;41(1):349-362
pubmed: 32880786
J Infect Dis. 2018 May 5;217(11):1728-1739
pubmed: 29741740
Int J Microbiol. 2010;2010:126049
pubmed: 20981303
Bull World Health Organ. 2008 May;86(5):408-16
pubmed: 18545744
Influenza Other Respir Viruses. 2023 Nov;17(11):e13227
pubmed: 38019696
PLoS Med. 2013;10(5):e1001444
pubmed: 23690754
Clin Chest Med. 2017 Mar;38(1):127-138
pubmed: 28159155
PLoS Pathog. 2013 Jan;9(1):e1003057
pubmed: 23326226
BMJ Open. 2019 Mar 13;9(3):e026735
pubmed: 30867203
PLoS One. 2020 Aug 21;15(8):e0237857
pubmed: 32822390
Influenza Other Respir Viruses. 2016 Sep;10(5):394-403
pubmed: 27232677