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TRACKING SARS-COV-2 TRANSMISSION AND CO-INFECTION WITH OTHER ACUTE RESPIRATORY PATHOGENS USING A SENTINEL SURVEILLANCE SYSTEM IN RIFT VALLEY, KENYA
  • +11
  • Vincent Ruttoh,
  • Samwel Symekher,
  • Janet Majanja,
  • Silvanos Opanda,
  • Esther Chitechi,
  • Meshack Wadegu,
  • Ronald Tanui,
  • Tonny Nyandwaro,
  • Peter Rotich,
  • Anne Mwangi,
  • Ibrahim Mwangi,
  • Robert Oira,
  • Audrey Musimbi,
  • Samson Nzou
Vincent Ruttoh
Kenya Medical Research Institute

Corresponding Author:vruttoh@kemri.go.ke

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Samwel Symekher
Kenya Medical Research Institute
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Janet Majanja
Kenya Medical Research Institute
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Silvanos Opanda
Kenya Medical Research Institute
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Esther Chitechi
Kenya Medical Research Institute
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Meshack Wadegu
Kenya Medical Research Institute
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Ronald Tanui
Pan African University Institute for Basic Sciences Technology and Innovation
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Tonny Nyandwaro
Kenya Medical Research Institute
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Peter Rotich
Kenya Medical Research Institute
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Anne Mwangi
Kenya Medical Research Institute
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Ibrahim Mwangi
Kenya Medical Research Institute
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Robert Oira
Kenya Medical Research Institute
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Audrey Musimbi
Kenya Medical Research Institute
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Samson Nzou
Kenya Medical Research Institute
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Abstract

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. 1271 patients of all ages presenting with influenza-like illness were recruited into the study. Nasopharyngeal swab specimens were screened using a multiplex RT–qPCR for SARS-CoV-2, Influenza A, Influenza B and RSV. Influenza A and RSV samples were subtyped, and all the SARS-CoV-2 positive samples were further screened for 12 viral and 7 bacterial respiratory pathogens. We had a prevalence of 13.93% SARS-CoV-2, Influenza A 5.7%, Influenza B 1.96% and 0.94%. 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 and Haemophilus influenzae, accounting for 16.4% and 10.7% of all the SARS-CoV-2 positive samples. Augmenting syndromic testing in ARI surveillance is crucial to inform evidence-based clinical and public health interventions.
29 May 2023Submitted to Influenza and other respiratory viruses
30 May 2023Submission Checks Completed
30 May 2023Assigned to Editor
02 Jun 2023Reviewer(s) Assigned
05 Jul 2023Review(s) Completed, Editorial Evaluation Pending
05 Jul 2023Editorial Decision: Revise Major
03 Sep 20231st Revision Received
26 Sep 2023Submission Checks Completed
26 Sep 2023Assigned to Editor
29 Sep 2023Review(s) Completed, Editorial Evaluation Pending
29 Sep 2023Editorial Decision: Revise Minor
29 Oct 20232nd Revision Received
30 Oct 2023Submission Checks Completed
30 Oct 2023Assigned to Editor
05 Nov 2023Editorial Decision: Accept