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. 2023 Dec 12;11(6):e0132823.
doi: 10.1128/spectrum.01328-23. Epub 2023 Oct 9.

Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022

John T Kayiwa  1 , Charity Nassuna  1 , Sophia Mulei  1 , Gladys Kiggundu  1 , Joweria Nakaseegu  1 , Maria Nabbuto  1 , Esther Amwine  1 , Bridget Nakamoga  1 , Sarah Nankinga  1 , Phiona Atuhaire  1 , Pheobe Nabiryo  1 , Pixy Alunzi  1 , Tony Mbaziira  1 , Paul Isabirye  1 , Noel Ayuro  1 , Nicholas Owor  1 , Jocelyn Kiconco  1 , Barnabas Bakamutumaho  1 , Earl Austin Middlebrook  2 , Pontiano Kaleebu  3 , Julius J Lutwama  1 , Andrew William Bartlow  2
Affiliations

Integration of SARS-CoV-2 testing and genomic sequencing into influenza sentinel surveillance in Uganda, January to December 2022

John T Kayiwa et al. Microbiol Spectr. .

Abstract

Respiratory pathogens cause high rates of morbidity and mortality globally and have high pandemic potential. During the SARS-CoV-2 pandemic, influenza surveillance was significantly interrupted because of resources being diverted to SARS-CoV-2 testing and sequencing. Based on recommendations from the World Health Organization, the Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 testing and genomic sequencing into the influenza surveillance program. We describe the results of influenza and SARS-CoV-2 testing of samples collected from 16 sentinel surveillance sites located throughout Uganda as well as SARS-CoV-2 testing and sequencing in other health centers. The surveillance system showed that both SARS-CoV-2 and influenza can be monitored in communities at the national level. The integration of SARS-CoV-2 detection and genomic surveillance into the influenza surveillance program will help facilitate the timely release of SARS-CoV-2 information for COVID-19 pandemic mitigation and provide important information regarding the persistent threat of influenza.

Keywords: ILI/SARI surveillance; NGS; bioinformatics; diagnostics; genomics; sentinel surveillance.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig 1
Fig 1
Map of Uganda showing the location of the ILI/SARI sentinel sites. The following sites are designated by a red star: Entebbe Regional Referral Hospital, Mukono General Hospital, Fort Portal Hospital, Mbarara Hospital, Arua Regional Referral Hospital, Bibia Health Center III—Arua, Karambi Health Center III—Kasese, Kiryandongo Hospital, Koboko Hospital, Logiri Health Center III, Tororo General Hospital. Kawaala Health Center IV, Kiswa Health Center III, Kitebi Health Center III, Nsambya Hospital, and Kibuli Hospital are all located in the Kampala district and are designated by the orange star.
Fig 2
Fig 2
The number of positive cases of SARS-CoV-2 (orange) and influenza (broken up into AH1, AH3, and Influenza B) at the surveillance sites throughout Uganda from January 2022 to December 2022 (Epi week 50). The lines denote the percent positive cases for all influenza cases (solid line) and SARS-CoV-2 (dashed line).
Fig 3
Fig 3
The number of positive cases of SARS-CoV-2 at both the ILI/SARI surveillance sites (orange) and in the community (green) from January 2022 to December 2022 (Epi week 50). The lines denote the percent positive cases of SARS-CoV-2 at surveillance sites (dashed line) and in the community (solid line).
Fig 4
Fig 4
The percent of Omicron lineages and sublineages detected at surveillance sites (orange) and in the community (green) from samples collected from January 2022 to December 2022 (Epi week 50).
See this image and copyright information in PMC

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