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

Journal Article · 08 October 2023 · Microbiology Spectrum

DOI: https://doi.org/10.1128/spectrum.01328-23 · OSTI ID:2329244

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

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1. Uganda Virus Research Inst., Entebbe (Uganda)
2. Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
3. Uganda Virus Research Inst., Entebbe (Uganda); Uganda Research Unit, Entebbe (Uganda)

The Uganda Virus Research Institute, National Influenza Center laboratory integrated SARS-CoV-2 polymerase chain reaction testing and genomic sequencing into the influenza surveillance program that was established in 2007. A total of 7,698 nasopharyngeal/oropharyngeal (NP/OP) swab samples were collected and analyzed from ILI/SARI sentinel sites across the country from January to December 2022. All samples were tested for influenza and SARS-CoV-2. Of these, 252 (3.3%), 162 (2.1%), and 589 (7.7%) were positive for influenza A, influenza B, and SARS-CoV-2, respectively. Out of 414 influenza-positive samples, 122 (29.5%) were AH1pdm09, 130 (31.4%) were AH3, and 162 (39.1%) were B-Victoria. All SARS-CoV-2 sequenced samples were of the Omicron variant, with subvariants of concern known to evade the immune system being detected, such as BQ.1 and XBB.2. Other SARS-CoV-2 positive samples collected from other health centers in the community outside the surveillance sites were included into SARS-CoV-2 genomic sequencing with similar patterns with respect to variants. In all, the ILI/SARI surveillance system has shown to be an efficient, cost-effective, and sustainable program, providing a ready platform to monitor the circulation of SARS-CoV-2 in communities at the national level while remaining vigilant for the persistent threat of influenza. The integration of SARS-CoV-2 detection and genomic surveillance into the influenza surveillance program will strengthen the laboratory response capacity, as well as facilitate the timely release of SARS-CoV-2 genomic information to be used to complement the multiple response strategies for COVID-19 pandemic mitigation.

• Research Organization: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
• Sponsoring Organization: USDOE National Nuclear Security Administration (NNSA); Defense Threat Reduction Agency (DTRA); CARES Foundation, Inc.
• Grant/Contract Number: 89233218CNA000001
• OSTI ID: 2329244
• Report Number(s): LA-UR--23-23309
• Journal Information: Microbiology Spectrum, Journal Name: Microbiology Spectrum Journal Issue: 6 Vol. 11; ISSN 2165-0497
• Publisher: American Society for MicrobiologyCopyright Statement
• Country of Publication: United States
• Language: English