Epidemiology of COVID-19 infections on routine polymerase chain reaction (PCR) and serology testing in Coastal Kenya

James Nyagwange; Leonard Ndwiga; Kelvin Muteru; Kevin Wamae; James Tuju; Covid Testing Team; Bernadette Kutima; John Gitonga; Henry Karanja; Daisy Mugo; Kadondi Kasera; Patrick Amoth; Nickson Murunga; Lawrence Babu; Edward Otieno; George Githinji; D J Nokes; Benjamin Tsofa; Benedict Orindi; Edwine Barasa; George Warimwe; Charles N Agoti; Philip Bejon; Lynette Isabella Ochola-Oyier

doi:10.12688/wellcomeopenres.17661.1

Epidemiology of COVID-19 infections on routine polymerase chain reaction (PCR) and serology testing in Coastal Kenya

Wellcome Open Res. 2022 Feb 23:7:69. doi: 10.12688/wellcomeopenres.17661.1. eCollection 2022.

Authors

James Nyagwange^#¹, Leonard Ndwiga^#¹, Kelvin Muteru^#¹, Kevin Wamae¹, James Tuju¹, Covid Testing Team¹, Bernadette Kutima¹, John Gitonga¹, Henry Karanja¹, Daisy Mugo¹, Kadondi Kasera², Patrick Amoth², Nickson Murunga¹, Lawrence Babu¹, Edward Otieno¹, George Githinji¹, D J Nokes¹, Benjamin Tsofa¹, Benedict Orindi¹, Edwine Barasa¹, George Warimwe¹, Charles N Agoti¹, Philip Bejon¹, Lynette Isabella Ochola-Oyier¹

Affiliations

¹ Kenya Medical Research Institute, Kilifi, Kenya.
² Ministry of Health, Nairobi, Kenya.

^# Contributed equally.

Abstract

Background: There are limited studies in Africa describing the epidemiology, clinical characteristics and serostatus of individuals tested for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. We tested routine samples from the Coastal part of Kenya between 17 ^th March 2020 and 30 ^th June 2021. Methods: SARS-CoV-2 infections identified using reverse transcription polymerase chain reaction (RT-PCR) and clinical surveillance data at the point of sample collection were used to classify as either symptomatic or asymptomatic. IgG antibodies were measured in sera samples, using a well validated in-house enzyme-linked immunosorbent assay (ELISA). Results: Mombasa accounted for 56.2% of all the 99,694 naso-pharyngeal/oro-pharyngeal swabs tested, and males constituted the majority tested (73.4%). A total of 7737 (7.7%) individuals were SARS-CoV-2 positive by RT-PCR. The majority (i.e., 92.4%) of the RT-PCR positive individuals were asymptomatic. Testing was dominated by mass screening and travellers, and even at health facility level 91.6% of tests were from individuals without symptoms. Out of the 97,124 tests from asymptomatic individuals 7,149 (7%) were positive and of the 2,568 symptomatic individuals 588 (23%) were positive. In total, 2458 serum samples were submitted with paired naso-pharyngeal/oro-pharyngeal samples and 45% of the RT-PCR positive samples and 20% of the RT-PCR negative samples were paired with positive serum samples. Symptomatic individuals had significantly higher antibody levels than asymptomatic individuals and become RT-PCR negative on repeat testing earlier than asymptomatic individuals. Conclusions: In conclusion, the majority of SARS-CoV-2 infections identified by routine testing in Coastal Kenya were asymptomatic. This reflects the testing practice of health services in Kenya, but also implies that asymptomatic infection is very common in the population. Symptomatic infection may be less common, or it may be that individuals do not present for testing when they have symptoms.

Keywords: COVID-19; ELISA; RT-PCR; SARS-CoV-2; clinical characteristics; epidemiology; serology.

Grants and funding

We are grateful to DJN whose funding from the National Institute for Health Research (NIHR) (project reference 17/63/82) using UK aid from the UK Government to support global health research, and the UK Department for International Development (DfID) and Wellcome [102975; 220985] provided reagents to initiate the testing. Also, the KEMRI-Wellcome Core award [203077] from Wellcome award to PB supports the ongoing testing and thereafter the National COVID Testing Africa AAPs/Centre Wellcome Award, [222574], to PB and L.I.O-O supports the ongoing testing. LIO-O and VO were supported by a Wellcome Trust Intermediate Fellowship awarded to L.I.O.-O. [107568]. This work was supported by the African Academy of Sciences (AAS) through a DELTAS Africa Initiative grant awarded to CNA [DEL-15-003]. The DELTAS Africa Initiative is an independent funding scheme of the AAS’ Alliance for Accelerating Excellence in Science in Africa (AESA) and supported by the New Partnership for Africa’s Development Planning and Coordinating Agency (NEPAD Agency) with funding from the Wellcome Trust [107769] and the UK government. Views expressed in this publication are those of the authors and not necessarily those of AAS, NEPAD Agency, Wellcome Trust or the UK government. GW is supported through a fellowship from the Oak foundation and JN is supported through funding from Wellcome [220991]. J.U.N is supported by a PATH grant [PATH grant # GAT.1890-01665713-SUB]. The following grants supported staff in the COVID testing team: funding received by Dr Marta Maia (BOHEMIA study funded UNITAID), Dr Francis Ndungu (Senior Fellowship and Research and Innovation Action (RIA) grants from EDCTP), Dr Eunice Nduati (USAID grant to IAVI: AID-OAA-A-16-00032), Bill and Melinda Gates Foundation GCE grant to Dr Abdirahman Abdi and Prof Jay Berkley and Prof. Anthony Scott (PCIVS grant from GAVI), a IAVI grant to Dr Eunice Nduati and a Wellcome Senior Fellowship to Prof Tom Williams.