key: cord-0274368-89v7g7m4 authors: Uyoga, S.; Adetifa, I. M. O.; Otiende, M.; Gitonga, J.; Mugo, D.; Nyagwange, J.; Karanja, H. K.; Tuju, J.; Makale, J.; Aman, R.; Mwangangi, M.; Amoth, P.; Kasera, K.; Ng'ang'a, W.; Kilonzo, N.; Chege, E.; Yegon, C.; Odhiambo, E.; Rotich, T.; Orgut, I.; Kihara, S.; Bottomley, C.; Kagucia, E. W.; Gallagher, K.; Etyang, A. O.; Voller, S.; Lambe, T.; Wright, D.; Barasa, E.; Tsofa, B.; Mwangangi, J.; Bejon, P.; Ochola-Oyier, L. I.; Warimwe, G. M.; Agweyu, A.; Scott, J. A. G. title: Prevalence of SARS-CoV-2 Antibodies from a one-year National Serosurveillance of Kenyan Blood Transfusion Donors date: 2021-07-07 journal: nan DOI: 10.1101/2021.07.06.21260038 sha: 13a7b97775af45705620ed10e76096021b9f8495 doc_id: 274368 cord_uid: 89v7g7m4 In tropical Africa, SARS-CoV-2 epidemiology is poorly described because of lack of access to testing and weak surveillance systems. Since April 2020, we followed SARS-CoV-2 seroprevalence in plasma samples across the Kenya National Blood Transfusion Service. We developed an IgG ELISA against full length spike protein. Validated in locally-observed, PCR-positive COVID-19 cases and in pre-pandemic sera, sensitivity was 92.7% and sensitivity was 99.0%. Using sera from 9,922 donors, we estimated national seroprevalence of SARS-CoV-2 antibodies at 4.3% in April-June 2020 and 9.1% in August-September 2020. The second COVID-19 wave peaked in November 2020. Here we estimate national seroprevalence in early 2021. Between January 3 and March 15, 2021, we collected 3,062 samples from donors aged 16-64 years. Among 3,018 samples that met our study criteria 1,333 were seropositive (crude seroprevalence 44.2%, 95% CI 42.4-46.0%). After Bayesian test-performance adjustment and population weighting to represent the national population distribution, the national estimate of seroprevalence was 48.5% (95% CI 45.2-52.1%). Seroprevalence varied little by age or sex but was higher in Nairobi, the capital city, and lower in two rural regions. Almost half of Kenyan adult donors had evidence of past SARS-CoV-2 infection by March 2021. Although high, the estimate is corroborated by other population-specific estimates in country. Between March and June, 2% of the population were vaccinated against COVID-19 and the country experienced a third epidemic wave. Natural infection is outpacing vaccine delivery substantially in Africa, and this reality needs to be considered as objectives of the vaccine programme are set. For high-income countries like Israel and the USA, vaccination has provided an 'exit' from the COVID-19 pandemic. For example, in surveillance of blood transfusion donors in the UK, 79% of adults had antibodies to SARS-CoV-2 by June 6, 2021 and 15% had serological evidence of natural infection, indicating that most population immunity was vaccine-derived 1 . Global inequity in COVID-19 vaccine distribution was highlighted at the G7 Summit which committed an extra one billion doses to low-income countries. This focus on doses rather than timing overlooks the pace of transmission in these settings. Since April 2020, we have undertaken surveillance of blood transfusion donors (aged 16-64 years) in Kenya 2,3 . Using sera from 9,922 donors, national seroprevalence of SARS-CoV-2 antibodies was estimated at 4.3% in April-June 2020 3 , and 9.1% in August-September 2020 2 . Here we estimate seroprevalence for January-March 2021. Plasma samples were collected from all 6 regional transfusion centres and assayed for antispike IgG using ELISA 3 . Validated among 910 pre-pandemic sera from coastal Kenya and 174 PCR-positive patients from Nairobi, specificity was 99.0% and sensitivity was 92.7%. We used Bayesian Multi-level Regression with Post-stratification (MRP) to adjust for the age, sex and regional distribution of blood donors compared to national figures. Donors were specified at county level but analysed in regions (adjacent counties) 3 . The surveillance was approved by the Scientific and Ethics Review Unit of Kenya Medical Research Institute (Protocol SSC 3426). . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted July 7, 2021. Between January 3 and March 15, 2021, we collected 3,062 samples (median sample date February 14). Sample numbers from each regional transfusion centre were 1145 (Nairobi), 879 (Mombasa), 431 (Kisumu), 250 (Embu), 200 (Nakuru) and 157 (Eldoret). Forty-four samples were excluded for reasons including missing information, age-ineligible donors, and collection in 2020 (see Figure) . Of 3,018 remaining samples, 1,333 were seropositive giving a crude seroprevalence of 44.2% (95% CI 42.4-46.0, Table) . After Bayesian population weighting and test-performance adjustment, the estimate of seroprevalence among adults 16-64 years in Kenya was 48.5% (95% CI 45.2-52.1%). This estimate varied little by age or sex but was higher in Nairobi, the country's capital city and lower in two rural regions in western Kenya, adjacent to Uganda. Blood transfusion donors are a convenience sample and may not represent the population as a whole, though they have provided useful epidemic intelligence in high income countries 1 . In Kenya, they provide an estimate of cumulative incidence which has grown from 4.3% to 9.1% to 48.5% over a period of 12 months 2,3 . This is consistent with estimates in other populations in Kenya: 35% among Nairobi residents sampled randomly in November 2020; 11% and 50% among antenatal clinic attendees in rural Kilifi and urban Nairobi, respectively, in August-September 2020; 42% among truckers in August-November 2020 2,4 . . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted July 7, 2021. ; https://doi.org/10.1101/2021.07.06.21260038 doi: medRxiv preprint The antibody assay was highly specific in Kenyan pre-pandemic samples and demonstrated consistent discrimination in a WHO multi-laboratory standardization exercise 5 . Sensitivity was estimated in individuals sampled a median 21 (minimum 7) days after a positive PCR-test. Antibody concentration, and test sensitivity, may decline with longer times after infection, implying that seroprevalence may be underestimated by our test-performance adjustments. Collectively these data suggest SARS-CoV-2 has progressed rapidly across Kenya and that half of all adults (16-64 years) were infected by February 2021, before a large third wave of SARS-CoV-2 infections began in March 2021. Kenya's COVID-19 vaccine programme also began in March 2021 and has reached 2% of the population to date. Elsewhere in Africa, data are sparse but high seroprevalence has been demonstrated; for example, 38% in Juba, South Sudan in October 2020 6 . Natural infection is outpacing vaccine delivery in Africa, and this reality needs to be considered as objectives of the vaccine programme are set. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted July 7, 2021. is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. The copyright holder for this preprint this version posted July 7, 2021. . CC-BY-NC-ND 4.0 International license It is made available under a is the author/funder, who has granted medRxiv a license to display the preprint in perpetuity. (which was not certified by peer review) The copyright holder for this preprint this version posted July 7, 2021. ; https://doi.org/10.1101/2021.07.06.21260038 doi: medRxiv preprint Weekly national Influenza and COVID-19 surveillance report Temporal trends of SARS-CoV-2 seroprevalence in transfusion blood donors during the first wave of the COVID-19 epidemic in Kenya Seroprevalence of anti-SARS-CoV-2 IgG antibodies in Kenyan blood donors High seroprevalence of SARS-CoV-2 eight months after introduction in Establishment of the WHO International Standard and Reference Panel for anti-SARS-CoV-2 antibody. World Health Organization Seroprevalence of Severe Acute Respiratory Syndrome Coronavirus 2 IgG in All authors had full access to all the data in the study and take responsibility for the integrity of the data and the accuracy of the data analysis.Concept and design: All authors.