COVID-19 transmission dynamics underlying epidemic waves in Kenya

Brand, Samuel; Ojal, John; Aziza, Rabia; Were, Vincent; Okiro, Emelda A.; Kombe, Ivy K.; Mburu, Caroline; Ogero, Morris; Agweyu, Ambrose; Warimwe, George M.; Nyagwange, James; Karanja, Henry; Gitonga, John N.; Mugo, Daisy; Uyoga, Sophie; Adetifa, Ifedayo; Scott, John A.; Otieno, Edward; Murunga, Nickson; Otiende, Mark; Ochola‐Oyier, Lynette Isabella; Agoti, Charles N.; Githinji, George; Kasera, Kadondi; Amoth, Patrick; Mwangangi, Mercy; Aman, Rashid; Ng’ang’a, Wangari; Tsofa, Benjamin; Bejon, Philip; Keeling, Matthew James; Nokes, D. James; Barasa, Edwine

doi:10.1126/science.abk0414

Cited by 60 publications

(77 citation statements)

References 47 publications

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“…However, we can conclude that asymptomatic infection is very common in our setting, and other lines of evidence confirm widespread transmission in Kenya without overwhelming the health system or high numbers of deaths ( Brand et al ., 2021 ).…”

Section: Discussionsupporting

confidence: 69%

“…By 30 th June 2021, the total number of confirmed cases in Kenya was 95,843, with 1,655 deaths ( WHO, 2021 ). In 2020 and up to June 2021, Kenya experienced three waves; the first wave was in July - August 2020, the second wave observed shortly after from November - December 2020 attributable to the epidemic spreading to new socio-economic groupings, and a third wave from April-May 2021 attributable to variants of concern ( Brand et al ., 2021 ).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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 17th March 2020 and 30th 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.

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Section: Discussionsupporting

confidence: 69%

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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“…Following confirmation of the first COVID-19 case on March 13, 2020, and through subsequent waves, the government of Kenya implemented various mitigation measures to control its spread, including closure of international borders, banning social gatherings, and lockdown of hotspots located primarily in urban and peri-urban regions of the country [15]). Despite these measures, the SARS-CoV-2 prevalence in capital city of Nairobi was reported as 35% in the first 8 month of the pandemic (in November 2020) [16], and studies predicted that 75% of the Nairobi's population would be infected by June 2021 [17].As at January 30, 2022, Kenya had reported five waves of COVID-19 pandemic, with a total of 331,324 confirmed cases and 5,488 deaths (case fatality ratio = 1.7%) [18]. By then, only 17.3% of the adult population had been vaccinated, in large part due to limited availability of vaccines, and a level of vaccine hesitancy [19][20][21].…”

Section: Introductionmentioning

confidence: 99%

Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic

Nasimiyu

Matoke-Muhia

Rono

et al. 2022

Preprint

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Background. Using classical and genomic epidemiology, we tracked the COVID-19 pandemic in Kenya over 23 months to determine the impact of SARS-CoV-2 variants on its progression. Methods. SARS-CoV-2 surveillance and testing data were obtained from the Kenya Ministry of Health, collected daily from 306 health facilities. COVID-19-associated fatality data were also obtained from these health facilities and communities. Whole SARS-CoV-2 genome sequencing were carried out on 1241 specimens. Results. Over the pandemic duration (March 2020 - January 2022) Kenya experienced five waves characterized by attack rates (AR) of between 65.4 and 137.6 per 100,000 persons, and intra-wave case fatality ratios (CFR) averaging 3.5%, two-fold higher than the national average COVID-19 associated CFR. The first two waves that occurred before emergence of global variants of concerns (VoC) had lower AR (65.4 and 118.2 per 100,000). Waves 3, 4, and 5 that occurred during the second year were each dominated by multiple introductions each, of Alpha (74.9% genomes), Delta (98.7%), and Omicron (87.8%) VoCs, respectively. During this phase, government-imposed restrictions failed to alleviate pandemic progression, resulting in higher attack rates spread across the country. Conclusions. The emergence of Alpha, Delta, and Omicron variants was a turning point that resulted in widespread and higher SARS-CoV-2 infections across the country.

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“…Among adult residents of the KHDSS area, we observed a sharp fall in all admissions to hospital in March 2020 reflecting the rapid imposition of travel restrictions at the start of the pandemic 30 . However, admissions returned to normal levels within 3 months, reflecting national trends in mobility, captured by Google Community Mobility Reports, which had normalised by October 2020 31 .…”

Section: Discussionmentioning

confidence: 89%

Impact of the COVID-19 epidemic on mortality in rural coastal Kenya

Otiende

Nyaguara

Bottomley

et al. 2022

Preprint

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Background: The impact of COVID-19 on all-cause mortality in sub-Saharan Africa remains unknown. Methods: We monitored mortality among 306,000 residents of Kilifi Health and Demographic Surveillance System, Kenya, through four COVID-19 waves from April 2020-September 2021. We calculated expected deaths using negative binomial regression fitted to baseline mortality data (2010-2019) and calculated excess mortality as observed-minus-expected deaths. We excluded deaths in infancy because of under-ascertainment of births during lockdown. In February 2021, after two waves of wild-type COVID-19, adult seroprevalence of anti-SARS-CoV-2 was 25.1%. We predicted COVID-19-attributable deaths as the product of age-specific seroprevalence, population size and global infection fatality ratios (IFR). We examined changes in cause of death by Verbal Autopsy (VA). Results: Between April 2020 and February 2021, we observed 1,000 deaths against 1,012 expected deaths (excess mortality -1.2%, 95% PI -6.6%, 5.8%). Based on SARS-CoV-2 seroprevalence, we predicted 306 COVID-19-attributable deaths (a predicted excess mortality of 30.6%) within this period. Monthly mortality analyses showed a significant excess among adults aged ≥45 years in only two months, July-August 2021, coinciding with the fourth (Delta) wave of COVID-19. By September 2021, overall excess mortality was 3.2% (95% PI -0.6%, 8.1%) and cumulative excess mortality risk was 18.7/100,000. By VA, there was a transient reduction in deaths attributable to acute respiratory infections in 2020. Conclusions: Normal mortality rates during extensive transmission of wild-type SARS-CoV-2 through February 2021 suggests that the IFR for this variant is lower in Kenya than elsewhere. We found excess mortality associated with the Delta variant but the cumulative excess mortality risk remains low in coastal Kenya compared to global estimates.

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COVID-19 transmission dynamics underlying epidemic waves in Kenya

Cited by 60 publications

References 47 publications

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

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

Imported SARS-COV-2 Variants of Concern Drove Spread of Infections Across Kenya During the Second Year of the Pandemic

Impact of the COVID-19 epidemic on mortality in rural coastal Kenya

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