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1.
Clin Infect Dis ; 74(2): 288-293, 2022 01 29.
Article in English | MEDLINE | ID: covidwho-1662110

ABSTRACT

BACKGROUND: Few studies have assessed the seroprevalence of antibodies against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among healthcare workers (HCWs) in Africa. We report findings from a survey among HCWs in 3 counties in Kenya. METHODS: We recruited 684 HCWs from Kilifi (rural), Busia (rural), and Nairobi (urban) counties. The serosurvey was conducted between 30 July and 4 December 2020. We tested for immunoglobulin G antibodies to SARS-CoV-2 spike protein, using enzyme-linked immunosorbent assay. Assay sensitivity and specificity were 92.7 (95% CI, 87.9-96.1) and 99.0% (95% CI, 98.1-99.5), respectively. We adjusted prevalence estimates, using bayesian modeling to account for assay performance. RESULTS: The crude overall seroprevalence was 19.7% (135 of 684). After adjustment for assay performance, seroprevalence was 20.8% (95% credible interval, 17.5%-24.4%). Seroprevalence varied significantly (P < .001) by site: 43.8% (95% credible interval, 35.8%-52.2%) in Nairobi, 12.6% (8.8%-17.1%) in Busia and 11.5% (7.2%-17.6%) in Kilifi. In a multivariable model controlling for age, sex, and site, professional cadre was not associated with differences in seroprevalence. CONCLUSION: These initial data demonstrate a high seroprevalence of antibodies to SARS-CoV-2 among HCWs in Kenya. There was significant variation in seroprevalence by region, but not by cadre.


Subject(s)
COVID-19 , SARS-CoV-2 , Antibodies, Viral , Bayes Theorem , Health Personnel , Humans , Kenya/epidemiology , Seroepidemiologic Studies , Spike Glycoprotein, Coronavirus
2.
J Clin Virol ; 146: 105061, 2022 01.
Article in English | MEDLINE | ID: covidwho-1636045

ABSTRACT

Many SARS-CoV-2 antibody detection assays have been developed but their differential performance is not well described. In this study we compared an in-house (KWTRP) ELISA which has been used extensively to estimate seroprevalence in the Kenyan population with WANTAI, an ELISA which has been approved for widespread use by the WHO. Using a wide variety of sample sets including pre-pandemic samples (negative gold standard), SARS-CoV-2 PCR positive samples (positive gold standard) and COVID-19 test samples from different periods (unknowns), we compared performance characteristics of the two assays. The overall concordance between WANTAI and KWTRP was 0.97 (95% CI, 0.95-0.98). For WANTAI and KWTRP, sensitivity was 0.95 (95% CI 0.90-0.98) and 0.93 (95% CI 0.87-0.96), respectively. Specificity for WANTAI was 0.98 (95% CI, 0.96-0.99) and 0.99 (95% CI 0.96-1.00) while KWTRP specificity was 0.99 (95% CI, 0.98-1.00) and 1.00 using pre-pandemic blood donors and pre-pandemic malaria cross-sectional survey samples respectively. Both assays show excellent characteristics to detect SARS-CoV-2 antibodies.


Subject(s)
COVID-19 , Spike Glycoprotein, Coronavirus , Antibodies, Viral , Cross-Sectional Studies , Enzyme-Linked Immunosorbent Assay , Humans , Immunoglobulin G , Kenya/epidemiology , SARS-CoV-2 , Sensitivity and Specificity , Seroepidemiologic Studies
3.
Science ; 374(6570): 989-994, 2021 Nov 19.
Article in English | MEDLINE | ID: covidwho-1526450

ABSTRACT

Policy decisions on COVID-19 interventions should be informed by a local, regional and national understanding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Epidemic waves may result when restrictions are lifted or poorly adhered to, variants with new phenotypic properties successfully invade, or infection spreads to susceptible subpopulations. Three COVID-19 epidemic waves have been observed in Kenya. Using a mechanistic mathematical model, we explain the first two distinct waves by differences in contact rates in high and low social-economic groups, and the third wave by the introduction of higher-transmissibility variants. Reopening schools led to a minor increase in transmission between the second and third waves. Socioeconomic and urban­rural population structure are critical determinants of viral transmission in Kenya.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , COVID-19/virology , COVID-19 Nucleic Acid Testing , Communicable Disease Control , Epidemics , Humans , Incidence , Kenya/epidemiology , Models, Biological , Seroepidemiologic Studies , Social Class , Socioeconomic Factors
6.
Open Forum Infect Dis ; 8(7): ofab314, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-1361796

ABSTRACT

In October 2020, anti-severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) immunoglobulin G seroprevalence among truck drivers and their assistants (TDA) in Kenya was 42.3%, higher than among healthcare workers and blood donors. Truck drivers and their assistants transport essential supplies during the coronavirus disease 2019 pandemic, placing them at increased risk of being infected and of transmitting SARS-CoV-2 over a wide geographical area.

7.
Nat Commun ; 12(1): 3966, 2021 06 25.
Article in English | MEDLINE | ID: covidwho-1281718

ABSTRACT

Observed SARS-CoV-2 infections and deaths are low in tropical Africa raising questions about the extent of transmission. We measured SARS-CoV-2 IgG by ELISA in 9,922 blood donors across Kenya and adjusted for sampling bias and test performance. By 1st September 2020, 577 COVID-19 deaths were observed nationwide and seroprevalence was 9.1% (95%CI 7.6-10.8%). Seroprevalence in Nairobi was 22.7% (18.0-27.7%). Although most people remained susceptible, SARS-CoV-2 had spread widely in Kenya with apparently low associated mortality.


Subject(s)
Antibodies, Viral/immunology , COVID-19/diagnosis , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , Adolescent , Adult , Antibodies, Viral/blood , Bayes Theorem , COVID-19/epidemiology , COVID-19/virology , Enzyme-Linked Immunosorbent Assay , Epidemics , Female , Humans , Immunoglobulin G/blood , Immunoglobulin G/immunology , Kenya/epidemiology , Male , Middle Aged , Prevalence , SARS-CoV-2/metabolism , SARS-CoV-2/physiology , Seroepidemiologic Studies , Spike Glycoprotein, Coronavirus/metabolism , Young Adult
8.
Eurosurveillance ; 25(19):7, 2020.
Article in English | ProQuest Central | ID: covidwho-1202500

ABSTRACT

Using electronic health records, we assessed the early impact of coronavirus disease (COVID-19) on routine childhood vaccination in England by 26 April 2020. Measles-mumps-rubella vaccination counts fell from February 2020, and in the 3 weeks after introduction of physical distancing measures were 19.8% lower (95% confidence interval: −20.7 to −18.9) than the same period in 2019, before improving in mid-April. A gradual decline in hexavalent vaccination counts throughout 2020 was not accentuated by physical distancing.

9.
Pediatr Infect Dis J ; 40(6): 503-512, 2021 06 01.
Article in English | MEDLINE | ID: covidwho-1197052

ABSTRACT

BACKGROUND: Severity of viral respiratory illnesses can be increased with bacterial coinfection and can vary by sex, but influence of coinfection and sex on human endemic coronavirus (CoV) species, which generally cause mild to moderate respiratory illness, is unknown. We evaluated CoV and pneumococcal co-detection by sex in childhood pneumonia. METHODS: In the 2011-2014 Pneumonia Etiology Research for Child Health study, nasopharyngeal and oropharyngeal (NP/OP) swabs and other samples were collected from 3981 children <5 years hospitalized with severe or very severe pneumonia in 7 countries. Severity by NP/OP detection status of CoV (NL63, 229E, OC43 or HKU1) and high-density (≥6.9 log10 copies/mL) pneumococcus (HDSpn) by real-time polymerase chain reaction was assessed by sex using logistic regression adjusted for age and site. RESULTS: There were 43 (1.1%) CoV+/HDSpn+, 247 CoV+/HDSpn-, 449 CoV-/HDSpn+ and 3149 CoV-/HDSpn- cases with no significant difference in co-detection frequency by sex (range 51.2%-64.0% male, P = 0.06). More CoV+/HDSpn+ pneumonia was very severe compared with other groups for both males (13/22, 59.1% versus range 29.1%-34.7%, P = 0.04) and females (10/21, 47.6% versus 32.5%-43.5%, P = 0.009), but only male CoV+/HDSpn+ required supplemental oxygen more frequently (45.0% versus 20.6%-28.6%, P < 0.001) and had higher mortality (35.0% versus 5.3%-7.1%, P = 0.004) than other groups. For females with CoV+/HDSpn+, supplemental oxygen was 25.0% versus 24.8%-33.3% (P = 0.58) and mortality was 10.0% versus 9.2%-12.9% (P = 0.69). CONCLUSIONS: Co-detection of endemic CoV and HDSpn was rare in children hospitalized with pneumonia, but associated with higher severity and mortality in males. Findings may warrant investigation of differences in severity by sex with co-detection of HDSpn and SARS-CoV-2.


Subject(s)
Coinfection/epidemiology , Coronavirus Infections/diagnosis , Pneumococcal Infections/diagnosis , Respiratory Tract Infections/diagnosis , Animals , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/virology , Child, Preschool , Coinfection/diagnosis , Coinfection/virology , Coronavirus , Coronavirus Infections/epidemiology , Coronavirus Infections/virology , Female , HIV Infections/epidemiology , HIV Infections/virology , Humans , Infant , Infant, Newborn , Logistic Models , Male , Nasopharynx/virology , Pneumococcal Infections/epidemiology , Pneumococcal Infections/virology , Pneumonia/diagnosis , Pneumonia/virology , Respiratory Tract Infections/epidemiology , Respiratory Tract Infections/virology , SARS-CoV-2/isolation & purification , Streptococcus pneumoniae
10.
BMC Public Health ; 21(1): 484, 2021 03 11.
Article in English | MEDLINE | ID: covidwho-1133589

ABSTRACT

BACKGROUND: Characterising the size and distribution of the population at risk of severe COVID-19 is vital for effective policy and planning. Older age, and underlying health conditions, are associated with higher risk of death from COVID-19. This study aimed to describe the population at risk of severe COVID-19 due to underlying health conditions across the United Kingdom. METHODS: We used anonymised electronic health records from the Clinical Practice Research Datalink GOLD to estimate the point prevalence on 5 March 2019 of the at-risk population following national guidance. Prevalence for any risk condition and for each individual condition is given overall and stratified by age and region with binomial exact confidence intervals. We repeated the analysis on 5 March 2014 for full regional representation and to describe prevalence of underlying health conditions in pregnancy. We additionally described the population of cancer survivors, and assessed the value of linked secondary care records for ascertaining COVID-19 at-risk status. RESULTS: On 5 March 2019, 24.4% of the UK population were at risk due to a record of at least one underlying health condition, including 8.3% of school-aged children, 19.6% of working-aged adults, and 66.2% of individuals aged 70 years or more. 7.1% of the population had multimorbidity. The size of the at-risk population was stable over time comparing 2014 to 2019, despite increases in chronic liver disease and diabetes and decreases in chronic kidney disease and current asthma. Separately, 1.6% of the population had a new diagnosis of cancer in the past 5 y. CONCLUSIONS: The population at risk of severe COVID-19 (defined as either aged ≥70 years, or younger with an underlying health condition) comprises 18.5 million individuals in the UK, including a considerable proportion of school-aged and working-aged individuals. Our national estimates broadly support the use of Global Burden of Disease modelled estimates in other countries. We provide age- and region- stratified prevalence for each condition to support effective modelling of public health interventions and planning of vaccine resource allocation. The high prevalence of health conditions among older age groups suggests that age-targeted vaccination strategies may efficiently target individuals at higher risk of severe COVID-19.


Subject(s)
COVID-19/epidemiology , Health Status , Adolescent , Adult , Age Factors , Aged , Child , Chronic Disease/epidemiology , Electronic Health Records , Female , Humans , Male , Middle Aged , Multimorbidity , Pregnancy , Prevalence , Public Health , Risk Factors , United Kingdom/epidemiology
11.
Science ; 371(6524): 79-82, 2021 01 01.
Article in English | MEDLINE | ID: covidwho-920888

ABSTRACT

The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Africa is poorly described. The first case of SARS-CoV-2 in Kenya was reported on 12 March 2020, and an overwhelming number of cases and deaths were expected, but by 31 July 2020, there were only 20,636 cases and 341 deaths. However, the extent of SARS-CoV-2 exposure in the community remains unknown. We determined the prevalence of anti-SARS-CoV-2 immunoglobulin G among blood donors in Kenya in April-June 2020. Crude seroprevalence was 5.6% (174 of 3098). Population-weighted, test-performance-adjusted national seroprevalence was 4.3% (95% confidence interval, 2.9 to 5.8%) and was highest in urban counties Mombasa (8.0%), Nairobi (7.3%), and Kisumu (5.5%). SARS-CoV-2 exposure is more extensive than indicated by case-based surveillance, and these results will help guide the pandemic response in Kenya and across Africa.


Subject(s)
Antibodies, Viral/blood , Blood Donors , COVID-19/epidemiology , Immunoglobulin G/blood , Adolescent , Adult , Aged , Communicable Disease Control , Humans , Kenya/epidemiology , Middle Aged , SARS-CoV-2/physiology , Seroepidemiologic Studies , Young Adult
12.
Lancet Glob Health ; 8(10): e1295-e1304, 2020 10.
Article in English | MEDLINE | ID: covidwho-796424

ABSTRACT

BACKGROUND: Each year, billions of US$ are spent globally on infectious disease research and development. However, there is little systematic tracking of global research and development. We present research on investments into infectious diseases research from funders in the G20 countries across an 18-year time period spanning 2000-17, comparing amounts invested for different conditions and considering the global burden of disease to identify potential areas of relative underfunding. METHODS: The study examined research awards made between 2000 and 2017 for infectious disease research from G20-based public and philanthropic funders. We searched research databases using a range of keywords, and open access data were extracted from funder websites. Awards were categorised by type of science, specialty, and disease or pathogen. Data collected included study title, abstract, award amount, funder, and year. We used descriptive statistics and Spearman's correlation coefficient to investigate the association between research investment and disease burden, using Global Burden of Disease 2017 study data. FINDINGS: The final 2000-17 dataset included 94 074 awards for infectious disease research, with a sum investment of $104·9 billion (annual range 4·1 billion to 8·4 billion) and a median award size of $257 176 (IQR 62 562-770 661). Pre-clinical research received $61·1 billion (58·2%) across 70 337 (74·8%) awards and public health research received $29·5 billion (28·1%) from 19 197 (20·4%) awards. HIV/AIDS received $42·1 billion (40·1%), tuberculosis received $7·0 billion (6·7%), malaria received $5·6 billion (5·3%), and pneumonia received $3·5 billion (3·3%). Funding for Ebola virus ($1·2 billion), Zika virus ($0·3 billion), influenza ($4·4 billion), and coronavirus ($0·5 billion) was typically highest soon after a high-profile outbreak. There was a general increase in year-on-year investment in infectious disease research between 2000 and 2006, with a decline between 2007 and 2017. Funders based in the USA provided $81·6 billion (77·8%). Based on funding per 2017 disability-adjusted life years (DALYs), HIV/AIDS received the greatest relative investment ($772 per DALY), compared with tuberculosis ($156 per DALY), malaria ($125 per DALY), and pneumonia ($33 per DALY). Syphilis and scabies received the least relative investment (both $9 per DALY). We observed weak positive correlation (r=0·30) between investment and 2017 disease burden. INTERPRETATION: HIV research received the highest amount of investment relative to DALY burden. Scabies and syphilis received the lowest relative funding. Investments for high-threat pathogens (eg, Ebola virus and coronavirus) were often reactive and followed outbreaks. We found little evidence that funding is proactively guided by global burden or pandemic risk. Our findings show how research investments are allocated and how this relates to disease burden and diseases with pandemic potential. FUNDING: Bill & Melinda Gates Foundation.


Subject(s)
Biomedical Research/economics , Communicable Diseases/economics , Global Health/economics , Research Support as Topic/statistics & numerical data , Humans , International Cooperation
13.
Euro Surveill ; 25(19)2020 05.
Article in English | MEDLINE | ID: covidwho-259289

ABSTRACT

Using electronic health records, we assessed the early impact of coronavirus disease (COVID-19) on routine childhood vaccination in England by 26 April 2020. Measles-mumps-rubella vaccination counts fell from February 2020, and in the 3 weeks after introduction of physical distancing measures were 19.8% lower (95% confidence interval: -20.7 to -18.9) than the same period in 2019, before improving in mid-April. A gradual decline in hexavalent vaccination counts throughout 2020 was not accentuated by physical distancing.


Subject(s)
Coronavirus Infections/epidemiology , Coronavirus , Disease Outbreaks/prevention & control , Measles-Mumps-Rubella Vaccine , Pandemics , Pneumonia, Viral/epidemiology , Vaccination/statistics & numerical data , Betacoronavirus , COVID-19 , Child, Preschool , England , Health Services Accessibility , Humans , Infant , Measles/prevention & control , Mumps/prevention & control , Quarantine , Rubella/prevention & control , SARS-CoV-2
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