Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.
Background Cholera globally affects 1.3–4.0 million people and causes 21 000–143 000 deaths annually. In June 2017, a cluster of diarrhoeal illness occurred among participants of an international scientific conference at a hotel in Nairobi, Kenya. Culture confirmed Vibrio cholerae, serotype Ogawa. We investigated to assess magnitude, identify likely exposures and suggest control measures. Methods We carried out a retrospective cohort study utilizing a structured questionnaire administered by telephone, email and internet-based survey. We calculated food-specific attack rates, risk ratios and in a nested-case control analysis, performed logistic regression to identify exposures independently associated with the outbreak. Results We interviewed 249 out of 456 conference attendees (response rate=54.6%). Mean age of respondents was 37.8 years, ±8.3 years, 131 (52.6%) were male. Of all the respondents, 137 (55.0%) were cases. Median incubation time was 35 (11–59) hours. Eating chicken (adjusted OR 2.49, 95% CI, 1.22–5.06) and having eaten lunch on Tuesday (adjusted OR 2.34, 95% CI 1.09–5.05) were independently associated with illness; drinking soda was protective (adjusted OR 0.17, 95% CI 0.07–0.42). Conclusion Point source outbreak, associated with chicken eaten at lunch on Tuesday 20th June 2017 occurred. We recommend better collaboration between the food and health sectors in food-borne outbreak investigations.
word count: 295 (with subheadings) Manuscript body ward count: 2586 Abstract 2 Background 3 Cholera affects 1.3-4 million people globally and causes 21000-143,000 deaths 4 annually. Nairobi County in Kenya reported cholera cases since April 2017. We investigated to 5 identify associated factors and institute control measures. 6 Methods 7We reviewed the line-list of patients admitted at the Kenyatta National referral Hospital, 8 Nairobi and performed descriptive epidemiology. We carried out a frequency-matched case 9 control study, using facility-based cases and community controls. We defined a case as acute 10 onset of watery diarrhoea of at least >3 stools/24hours with or without vomiting in person of 11 any age, admitted in Kenyatta National Hospital as from July 1 st , 2017. We calculated odds 12 ratios and their respective 95% confidence intervals. We also took water samples at water 13 reservoirs, distribution and consumer points, and made observation on hygiene and sanitation 14 conditions in the community. 15 16 Results 17We reviewed 71 line-listed cases; median age 30 years (range 2-86 years); 45 (63%) 18 were male. First case was admitted on 14 th April 2017. Culture was performed on 44 cases, 30 19 (68%) was positive for Vibrio cholerae, biotype El-Tor, serotype Ogawa. There were 2 deaths 20 (case fatality ratio 2.8%). Age-group ≥25 years was most affected. Drinking unchlorinated 21 water (aOR 14.57, 95% CI 4.44-47.83), eating in public places (aOR 9.45, 95% CI 3.07-29.12) 22 sourcing water from non-Nairobi city water company source (aOR 4.92, 95% CI 1.56-15.52) 23and having drank untreated water in the previous week before the outbreak (aOR 3.21, 95% CI 24 1.12-9.24) were independently associated with being a case in the outbreak. Out of 28 water 25 samples, 4 (14%) had >180 coliforms/100mls; all were at consumer points. 26 3 27 Conclusion 28Poor water quality and sanitation were responsible for this outbreak. We recommended 29 adequate, clean water supply to unplanned settlements in Nairobi County, as well education of 30 residents on water treatment at the household level. 31 32 Author summary 33 Cholera, a disease causing outbreaks in areas with low standards of hygiene and sanitation has 34 afflicted humans for millennia. It is caused by a bacterium, Vibrio Cholerae, transmitted 35 mainly through water contaminated by faecal matter. The resultant disease is acute watery 36 diarrhoea, which causes death rapidly due to dehydration and shock. Virtually brought under 37 control in the developed world due to improvements in hygiene, the disease still ravages many 38 communities in low and middle income countries, as well as regions affected by conflict or 39 natural disasters. In outbreak situations, rapid response in water treatment, sanitation 40 improvement and setting up of cholera treatment centres for rehydration therapy reduces 41 impact and saves lives. Long-term control can only be achieved through sustainable 42 improvements in sanitation and standards of living. Case control studies in outbre...
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