ABSTRACT
Background: Emergence of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants may contribute to prolonging the pandemic and increasing morbidity, and mortality related to coronavirus disease 2019 (COVID-19). We describe the dynamics of circulating SARS-CoV-2 variants identified during the different COVID-19 waves that occurred in Mali between April 2021 and October 2021. Methods: We sequenced respiratory SARS-CoV-2 complete spike (S) gene from positive samples. Generated sequences were aligned by Variant Reporter v3.0 using Wuhan-1 strain as a reference. Mutations were noted using the GISAID and Nextclade platforms. Results: Of 16,797 nasopharyngeal swab samples tested, 6.0 % (1008/16,797) were RT-qPCR positive for SARS-CoV-2. Of these, 16.07% (162/1008) had a Ct value ≤ 28 and were amplified and sequenced. We recovered complete S-gene sequence from 80 of 162 [49.8%] samples. We identified seven distinct variants including Delta [62.5%], Alpha [1.2%], Beta [1.2%], Eta [30.0%], 20B [2.5%], 19B and 20A [1.2% each]. Conclusion and perspectives: Our results show the presence of several SARS-CoV-2 variants during COVID-19 waves in Mali between April and October 2021. The continued emergence of new variants highlights the need to strengthen local real-time sequencing capacity, and genomic surveillance for better and coordinated national responses to SARS-CoV-2.
ABSTRACT
In response to the COVID-19 pandemic, COVID-19 vaccines have been developed, and the World Health Oraganization (WHO) has granted emergency use listing to multiple vaccines. Studies of vaccine immunogenicity data from implementing COVID-19 vaccines by national immunization programs in single studies spanning multiple countries and continents are limited but critically needed to answer public health questions on vaccines, such as comparing immune responses to different vaccines and among different populations.
Subject(s)
COVID-19 , Vaccines , COVID-19/prevention & control , COVID-19 Vaccines , Cohort Studies , Humans , Pandemics/prevention & controlABSTRACT
Mali, like the rest of the world, has seen a rapid spread of COVID-19 since the first report of imported cases. Despite being a low-income country, Mali has leveraged scientific research resources via coordinated approaches to enable public health emergency planning and response to the COVID-19 pandemic. Mali's approach includes the harmonization of research activities; leveraging of research laboratory capacity of the University Clinical Research Center, Mali International Center for Excellence and three other in-country laboratories for community COVID-19 testing; strengthening relationships amongst local and international stakeholders; and collaboration with the Ministry of Health to integrate scientific evidence into public policy and emergency management of COVID-19 through a platform of consultation and open communication. The country has implemented national coordination of its COVID-19 response by establishing a COVID-19 Scientific Advisory Committee and a COVID-19 Technical Coordination Committee, both within the Ministry of Health and working collaboratively with other stakeholders. Members of Mali's COVID-19 Scientific Advisory Committee also serve as leaders of its principal academic and government clinical and public health research entities. This centralised approach has enabled the prioritisation of COVID-19 control activities, informed allocation of resources, evidence-based public health practices and timely decision-making in the pandemic setting. Though challenges remain, lessons learned from Mali's harnessing of clinical research capacity to guide and support its COVID-19 response can be applied to future global health research challenges and illustrate the power of building public health-responsive research capacity in resource-limited settings through international collaboration.