Genomic epidemiology of SARS-CoV-2 in Mozambique

<strong>Abstract: </strong>Mozambique reported the first case of coronavirus disease 2019 (COVID-19) in March 2020. Since then, the virus has spread to all provinces in the country. Here we set out to perform a retrospective molecular epidemiological analysis of the first 25 months of the epidemic in Mozambique. In total, 1 146 whole genome sequences from Mozambique were phylogenetically analyzed against a globally representative set of references to put the epidemic in the country into context. The domestic pandemic was marked by four successive waves of infection, with the first wave associated with B.1 ancestral lineages, while the Beta, Delta, and Omicron Variants of Concern (VOCs) were responsible for the majority of cases and death during the second, third, and fourth waves. Viral exchanges between Mozambique and the outside world mimicked pandemic waves, with most exchanges occurring during the second, third, and forth waves and most imports and exports being attributed to South Africa. Due to a health system already under constraint and paucity of data in Mozambique, there is a need to continue to strengthen and support genomic surveillance in the country as VOCs and Variants of interests (VOIs) are often reported from the southern African region.