The COVID-19 pandemic is one of the fastest evolving pandemics in recent history. As such, the SARS-CoV-2 viral evolution needs to be continuously tracked. This study sequenced 1123 SARS-CoV-2 genomes from patient isolates (121 from arriving travellers and 1002 from communities) to track the molecular evolution and spatio-temporal dynamics of the SARS-CoV-2 variants in Ghana. The data show that initial local transmission was dominated by B.1.1 lineage, but the second wave was overwhelmingly driven by the Alpha variant. Subsequently, an unheralded variant under monitoring, B.1.1.318, dominated transmission from April to June 2021 before being displaced by Delta variants, which were introduced into community transmission in May 2021. Mutational analysis indicated that variants that took hold in Ghana harboured transmission enhancing and immune escape spike substitutions. The observed rapid viral evolution demonstrates the potential for emergence of novel variants with greater mutational fitness as observed in other parts of the world.

Newcastle Disease (ND) has been identified as a major constraint to local poultry production with its impact being felt more in rural poultry production which forms about 80% of Ghana poultry population. However documented evidence on ND virus activity in rural poultry in Ghana is still lacking. Hence, this study was conducted to evaluate the level of circulating antibodies against ND using the Haemagglutination Inhibition (HI) technique. Sera collected from unvaccinated 292 chickens and 153 guinea fowls randomly selected from households and a live bird market in Kumasi and its environs were evaluated for Newcastle disease virus antibodies. Results showed 81.8 % (239/292) of local chickens and 24.2 % (37/153) of guinea fowls tested positive for ND antibodies.Comparison was made between the seroprevalence of ND antibodies in household and live bird market as well as between sexes. Significantly higher prevalence rate (p<0.05) was observed with chickens sampled from households compared to those from the live bird market. Higher ranges of titers were also observed in chickens from households than those from live bird markets. The presence of ND antibodies in these unvaccinated local chickens and guinea fowls indicated the presence of the virus amongst the rural poultry population, hence aneed for improvement in vaccine campaignand delivery against ND for rural poultry especially with the use of thermostable and improved oral or feed-based vaccine delivery systems.

This study sequenced 1077 SARS-CoV-2 genomes from patient isolates (106 from arriving travellers and 971 from communities) to track the molecular evolution and spatio-temporal dynamics of the SARS-CoV-2 variants in Ghana. The data show that initial local transmission was dominated by B.1.1 lineages, but the second wave in Ghana was overwhelmingly driven by the Alpha variant, which was detected in community cases from January 2021, with Eta also contributing to reported cases. Subsequently, an unheralded variant under monitoring, B.1.1.318, dominated transmission from April to June 2021 before being displaced by Delta (B.1.1.617) and Delta Plus (AY.*) variants, which were introduced into community transmission in May 2021 and have remained dominant to date. Mutational analysis indicated that variants that took hold in Ghana harboured transmission enhancing and immune escape spike substitutions. The apparent rapid viral evolution observed demonstrate the potential for emergence of novel variants with greater mutational fitness.