SARS-CoV-2 genomic monitoring in the Sao Paulo State unveils new sublineages of the AY.43 strain (preprint)

Delta VOC is highly diverse and more than 120 sublineages have been identified in Pango lineages with the continuous description of emerging ones. Brazil is now one of the most vaccinated countries against SARS-CoV-2 in the world which can enhance the emergence of viral mutations related to improved viral fitness. In this study, we identified two novel sublineages of the AY.43 lineage which were classified as AY.43.1 and AY.43.2 as observed on the specific clustering on the obtained phylogenetic tree. The novel sublineages were defined by the following characteristic nonsynonymous mutations ORF1ab:A4133V and ORF3a:T14I for AY.43.1 and ORF1ab:G1155C for AY.43.2. The majority of the analyzed sequences of both lineages were Brazilian, which shows that probably these two emerging sublineages have Brazilian origin. It is still unknown how these two sublineages are disseminated in São Paulo State and Brazil and their potential impact on the ongoing vaccination process. However, the performed study reinforces the importance of the SARS-CoV-2 genome monitoring for timely identification of emerging SARS-CoV-2 variants which can impact the ongoing SARS-CoV-2 vaccination and public health policies

SARS-CoV-2 Delta variant of concern in Brazil - multiple introductions, communitary transmission, and early signs of local evolution (preprint)

The dissemination of the Delta VOC in Brazil is still unclear, despite the frequent reports of isolated cases from different Brazilian states. In this report we characterize the dissemination of the Delta VOC in Brazil and where the introductions of this lineage fall within the global Delta phylogeny. We also examined the mutational profile of the largest clade within the Brazilian Delta VOCs, with a focus on samples which were obtained in the State of Sao Paulo, and especially in the city of Sao Paulo, the largest metropolis of South America, and a national and international transportation hub.

Severe airport sanitarian control could slow down the spreading of COVID-19 pandemics in Brazil (preprint)

Background. We investigated a likely scenario of COVID-19 spreading in Brazil through the complex airport network of the country, for the 90 days after the first national occurrence of the disease. After the confirmation of the first imported cases, the lack of a proper airport entrance control resulted in the infection spreading in a manner directly proportional to the amount of flights reaching each city, following first occurrence of the virus coming from abroad. Methodology. We developed a SIR (Susceptible-Infected-Recovered) model divided in a metapopulation structure, where cities with airports were demes connected by the number of flights. Subsequently, we further explored the role of Manaus airport for a rapid entrance of the pandemic into indigenous territories situated in remote places of the Amazon region. Results. The expansion of the SARS-CoV-2 virus between cities was fast, directly proportional to the airport closeness centrality within the Brazilian air transportation network. There was a clear pattern in the expansion of the pandemic, with a stiff exponential expansion of cases for all cities. The more an airport showed closeness centrality, the greater was its vulnerability to SARS-CoV-2. Conclusions. We discussed the weak pandemic control performance of Brazil in comparison with other tropical, developing countries, namely India and Nigeria. Finally, we proposed measures for containing virus spreading taking into consideration the scenario of high poverty.