Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil

Abstract

The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. Novel SARS-CoV-2 lineages P.1 and P.2, first identified respectively in Manaus and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed a whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraiba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) aiming to identify SARS-CoV-2 mutations that could be involved in the surge of COVID19 cases in Brazil. Here, we showed a widespread dispersion of P.1 and P.2 across Brazilian regions. Except for Manaus, P.2 was the predominant lineage identified country-wise. P.2 lineage was estimated to have originated in February, 2020 and has diverged into new clades. Interstate transmission of P.2 was detected since March, but reached its peak in December, 2020 and January, 2021. Transmission of P.1 was also high in December. P.1 origin was inferred to have happened in August 2020. We also confirmed the presence of the variant under investigation (VUI) NP13L recently described in the southernmost region of Brazil to have spread across the Northeastern states. P.1, P.2 and NP13L are descended from the ancient B.1.1.28 strain, although during the first phase of the pandemic in Brazil presence of B.1.1.33 strain was also reported. Here, for the first time, we investigate the possible occurrence of a new variant of concern descending from B.1.1.33 that also carries the E484K mutation. Indeed, the recurrent report of many novel SARS-CoV-2 genetic variants in Brazil could be due to the absence of effective control measures resulting in high SARS-CoV2 transmission rates. Altogether, our findings provided a landscape of the critical state of SARS-CoV-2 across Brazil and confirm the need to sustain continuous sequencing of the SARS-CoV-2 isolates worldwide in order to early identify novel variants of concern and to monitor for vaccine effectiveness.

Emergence of the novel SARS-CoV-2 lineage VUI-NP13L and massive spread of P.2 in South Brazil

“…The geographic distribution of lineages was evaluated in four RS-sampled regions since the first detection of VUI-NP13L in our sampling (Fig. 4 Southeast Brazil, on 9 March 2020 and then disseminated across the country 16,24,37,38 . This lineage was also associated with outbreaks in Argentina and Uruguay, countries bordering RS 38,39 .…”

Emergence of the novel SARS-CoV-2 lineage P.4.1 and massive spread of P.2 in South Brazil

“…Sequences evaluated in our study are restricted to 2020; therefore, we cannot rule out if the lineages are still active across southern Brazil. 16,18,20,23 . This lineage was also associated with secondary outbreaks in Argentina and Uruguay, countries bordering RS 18,24 .…”

“…Although P.4.1 probably emerged in Goiás or São Paulo around Jun-Jul 2020, this lineage was only identified in South Brazil at the beginning of October 2020. According to an independent phylodynamic reconstruction, P.4.1 rapidly arrived in the southeastern and northeastern regions of Brazil and seems to have been exported to Japan, the Netherlands and England 23 . The success of the spread of P.4.1, beyond having important mutations in the spike protein (V1176F, D614G), also shared by P.2 and P.1 lineages, could be justified by the unique amino acid changes in ORF1a 16,26,27 .…”

Second Wave Analysis and Confirmed Forecasts of the SARS-Cov-2 Epidemic Outbreak in São Paulo, Brazil

“…Adding to model a time-varying fatality rate (t) by data fitting to the first 90 days after March 1 st , 2020 (Figure 5b) would further improve the values of SD and RMS to 0.05 and 0.06 respectively. Novel SARS-CoV-2 lineage P.1 first identified in Manaus has been associated with potentially higher transmission rates, and now it is widespread across all Brazilian regions [17,18]. On the other hand, a preliminary study conducted by Institute Butantan [19], suggests the vaccination in Brazil by CoronaVac can neutralize variants P.1 and P.2 of SARS-CoV-2.…”