Turnover of SARS-CoV-2 lineages shaped the pandemic and enabled the emergence of new variants in the state of Rio de Janeiro, Brazil

Júnior, Francisco de Assis Martins; Lamarca,; Almeida, Luiz Gonzaga Paula de; Cavalcante,; Machado,; Martins, Yasmmin; Brustolini,; Gerber,; Guimaraes, M. S.; Gonçalves, Bruno; Mariani, Leonardo; Cruz, N.; Souza, de; Carvalho, de; Ribeiro, Martha S.; Carvalho, Hélder; Silva, da; Garcia, Justin R.; Cavalcanti,; Mello, De; Struchiner,; Tanuri,; Vasconcelos, de

doi:10.1101/2021.07.20.21260890

Cited by 2 publications

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“…P.2 was firstly reported in November 2020 in samples from the state of Rio de Janeiro and was estimated to have first diverged in late July [ 5 ]. By December 2020, it was already prevalent in samples from the Brazilian states of Rio Grande do Sul Amazonas and Rio de Janeiro [ 3 , 6 , 7 ]. P.1 was first detected in the state of Amazonas in mid-December 2020, with a proposed emergence around November [ 3 , 4 ].…”

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confidence: 99%

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

et al. 2021

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The sharp increase of COVID-19 cases in late 2020 has made Brazil the new epicenter of the ongoing SARS-CoV-2 pandemic. The novel viral lineages P.1 (Variant of Concern Gamma) and P.2, respectively identified in the Brazilian states of Amazonas and Rio de Janeiro, have been associated with potentially higher transmission rates and antibody neutralization escape. In this study, we performed the whole-genome sequencing of 185 samples isolated from three out of the five Brazilian regions, including Amazonas (North region), Rio Grande do Norte, Paraíba and Bahia (Northeast region), and Rio de Janeiro (Southeast region) in order to monitor the spread of SARS-CoV-2 lineages in Brazil in the first months of 2021. Here, we showed a widespread dispersal of P.1 and P.2 across Brazilian regions and, except for Amazonas, P.2 was the predominant lineage identified in the sampled states. We estimated the origin of P.2 lineage to have happened in February, 2020 and identified that it has differentiated 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 and its origin was inferred to have happened in August 2020. We also confirmed the presence of lineage P.7, recently described in the southernmost region of Brazil, to have spread across the Northeastern states. P.1, P.2 and P.7 are descended from the ancient B.1.1.28 strain, which co-dominated the first phase of the pandemic in Brazil with the B.1.1.33 strain. We also identified the occurrence of a new lineage descending from B.1.1.33 that convergently carries the E484K mutation, N.9. 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 identify novel variants of interest and monitor for vaccine effectiveness.

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confidence: 99%

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

et al. 2021

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“…The VOC P.1, which harbors the mutations of concern S:K417T/E484K/N501Y among its lineage defining mutations [6], originated in the Amazonas state in mid-November [7,8] and rapidly spread across Brazil and to over 50 countries globally [9]. The lineages P.2, P.4, and P.5, carrying the concerning amino acid changes S:E484K, S:L452R, and S:E484Q/N501T, respectively, were also initially detected in samples from Brazil [10][11][12][13][14][15]. The lineage P.3 (former VOI Theta) emerged in the Philippines, and it includes substitutions S:E484K/N501Y/P681H among the lineage-defining mutations; the first sample was collected on 8 January 2021, and later it further spread to the USA, Germany, and Malaysia, among other countries [16].…”

Section: Introductionmentioning

confidence: 99%

Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay

Rego

Salazar

Paz

et al. 2021

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Uruguay controlled the viral dissemination during the first nine months of the SARS-CoV-2 pandemic. Unfortunately, towards the end of 2020, the number of daily new cases exponentially increased. Herein, we analyzed the country-wide genetic diversity of SARS-CoV-2 between November 2020 and April 2021. We identified that the most prevalent viral variant during the first epidemic wave in Uruguay (December 2020–February 2021) was a B.1.1.28 sublineage carrying Spike mutations Q675H + Q677H, now designated as P.6, followed by lineages P.2 and P.7. P.6 probably arose around November 2020, in Montevideo, Uruguay’s capital department, and rapidly spread to other departments, with evidence of further local transmission clusters; it also spread sporadically to the USA and Spain. The more efficient dissemination of lineage P.6 with respect to P.2 and P.7 and the presence of mutations (Q675H and Q677H) in the proximity of the key cleavage site at the S1/S2 boundary suggest that P.6 may be more transmissible than other lineages co-circulating in Uruguay. Although P.6 was replaced by the variant of concern (VOC) P.1 as the predominant lineage in Uruguay since April 2021, the monitoring of the concurrent emergence of Q675H + Q677H in VOCs should be of worldwide interest.

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Turnover of SARS-CoV-2 lineages shaped the pandemic and enabled the emergence of new variants in the state of Rio de Janeiro, Brazil

Cited by 2 publications

References 59 publications

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

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

Emergence and Spread of a B.1.1.28-Derived P.6 Lineage with Q675H and Q677H Spike Mutations in Uruguay

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