Genomic surveillance of SARS-CoV-2 tracks early interstate transmission of P.1 lineage and diversification within P.2 clade in Brazil
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Abstract
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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SciScore for 10.1101/2021.03.21.21253418: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The present study was approved by Ethical Review Board/Brazilian Commission of Ethical Study (Research Ethics Committee of: Universidade Federal Rio Grande do Norte - CAAE 36287120.2.0000.5537 Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Ninety-two males and 93 females were included, with age ranging between 11-90 years and with CT values between 8.70 to 29.00 (Appendix 1 Table S1). Table 2: Resources
Software and Algorithms Sentences Resources Modifications were clustering aligned sequences by 0.99985 similarity with CD-hit [14], keeping only the oldest record of each cluster and removing restrictions by … SciScore for 10.1101/2021.03.21.21253418: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
Institutional Review Board Statement IRB: The present study was approved by Ethical Review Board/Brazilian Commission of Ethical Study (Research Ethics Committee of: Universidade Federal Rio Grande do Norte - CAAE 36287120.2.0000.5537 Randomization not detected. Blinding not detected. Power Analysis not detected. Sex as a biological variable Ninety-two males and 93 females were included, with age ranging between 11-90 years and with CT values between 8.70 to 29.00 (Appendix 1 Table S1). Table 2: Resources
Software and Algorithms Sentences Resources Modifications were clustering aligned sequences by 0.99985 similarity with CD-hit [14], keeping only the oldest record of each cluster and removing restrictions by country. CD-hitsuggested: (CD-HIT, RRID:SCR_007105)All sequence alignment steps were conducted using MAFFT [15]. MAFFTsuggested: (MAFFT, RRID:SCR_011811)Simultaneously, the substitution model was selected with ModelFinder [16] using the global sequences as a proxy for genomic diversity within the larger alignment. ModelFindersuggested: NoneWe extracted P.1 and P.2 clades from the resulting maximum likelihood phylogeny to infer divergence dates and spatial dispersion with BEAST v1.10.4 [17]. BEASTsuggested: (BEAST, RRID:SCR_010228)After evaluating with TempEst [18] the correlation between root-to-tip distances and sampling dates (Figure S1), we selected the strict clock model to date P. TempEstsuggested: (TempEst, RRID:SCR_017304)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: An explicit section about the limitations of the techniques employed in this study was not found. We encourage authors to address study limitations.Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- Thank you for including a funding statement. Authors are encouraged to include this statement when submitting to a journal.
- No protocol registration statement was detected.
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