Replacement of the Gamma by the Delta variant in Brazil: Impact of lineage displacement on the ongoing pandemic
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Abstract
The coronavirus disease 2019 (COVID-19) epidemic in Brazil was driven mainly by the spread of Gamma (P.1), a locally emerged variant of concern (VOC) that was first detected in early January 2021. This variant was estimated to be responsible for more than 96 per cent of cases reported between January and June 2021, being associated with increased transmissibility and disease severity, a reduction in neutralization antibodies and effectiveness of treatments or vaccines, and diagnostic detection failure. Here we show that, following several importations predominantly from the USA, the Delta variant rapidly replaced Gamma after July 2021. However, in contrast to what was seen in other countries, the rapid spread of Delta did not lead to a large increase in the number of cases and deaths reported in Brazil. We suggest that this was likely due to the relatively successful early vaccination campaign coupled with natural immunity acquired following prior infection with Gamma. Our data reinforce reports of the increased transmissibility of the Delta variant and, considering the increasing concern due to the recently identified Omicron variant, argues for the necessity to strengthen genomic monitoring on a national level to quickly detect the emergence and spread of other VOCs that might threaten global health.
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SciScore for 10.1101/2021.12.27.21268309: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Depending on the partner institution, library preparation and sequencing was done either on the Illumina and/or Oxford Nanopore Platform. Oxford Nanoporesuggested: (Oxford Nanopore Technologies, RRID:SCR_003756)Viral RNA was extracted from nasopharyngeal swabs using an automated protocol and tested for SARS-CoV-2 by multiplex real-time PCR assays: (i) the Allplex 2019-nCoV Assay (Seegene) targeting the envelope (E), the RNA dependent RNA polymerase (RdRp) and the nucleocapsid (N) genes; (ii) the Charité: SARS-CoV2 (E/RP) assay (Bio- Manguinhos/Fiocruz) targeting the E gene, and (iii) the … SciScore for 10.1101/2021.12.27.21268309: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources Depending on the partner institution, library preparation and sequencing was done either on the Illumina and/or Oxford Nanopore Platform. Oxford Nanoporesuggested: (Oxford Nanopore Technologies, RRID:SCR_003756)Viral RNA was extracted from nasopharyngeal swabs using an automated protocol and tested for SARS-CoV-2 by multiplex real-time PCR assays: (i) the Allplex 2019-nCoV Assay (Seegene) targeting the envelope (E), the RNA dependent RNA polymerase (RdRp) and the nucleocapsid (N) genes; (ii) the Charité: SARS-CoV2 (E/RP) assay (Bio- Manguinhos/Fiocruz) targeting the E gene, and (iii) the GeneFinder COVID-19 Plus RealAmp Kit (Osang Healthcare, South Korea) supplied by the Brazilian Ministry of Health (BrMoH), Butantan Institute and the Pan-American Health Organization (OPAS) Bio-suggested: NoneManguinhos/Fiocruzsuggested: NoneGeneFindersuggested: (GENEFINDER, RRID:SCR_009190)Results from OddPub: Thank you for sharing your code and data.
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.
Results from scite Reference Check: We found no unreliable references.
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