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1.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-21263755

Résumé

The SARS-CoV-2 has infected almost 200 million people worldwide by July 2021 and the pandemic has been characterized by infection waves of viral lineages showing distinct fitness profiles. The simultaneous infection of a single individual by two distinct SARS-CoV-2 lineages provides a window of opportunity for viral recombination and the emergence of new lineages with differential phenotype. Several hundred SARS-CoV-2 lineages are currently well characterized but two main factors have precluded major coinfection/codetection analysis thus far: i) the low diversity of SARS-CoV-2 lineages during the first year of the pandemic which limited the identification of lineage defining mutations necessary to distinguish coinfecting viral lineages; and the ii) limited availability of raw sequencing data where abundance and distribution of intrasample/intrahost variability can be accessed. Here, we have put together a large sequencing dataset from Brazilian samples covering a period of 18 May 2020 to 30 April 2021 and probed it for unexpected patterns of high intrasample/intrahost variability. It enabled us to detect nine cases of SARS-CoV-2 coinfection with well characterized lineage-defining mutations. In addition, we matched these SARS-CoV-2 coinfections with spatio-temporal epidemiological data confirming their plausibility with the co-circulating lineages at the timeframe investigated. These coinfections represent around 0.61% of all samples investigated. Although our data suggests that coinfection with distinct SARS-CoV-2 lineages is a rare phenomenon, it is likely an underestimation and coinfection rates warrants further investigation. DATA SUMMARYThe raw fastq data of codetection cases are deposited on gisaid.org and correlated to gisaid codes: EPI_ISL_1068258, EPI_ISL_2491769, EPI_ISL_2491781, EPI_ISL_2645599, EPI_ISL_2661789, EPI_ISL_2661931, EPI_ISL_2677092, EPI_ISL_2777552, EPI_ISL_3869215. Supplementary data are available on https://doi.org/10.6084/m9.figshare.16570602.v1. The workflow code used in this study is publicly available on: https://github.com/dezordi/IAM_SARSCOV2.

2.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-21253946

Résumé

Mutations at both the receptor-binding domain (RBD) and the amino (N)-terminal domain (NTD) of the SARS-CoV-2 Spike (S) glycoprotein can alter its antigenicity and promote immune escape. We identified that SARS-CoV-2 lineages circulating in Brazil with mutations of concern in the RBD independently acquired convergent deletions and insertions in the NTD of the S protein, which altered the NTD antigenic-supersite and other predicted epitopes at this region. These findings support that the ongoing widespread transmission of SARS-CoV-2 in Brazil is generating new viral lineages that might be more resistant to neutralization than parental variants of concern.

3.
Preprint Dans Anglais | bioRxiv | ID: ppbiorxiv-434969

Résumé

The SARS-CoV-2 epidemic in Brazil was dominated by two lineages designated as B.1.1.28 and B.1.1.33. Two SARS-CoV-2 variants harboring mutations at the receptor-binding domain of the Spike (S) protein, designated as lineages P.1 and P.2, evolved within lineage B.1.1.28 and are rapidly spreading in Brazil. Lineage P.1 is considered a Variant of Concern (VOC) because of the presence of multiple mutations in the S protein (including K417T, E484K, N501Y), while lineage P.2 only harbors mutation S:E484K and is considered a Variant of Interest (VOI). Here we report the identification of a new SARS-CoV-2 VOI within lineage B.1.1.33 that also harbors mutation S:E484K and was detected in Brazil between November 2020 and February 2021. This VOI displayed four non-synonymous lineage-defining mutations (NSP3:A1711V, NSP6:F36L, S:E484K, and NS7b:E33A) and was designated as lineage N.9. The VOI N.9 probably emerged in August 2020 and has spread across different Brazilian states from the Southeast, South, North and Northeast regions.

4.
Preprint Dans Anglais | medRxiv | ID: ppmedrxiv-20249026

Résumé

BackgroundUruguay is one of the few countries in the Americas that successfully contained the COVID-19 epidemic during the first half of 2020. Nevertheless, the intensive human mobility across the dry border with Brazil is a major challenge for public health authorities. We aimed to investigate the origin of SARS-CoV-2 strains detected in Uruguayan localities bordering Brazil as well as to measure the viral flux across this [~]1,100 km uninterrupted dry frontier. MethodsUsing complete SARS-CoV-2 genomes from the Uruguayan-Brazilian bordering region and phylogeographic analyses, we inferred the virus dissemination frequency between Brazil and Uruguay and characterized local outbreak dynamics during the first months (May-July) of the pandemic. FindingsPhylogenetic analyses revealed multiple introductions of SARS-CoV-2 Brazilian lineages B.1.1.28 and B.1.1.33 into Uruguayan localities at the bordering region. The most probable sources of viral strains introduced to Uruguay were the Southeast Brazilian region and the state of Rio Grande do Sul. Some of the viral strains introduced in Uruguayan border localities between early May and mid-July were able to locally spread and originated the first outbreaks detected outside the metropolitan region. The viral lineages responsible for Uruguayan suburban outbreaks were defined by a set of between four and 11 mutations (synonymous and non-synonymous) respect to the ancestral B.1.1.28 and B.1.1.33 viruses that arose in Brazil, supporting the notion of a rapid genetic differentiation between SARS-CoV-2 subpopulations spreading in South America. InterpretationAlthough Uruguayan borders have remained essentially closed to non-Uruguayan citizens, the inevitable flow of people across the dry border with Brazil allowed the repeated entry of the virus into Uruguay and the subsequent emergence of local outbreaks in Uruguayan border localities. Implementation of coordinated bi-national surveillance systems are crucial to achieve an efficient control of the SARS-CoV-2 spread across this kind of highly permeable borderland regions around the world. Research in contextO_ST_ABSEvidence before this studyC_ST_ABSSince the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causative agent of coronavirus disease 19 (COVID-19), was first detected in South America on February 26, 2020, it has rapidly spread through the region, causing nearly 350,000 deaths by December, 2020. In contrast to most American countries, Uruguay avoided an early exponential growth of SARS-CoV-2 cases and during the first six months of the pandemic it registered the lowest incidence of SARS-CoV-2 cases and deaths among South American countries. The intensive cross-border human mobility through the [~]1,100 km uninterrupted dry frontier between Uruguay and Brazil, might poses a major challenge for long-term control of the epidemic in Uruguay. Previous genomic studies conducted in Uruguay have analyzed sequences mostly sampled at the capital city, Montevideo, and detected prevalent SARS-CoV-2 lineages different from those described in Brazil, thus finding no evidence of frequent viral exchanges between these countries. Added value of this studyHere we present the first genomic study of SARS-CoV-2 strains detected in different Uruguayan and Brazilian localities along the bordering region. The samples analyzed include 30% (n = 59) of all laboratory confirmed SARS-CoV-2 cases from Uruguayan departments at the Brazilian border between March and July, 2020, as well as 68 SARS-CoV-2 sequences from individuals diagnosed in the southernmost Brazilian state of Rio Grande do Sul between March and August, 2020. We demonstrate that SARS-CoV-2 viral lineages that widely spread in the Southeastern Brazilian region (B.1.1.28 and B.1.1.33) were also responsible for most viral infections in Rio Grande do Sul and neighboring Uruguayan localities. We further uncover that major outbreaks detected in Uruguayan localities bordering Brazil in May and June, 2020, were originated from two independent introduction events of the Brazilian SARS-CoV-2 lineage B.1.1.33, unlike previous outbreaks in the Uruguayan metropolitan region that were seeded by European SARS-CoV-2 lineages. Implications of all the available evidenceOur findings confirm that although Uruguayan borders have remained essentially closed to non-Uruguayan citizens, dissemination of SARS-CoV-2 across the Uruguayan-Brazilian frontier was not fully suppressed and had the potential to ignite local transmission chains in Uruguay. These findings also highlight the relevance of implementing bi-national public health cooperation workforces combining epidemiologic and genomic data to monitor the viral spread throughout this kind of highly permeable dry frontiers around the world.

5.
Preprint Dans Anglais | bioRxiv | ID: ppbiorxiv-158006

Résumé

Despite all efforts to control the COVID-19 spread, the SARS-CoV-2 reached South America within three months after its first detection in China, and Brazil became one of the hotspots of COVID-19 in the world. Several SARS-CoV-2 lineages have been identified and some local clusters have been described in this early pandemic phase in Western countries. Here we investigated the genetic diversity of SARS-CoV-2 during the early phase (late February to late April) of the epidemic in Brazil. Phylogenetic analyses revealed multiple introductions of SARS-CoV-2 in Brazil and the community transmission of a major B.1.1 lineage defined by two amino acid substitutions in the Nucleocapsid and ORF6. This SARS-CoV-2 Brazilian lineage was probably established during February 2020 and rapidly spread through the country, reaching different Brazilian regions by the middle of March 2020. Our study also supports occasional exportations of this Brazilian B.1.1 lineage to neighboring South American countries and to more distant countries before the implementation of international air travels restrictions in Brazil.

6.
Preprint Dans Anglais | bioRxiv | ID: ppbiorxiv-069039

Résumé

Genomic surveillance has become a useful tool for better understanding virus pathogenicity, origin and spread. Obtaining accurately assembled, complete viral genomes directly from clinical samples is still a challenging. Here, we describe three protocols using a unique primer set designed to recover long reads of SARS-CoV-2 directly from total RNA extracted from clinical samples. This protocol is useful, accessible and adaptable to laboratories with varying resources and access to distinct sequencing methods: Nanopore, Illumina and/or Sanger.

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