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1.
Frontiers in medicine ; 9, 2022.
Article in English | EuropePMC | ID: covidwho-2058471

ABSTRACT

Recombination events have been described in the Coronaviridae family. Since the beginning of the SARS-CoV-2 pandemic, a variable degree of selection pressure has acted upon the virus, generating new strains with increased fitness in terms of viral transmission and antibody scape. Most of the SC2 variants of concern (VOC) detected so far carry a combination of key amino acid changes and indels. Recombination may also reshuffle existing genetic profiles of distinct strains, potentially giving origin to recombinant strains with altered phenotypes. However, co-infection and recombination events are challenging to detect and require in-depth curation of assembled genomes and sequencing reds. Here, we present the molecular characterization of a new SARS-CoV-2 recombinant between BA.1.1 and BA.2.23 Omicron lineages identified in Brazil. We characterized four mutations that had not been previously described in any of the recombinants already identified worldwide and described the likely breaking points. Moreover, through phylogenetic analysis, we showed that the newly named XAG lineage groups in a highly supported monophyletic clade confirmed its common evolutionary history from parental Omicron lineages and other recombinants already described. These observations were only possible thanks to the joint effort of bioinformatics tools auxiliary in genomic surveillance and the manual curation of experienced personnel, demonstrating the importance of genetic, and bioinformatic knowledge in genomics.

2.
Front Med (Lausanne) ; 9: 930380, 2022.
Article in English | MEDLINE | ID: covidwho-2043487

ABSTRACT

The year of 2021 was marked by the emergence and dispersal of a number of SARS-CoV-2 lineages, resulting in the "third wave" of COVID-19 in several countries despite the level of vaccine coverage. Soon after the first confirmed cases of COVID-19 by the Delta variant in Brazil, at least seven Delta sub-lineages emerged, including the globally spread AY.101 and AY.99.2. In this study we performed a detailed analysis of the COVID-19 scenario in Brazil from April to December 2021 by using data collected by the largest private medical diagnostic company in Latin America (Dasa), and SARS-CoV-2 genomic sequences generated by its SARS-CoV-2 genomic surveillance project (GENOV). For phylogenetic and Bayesian analysis, SARS-CoV-2 genomes available at GISAID public database were also retrieved. We confirmed that the Brazilian AY.99.2 and AY.101 were the most prevalent lineages during this period, overpassing the Gamma variant in July/August. We also estimated that AY.99.2 likely emerged a few weeks after the entry of the B.1.617.2 in the country, at some point between late April and May and rapidly spread to other countries. Despite no increased fitness described for the AY.99.2 lineage, a rapid shift in the composition of Delta SARS-CoV-2 lineages prevalence in Brazil took place. Understanding the reasons leading the AY.99.2 to become the dominant lineage in the country is important to understand the process of lineage competitions that may inform future control measures.

3.
Arch Virol ; 167(11): 2271-2273, 2022 Nov.
Article in English | MEDLINE | ID: covidwho-1935816

ABSTRACT

In January 2022, our genomic surveillance network identified a SARS-CoV-2 BA.1 and BA.2 coinfection in a sample from a patient residing in Brazil. Our results suggest that the true number of SARS-CoV-2 coinfections remains largely underestimated.


Subject(s)
COVID-19 , Coinfection , Brazil/epidemiology , COVID-19/epidemiology , Coinfection/epidemiology , Genomics , Humans , SARS-CoV-2/genetics
4.
Frontiers in medicine ; 9, 2022.
Article in English | EuropePMC | ID: covidwho-1918901

ABSTRACT

The year of 2021 was marked by the emergence and dispersal of a number of SARS-CoV-2 lineages, resulting in the “third wave” of COVID-19 in several countries despite the level of vaccine coverage. Soon after the first confirmed cases of COVID-19 by the Delta variant in Brazil, at least seven Delta sub-lineages emerged, including the globally spread AY.101 and AY.99.2. In this study we performed a detailed analysis of the COVID-19 scenario in Brazil from April to December 2021 by using data collected by the largest private medical diagnostic company in Latin America (Dasa), and SARS-CoV-2 genomic sequences generated by its SARS-CoV-2 genomic surveillance project (GENOV). For phylogenetic and Bayesian analysis, SARS-CoV-2 genomes available at GISAID public database were also retrieved. We confirmed that the Brazilian AY.99.2 and AY.101 were the most prevalent lineages during this period, overpassing the Gamma variant in July/August. We also estimated that AY.99.2 likely emerged a few weeks after the entry of the B.1.617.2 in the country, at some point between late April and May and rapidly spread to other countries. Despite no increased fitness described for the AY.99.2 lineage, a rapid shift in the composition of Delta SARS-CoV-2 lineages prevalence in Brazil took place. Understanding the reasons leading the AY.99.2 to become the dominant lineage in the country is important to understand the process of lineage competitions that may inform future control measures.

5.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-336124

ABSTRACT

Since the emergence of the variant of concern (VOC) B.1.1.529 (Omicron) in November 2021 1 , nearly 100 sublineages have been assigned by Pango. Recently, the co-circulation of Omicron and Delta lineages, as well as its diverse set of sublineages, has brought to attention the identification of several recombinant events. A putative new recombinant and two XE recombinants were identified in children by the GENOV surveillance program (https://dasa.com.br/en/genov/) from Dasa, Brazil. All three children haven’t traveled abroad nor their relatives, indicating that the infections by recombinants likely occurred in São Paulo city.

6.
J Virol Methods ; 296: 114241, 2021 10.
Article in English | MEDLINE | ID: covidwho-1309315

ABSTRACT

SARS-CoV-2 is the etiologic agent of coronavirus disease 2019 (COVID-19) and is mainly detected by RT-PCR methods from upper respiratory specimens, as recommended by the World Health Organization. Oro/nasopharyngeal swabbing can be discomfortable to the patients, requires trained healthcare personnel and may generate aerosol, increasing the risk of nosocomial infections. In this study, we describe two SARS-CoV-2 RNA extraction-free single RT-PCR protocols on saliva samples and compared the results with the paired oro/nasopharyngeal swab specimens from 400 patients. The two saliva protocols demonstrated a substantial agreement when compared to the oro/nasopharyngeal swab protocol. Moreover, the positivity rate of saliva protocols increased according to the disease period. The 95 % limit of detection of one of the therefore implemented saliva protocol was determined as 9441 copies/mL. Our results support the conclusion that RNA extraction-free RT-PCR using self-collected saliva specimens is an alternative to nasopharyngeal swabs, especially in the early phase of symptom onset.


Subject(s)
COVID-19 Testing/methods , COVID-19/virology , SARS-CoV-2/isolation & purification , Saliva/virology , COVID-19/diagnosis , Cross Infection/diagnosis , Diagnostic Tests, Routine , Health Personnel , Humans , Nasopharynx/virology , RNA, Viral/genetics , SARS-CoV-2/genetics , Specimen Handling/methods , World Health Organization
7.
Emerg Infect Dis ; 27(3): 970-972, 2021 03.
Article in English | MEDLINE | ID: covidwho-1048946

ABSTRACT

In December 2020, research surveillance detected the B.1.1.7 lineage of severe acute respiratory syndrome coronavirus 2 in São Paulo, Brazil. Rapid genomic sequencing and phylogenetic analysis revealed 2 distinct introductions of the lineage. One patient reported no international travel. There may be more infections with this lineage in Brazil than reported.


Subject(s)
COVID-19 , Phylogeny , SARS-CoV-2/isolation & purification , Travel , Adult , Brazil , COVID-19/epidemiology , COVID-19/virology , Female , Genome, Viral , Humans , Male , Young Adult
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