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1.
J Virol Methods ; 308: 114587, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-1936900

ABSTRACT

PURPOSE: To evaluate filter paper as a means to transport oro/nasopharyngeal samples from laboratories with few resources for SARS-CoV-2 detection by RT-qPCR in a central laboratory that usually performs this technique as routine. METHODS: A total of 40 specimens were evaluated in parallel by RT-qPCR carried out after RNA extraction using two different protocols: direct RNA extraction (Protocol A - reference method) and RNA extraction after impregnation in filter paper (Protocol B). RESULTS: The RT-qPCR for SARS-CoV-2 using Protocol B presented 97.22% (35/36) of agreement for SARS-CoV-2-positive samples when compared to the reference method (Protocol A), even for specimens with low viral load (increased Ct values). Noteworthy, three clinical specimens which were categorized as inconclusive by Protocol A presented amplification of both N1 and N2 targets using Protocol B, presenting positive results for SARS-CoV-2. CONCLUSION: The use of filter paper to transport oro/nasopharyngeal clinical samples presented very satisfactory results to detect SARS-CoV-2 by RT-qPCR. In addition, it proved to be a feasible and sensitive approach, being able to generate the detection of SARS-CoV-2 even at low concentrations, without presenting false-negative results.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , COVID-19 Testing , Clinical Laboratory Techniques/methods , Humans , RNA, Viral/analysis , RNA, Viral/genetics , SARS-CoV-2/genetics , Sensitivity and Specificity
2.
Microbiol Spectr ; 10(1): e0151121, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1794530

ABSTRACT

The SARS-CoV-2 P.1 lineage emerged in Amazonas (AM), North Brazil and its evolution has been dynamically reported associated with increased transmissibility and/or immune evasion. Here, we evaluated the lineages circulating in 29 cities in Rio Grande do Sul (RS), Southern Brazil between March 2020 and May 2021 and investigated the genetic events associated with the emergence of the P.1. A total of 202 oro/nasopharyngeal SARS-CoV-2 specimens from patients during routine hospital care were submitted to whole-genome sequencing. Phylogenetic and Bayesian Evolutionary Analyses of the P.1 lineage were carried out to determine the relationship between sequences from RS and AM and dated their common ancestor and origin. One hundred six (53%) sequences were assigned as P.1 and most carried the 22 lineage-defining mutations. All the P.1 sequences included other important mutations, such as P314L and R203K/G204R, and revealed a high genetic diversity in the phylogenetic tree. The time-scaled inference suggests that the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM, but the origin of some sequences from RS is unknown. Further, the common ancestor of sequences from RS is dated to mid-June/July 2020, earlier than those previously reported from AM. Our results demonstrate that there is a high degree of genetic diversity among P.1 sequences, which suggests a continuous evolution and community spread of the virus. Although the first P.1 outbreak was reported in AM, the lineage was associated with multiple introductory events and had already been circulating in Southern Brazil prior to November 2020. IMPORTANCE The SARS-CoV-2 P.1 lineage is associated with increased transmissibility and/or immune evasion and presents a dynamic evolution in Brazil. The significance of our research relies in the fact that we evaluated the SARS-CoV-2 lineages circulating in Southern Brazil between March 2020 and May 2021. This evaluation allowed us to detect the genetic events associated with the emergence of the P.1 and its sublineages. This study is important because we were able to establish that the common ancestor of P.1 sequences from Rio Grande do Sul, Southern Brazil, is dated of mid-June/July 2020, earlier than the P.1 sequences previously reported from Amazonas (AM) state. Noteworthy, the high degree of genetic diversity among P.1 sequences found in this study suggests a continuous evolution and community spread of the virus. Moreover, the oldest P.1 sequences from different Brazilian states share a ancestor with those from AM.


Subject(s)
COVID-19/virology , Genome, Viral , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Brazil/epidemiology , COVID-19/epidemiology , Child , Child, Preschool , Female , Genomics , Humans , Infant , Male , Middle Aged , Mutation , Phylogeny , SARS-CoV-2/classification , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/genetics , Whole Genome Sequencing , Young Adult
3.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-324932

ABSTRACT

Background: The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) variant of concern (VOC) Gamma (P.1) has increased transmissibility and resulted in elevated hospitalization, intensive care unit occupancy and mortality rates in Brazil. It is not known whether this VOC is also associated with more severe clinical course of disease. Methods This was a retrospective cohort study with non-elderly patients hospitalized for COVID-19 from June to December/2020 (first period) and February to May/2021 (second period) at a reference hospital in Brazil. Two cohorts were performed: the main cohort, composed by patients with SARS-CoV-2 lineages confirmed by whole genome sequencing;and the sensitivity cohort, composed by all eligible patients admitted before and after the emergence of Gamma. The primary outcome was the incidence rate of need of advanced ventilatory support. Results In the main cohort a total of 86 (43 Gamma and 43 non-Gamma) patients were included. Baseline characteristics were similar, except that Gamma patients had lower median Charlson’s comorbidity score. The crude and adjusted incidence rates of advanced respiratory support (adjusted Hazard Ratio [aHR], 1.78;95% Confidence Interval [CI], 1.05–3.03), invasive respiratory support (aHR, 2.64;95% CI, 1.34–5.19) and 28-day mortality from onset of symptoms (aHR, 4.73;95% CI, 1.15–19.41) and adjusted 28-day mortality from hospital admission (aHR, 3.72;95% CI, 1.19–11.65) were significantly higher in patients infected by Gamma. These patients had significantly lower days alive and free of supplemental oxygen support. The sensitivity cohort included 433 patients: 259 from the first and 174 from the second period (before and after the emergence of Gamma, respectively). Baseline characteristics were similar, except for a higher incidence of severe distress respiratory syndrome in patients from second group at admission. Patients from the second period had significantly higher incidence rates of advanced respiratory support (aHR, 2.04;95% CI, 1.60–2.59), invasive ventilatory support (aHR, 2.72;95%CI, 2.05–3.62), and 28-day mortality from the onset of symptoms (aHR, 2.62;95%CI, 1.46–4.72). Conclusions Our study suggests that in non-elderly hospitalized patients, COVID-19 caused by Gamma VOC may present a more severe clinical course, with increased need of advanced respiratory support and higher 28-day mortality.

7.
Euro Surveill ; 26(12)2021 03.
Article in English | MEDLINE | ID: covidwho-1154192

ABSTRACT

The emergence of SARS-CoV-2 P.1 lineage coincided with a surge in hospitalisations in the North region of Brazil. In the South region's Rio Grande do Sul state, severe COVID-19 case numbers rose 3.8 fold in February 2021. During that month, at a COVID-19 referral hospital in this state, whole-genome sequencing of a subset of cases' specimens (n = 27) revealed P.1 lineage SARS-CoV-2 in most (n = 24). Findings raise concerns regarding a possible association between lineage P.1 and rapid case and hospitalisation increases.


Subject(s)
COVID-19/diagnosis , COVID-19/virology , SARS-CoV-2/isolation & purification , Brazil/epidemiology , Hospitalization/statistics & numerical data , Humans , Whole Genome Sequencing
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