ABSTRACT
Introduction: The demand for molecular diagnosis of pathogens has surged dramatically since the onset of the COVID-19 pandemic. In this context, different diagnostic tests have been developed to identify SARS-CoV-2 in patient samples. The emergence of new variants of SARS-CoV-2 raises questions about whether the molecular tests available for diagnosis continue to be effective in detecting the virus in biological samples. Objective: This study analyzed the viability of molecular targets directed to N, E and RdRp genes available against the new variants of SARS-CoV-2. Methodology: For this, we used bioinformatics tools to analyze SARS-CoV-2 genomic data of different variants deposited in GSAID and NCBI virus genomic databases to assess the accuracy of molecular tests available for the diagnosis of COVID-19. We also developed software for analyzing mutation frequencies in different molecular targets from the mutation database. Results: Mutation frequency analysis revealed a high rate of mutations in the N, E and RdRp genes and targets, although the target regions were more conserved. Only three SNPs were recurrent in the sequences of the variants identified in different continents and all in different targets. On the other hand, the registered mutations are not consistent and do not appear frequently in isolates of the same variant in all regions of the world. Conclusion: Our data suggest that the molecular targets designed for the first SARS-CoV-2 variants remain valid for the identification of new virus variants despite the large number of identified haplotypes. However, false negative test failures can be identified by using more than one molecular target for the same sample. Genomic regions that are under evolutive selective pressure should be avoided in the use of the diagnostic, once the emergence of new variants may affect the efficiency of molecular testing on a global scale.
Subject(s)
COVID-19 , Heart FailureABSTRACT
Objective: To evaluate serum levels of S100A9 as an inflammatory marker of unfavorable outcomes in patients with COVID-19 in a cross-section study.Material: Participants in this study were allocated from reference care units for the diagnosis of COVID-19 in the western region of Bahia, Brazil, from May 2020 to June 2021.Methods: Blood samples were collected from control group, patients with RT-qPCR positive for COVID-19 with different clinical manifestations of the disease and cured COVID-19 patients. Cytokines and inflammatory mediators (S100A9, D-dimer IL-6, IL-10, TNF-a, IL-12p70) were analyzed by ELISA/CBA.Results: Hospitalized COVID-19 patients presented increased production of S100A9, IL-6, IL-10, TNF-α, IL-12p70, and D-dimer when compared with not hospitalized patients, not infected or cured. Spearman analysis revealed a positive correlation between S100A9 and inflammatory cytokines/D-dimer. ROC curve analyses demonstrated accurate sensitivity and specificity for S100A9 and IL-6.Conclusion: S100A9 serum levels were elevated in hospitalized patients associated with unfavorable outcomes and poor prognosis in COVID-19. Thus, using S100A9 in association with other standardized parameters in clinical protocols may be a useful tool to predict critical clinical evolution during SARS-COV-2 infection.
Subject(s)
COVID-19ABSTRACT
It is not clear if COVID-19 can be indirectly transmitted. It is not possible to conclude the role of environment in transmission of SARS-CoV-2 without studying areas in which people transit in great amounts, such as market areas. In this work we aimed to better understand the role of environment in the spread of COVID-19. We investigated the presence of SARS-CoV-2 in inanimate objects as well as in the air and in the sewage using RT-qPCR. We studied both, a reference market area and a COVID-19 reference hospital at Barreiras city, Brazil. We collected and analyzed a total of 268 samples from mask fronts, cell phones, paper moneys, card machines, sewage, air and bedding during the ascendant phase of the epidemiological curve of COVID-19 in Barreiras. As a result, we detected the human RNAse P gene in most of samples, which indicates the presence of human cells in specimens. However, we did not detect any trace of SARS-CoV-2 in all samples analyzed. To rule out the possibility of problems in sampling method we tested detection of SARS-CoV-2 by RT-qPCR in laboratory conditions to reproduce environmental temperature and humidity. As a result, we showed detection of the virus in different conditions. We conclude that our sampling method reliable and that, strikingly, the environment and inanimate materials do not have an important role in COVID-19 transmission.
Subject(s)
COVID-19ABSTRACT
IntroductionMolecular diagnosis of SARS-CoV-2 is a huge challenge to many countries around the world. The cost of tests to check infected people is inaccessible since specialized teams and equipment are not disposable in remote locations. Herein, we compared the fitness of two primers sets to the SARS-CoV-2 N gene in the molecular diagnosis of COVID-19. Materials and MethodsThe 1029 patient samples were tested to presense/abscence molecular test using in house US CDC protocol. We compared the fitness of two primers sets to two different regions of N gene targets. ResultsBoth targets, N1 and N2 displayed similar fitness during testing with no differences between Ct or measurable viral genome copies. In addition, we verified security ranges Cts related to positive diagnostic with Ct above 35 value failuring in 66,6% after retesting of samples. Main conclusionOur data suggest that it is secure to use just one primer set to the N gene to identify SARS-CoV-2 in samples and the labs should be careful to set positive samples in high Ct values using high cutoffs.
Subject(s)
COVID-19 , HallucinationsABSTRACT
Background: Molecular diagnosis of SARS-CoV-2 is a huge challenge to many countries around the world. The cost of tests to check infected people is inaccessible since specialized teams and equipment are not disposable in remote locations. Herein, we compared the fitness of two primers sets to the SARS-CoV-2 N gene in the molecular diagnosis of COVID-19.Methods: The 1029 patient samples were tested to presense/abscence molecular test using in house US CDC protocol. We compared the fitness of two primers sets to two different regions of N gene targets.Findings: Both targets, N1 and N2 displayed similar fitness during testing with no differences between Ct or measurable viral genome copies. In addition, we verified security ranges Cts related to positive diagnostic with Ct above 35 value failuring in 66,6% after retesting of samples.Interpretation: Our data suggest that it is secure to use just one primer set to the N gene to identify SARS-CoV-2 in samples and the labs should be careful to set positive samples in high Ct values using high cutoffs.Funding: Associação Baiana de Produtores de Algodão (ABAPA); Associação Baiana de Agricultores Irrigantes da Bahia (AIBA); Fundação de Amparo à Pesquisa do Estado da Bahia (FAPESB) (Grant Number: #1381/2020); FINEP (Grant Number: # 0418000600); CNPq; CAPES, MEC, MCTIC.Declaration of Interests: None to declare.Ethics Approval Statement: The Research Ethics Committee of UFOB approved this study in 2020 (license number: 30629520.6.0000.0008). All clinical investigations were conducted according to the Declaration of Helsinki.