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2022 ◽  
Vol 42 (3) ◽  
pp. 363-366
Author(s):  
Sang Hyuk Park ◽  
Hyun-Ki Kim ◽  
Hang Kang ◽  
Jung Heon Kim ◽  
Jaeseung Lee ◽  
...  

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 123
Author(s):  
Nicolò Musso ◽  
Paolo Giuseppe Bonacci ◽  
Dafne Bongiorno ◽  
Stefano Stracquadanio ◽  
Dalida Angela Bivona ◽  
...  

Background: The SARS-CoV-2 virus has assumed considerable importance during the COVID-19 pandemic. Its mutation rate is high, involving the spike (S) gene and thus there has been a rapid spread of new variants. Herein, we describe a rapid, easy, adaptable, and affordable workflow to uniquely identify all currently known variants through as few analyses. Our method only requires two conventional PCRs of the S gene and two Sanger sequencing reactions, and possibly another PCR/sequencing assay on a N gene portion to identify the B.1.160 lineage. Methods: We selected an S gene 1312 bp portion containing a set of SNPs useful for discriminating all variants. Mathematical, statistical, and bioinformatic analyses demonstrated that our choice allowed us to identify all variants even without looking for all related mutations, as some of them are shared by different variants (e.g., N501Y is found in the Alpha, Beta, and Gamma variants) whereas others, that are more informative, are unique (e.g., A57 distinctive to the Alpha variant). Results: A “weight” could be assigned to each mutation that may be present in the selected portion of the S gene. The method’s robustness was confirmed by analyzing 80 SARS-CoV-2-positive samples. Conclusions: Our workflow identified the variants without the need for whole-genome sequencing and with greater reliability than with commercial kits.


2021 ◽  
Vol 9 ◽  
Author(s):  
Shenjiao Wang ◽  
Xin Zou ◽  
Zhifeng Li ◽  
Jianguang Fu ◽  
Huan Fan ◽  
...  

Background: At present, the global sever acute respiratory syndrome coronavirus 2 (SARS-CoV-2) situation is still grim, and the risk of local outbreaks caused by imported viruses is high. Therefore, it is necessary to monitor the genomic variation and genetic evolution characteristics of SARS-CoV-2. The main purpose of this study was to detect the entry of different SARS-CoV-2 variants into Jiangsu Province, China.Methods: First, oropharyngeal swabs were collected from 165 patients (55 locally confirmed cases and 110 imported cases with confirmed and asymptomatic infection) diagnosed with SARS-CoV-2 infection in Jiangsu Province, China between January 2020 and June 2021. Then, whole genome sequencing was used to explore the phylogeny and find potential mutations in genes of the SARS-CoV-2. Last, association analysis among clinical characteristics and SARS-CoV-2 Variant of Concern, pedigree surveillance analysis of SARS-COV-2, and single nucleotide polymorphisms (SNPs) detection in SARS-COV-2 samples was performed.Results: More men were infected with the SARS-CoV-2 when compared with women. The onset of the SARS-CoV-2 showed a trend of younger age. Moreover, the number of asymptomatic infected patients was large, similar to the number of common patients. Patients infected with Alpha (50%) and Beta (90%) variants were predominantly asymptomatic, while patients infected with Delta (17%) variant presented severe clinical features. A total of 935 SNPs were detected in 165 SARS-COV-2 samples. Among which, missense mutation (58%) was the dominant mutation type. About 56% of SNPs changes occurred in the open reading frame 1ab (ORF1ab) gene. Approximately, 20% of SNP changes occurred in spike glycoprotein (S) gene, such as p.Asp501Tyr, p.Pro681His, and p.Pro681Arg. In total, nine SNPs loci in S gene were significantly correlated with the severity of patients. It is worth mentioning that amino acid substitution of p.Asp614Gly was significantly positively correlated with the clinical severity of patients. The amino acid replacements of p.Ser316Thr and p.Lu484Lys were significantly negatively correlated with the course of disease.Conclusion: Sever acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may further undergo a variety of mutations in different hosts, countries, and weather conditions. Detecting the entry of different virus variants of SARS-CoV-2 into Jiangsu Province, China may help to monitor the spread of infection and the diversity of eventual recombination or genomic mutations.


2021 ◽  
Author(s):  
Dirk Eggink ◽  
Stijn P. Andeweg ◽  
Harry Vennema ◽  
Noortje van Maarseveen ◽  
Klaas Vermaas ◽  
...  

Infections by the Omicron SARS-CoV-2 variant are rapidly increasing worldwide. Among 70,983 infected individuals (age ≥ 12 years), we observed an increased risk of S-gene target failure, predictive of the Omicron variant, in fully vaccinated (odds ratio: 5.0; 95% confidence interval: 4.0-6.1) and previously infected individuals (OR: 4.9: 95% CI: 3.1-7.7) compared with infected naive individuals. This suggests a substantial decrease in protection from vaccine- or infection-induced immunity against SARS-CoV-2 infections caused by the Omicron variant compared with the Delta variant.


Viruses ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 2548
Author(s):  
Gabriel E. Wagner ◽  
Massimo G. Totaro ◽  
André Volland ◽  
Michaela Lipp ◽  
Sabine Saiger ◽  
...  

Rapid molecular surveillance of SARS-CoV-2 S-protein variants leading to immune escape and/or increased infectivity is of utmost importance. Among global bottlenecks for variant monitoring in diagnostic settings are sequencing and bioinformatics capacities. In this study, we aimed to establish a rapid and user-friendly protocol for high-throughput S-gene sequencing and subsequent automated identification of variants. We designed two new primer pairs to amplify only the immunodominant part of the S-gene for nanopore sequencing. Furthermore, we developed an automated “S-Protein-Typer” tool that analyzes and reports S-protein mutations on the amino acid level including a variant of concern indicator. Validation of our primer panel using SARS-CoV-2-positive respiratory specimens covering a broad Ct range showed successful amplification for 29/30 samples. Restriction to the region of interest freed sequencing capacity by a factor of 12–13, compared with whole-genome sequencing. Using either the MinION or Flongle flow cell, our sequencing strategy reduced the time required to identify SARS-CoV-2 variants accordingly. The S-Protein-Typer tool identified all mutations correctly when challenged with our sequenced samples and 50 deposited sequences covering all VOCs (December 2021). Our proposed S-protein variant screening offers a simple, more rapid, and low-cost entry into NGS-based SARS-CoV-2 analysis, compared with current whole-genome approaches.


2021 ◽  
Author(s):  
Ana Caroline Mesquita Cruz ◽  
Mayana Aguiar Vasconcelos

Introdução: Síndrome dos Ovários Policísticos (SOP) é uma doença crônica caracterizada como um distúrbio hormonal que pode afetar de 5 a 10% das mulheres em idade reprodutiva. Tal patologia está relacionada a altos índices de obesidade, resistência à insulina, diabetes mellitus 2 e problemas cardiovasculares causando repercussões à saúde ao longo da vida das portadoras. A SOP pode apresentar sintomas clínicos como hirsutismo, irregularidade menstrual, acne e infertilidade o que pode afetar diretamente a questão psicossocial nas portadoras. Os profissionais da nutrição precisam ter conhecimento frente a essa síndrome, pois a alteração do estilo de vida tem se instituído como tratamento de primeira linha em mulheres com SOP e obesidade. Objetivo: Compreender a fisiopatologia e a importância da abordagem dietoterápica em mulheres com SOP. Metodologia: coleta disponibilizada a partir de artigos científicos encontrados em sites de base de dados Pubmed, Scielo e Lilac, publicados nos últimos 10 anos. Foram utilizados os descritores "síndrome dos ovários policísticos", "síndrome metabólica", "obesidade" e "auxilio nutricional". Resultados: A fisiopatologia da SOP envolve o descontrole na esteroidogênese ovariana por um defeito intrínseco nas células da teca, redução da sensibilidade à insulina (atribuída a um defeito pós-receptor nas vias de sinalização da insulina), excesso de estresse oxidativo, além dos fatores genéticos e ambientais, porém o (s) gene (s) responsáveis pela SOP permanecem indefinidos. Dietas sem sido estudadas como método não medicamentoso e estudos mostram os benefícios da alteração do estilo de vida com a prática de atividade física e uma abordagem dietoterápica tem auxiliado na redução de peso em pacientes obesas com SOP o que afeta diretamente em uma melhora no ambiente hormonal e na composição corporal. No entanto, vale ressaltar que essas anormalidades metabólicas também podem estar presentes em pacientes não obesas. Alimentos in natura ou minimamente processados tem sido estudados principalmente por auxiliarem na prevenção de síndrome metabólica, diabetes mellitus tipo 2, doenças cardiometabólicas além de contribuir para a diminuição do estresse oxidativo nessa síndrome. Conclusão: Pode-se concluir que a orientação nutricional tem se constituído um modulador positivo mediante a sintomatologia e a nível metabólico na SOP.


2021 ◽  
Author(s):  
Rosanna C Barnard ◽  
Nicholas G Davies ◽  
Carl A B Pearson ◽  
Mark Jit ◽  
W John Edmunds

The Omicron B.1.1.529 SARS-CoV-2 variant was first detected in late November 2021 and has since spread to multiple countries worldwide. We model the potential consequences of the Omicron variant on SARS-CoV-2 transmission and health outcomes in England between December 2021 and April 2022, using a deterministic compartmental model fitted to epidemiological data from March 2020 onwards. Because of uncertainty around the characteristics of Omicron, we explore scenarios varying the extent of Omicron's immune escape and the effectiveness of COVID-19 booster vaccinations against Omicron, assuming the level of Omicron's transmissibility relative to Delta to match the growth in observed S gene target failure data in England. We consider strategies for the re-introduction of control measures in response to projected surges in transmission, as well as scenarios varying the uptake and speed of COVID-19 booster vaccinations and the rate of Omicron's introduction into the population. These results suggest that Omicron has the potential to cause substantial surges in cases, hospital admissions and deaths in populations with high levels of immunity, including England. The reintroduction of additional non-pharmaceutical interventions may be required to prevent hospital admissions exceeding the levels seen in England during the previous peak in winter 2020-2021.


2021 ◽  
Author(s):  
Vidhya N M ◽  
Kumaresan A ◽  
Kalaivani V ◽  
Rajesh Kumar A ◽  
Gurunathan Subramanian ◽  
...  

Emergence of Severe Acute Respiratory Syndrome Corona Virus-2 (SARS-CoV-2) Variants of Concern (VOC) possessing improved virulence, transmissibility and/or immune-escape capabilities has raised significant public health concerns. In order to identify VOCs, WHO recommends Whole-Genome Sequencing approach, which is costly and involves longer completion time. Hence, potential role of commercial multiplex RT-PCR kit to screen variants rapidly is being attempted in this study. A total of 1200 suspected COVID samples from different districts of Tamil Nadu State (India) were screened with Thermo TaqPath RT-PCR kit and Altona Realstar RT-PCR Assay kit. Among 1200 screened, S-gene target failure (SGTF) phenomenon were identified in 112 samples while testing with TaqPath RT-PCR Kit. 100% concordant results were observed between SGTF phenomenon and whole-genome sequencing (WGS) results in detecting SARS-CoV-2 VOC B.1.1.7. TaqPath RT-PCR assay testing can be utilized by laboratories to screen rapidly the VOC B.1.1.7 variants, thus enabling early detection of B.1.1.7 variant infection and transmission in population. This in turn will pave way to implement suitable preventive measures by appropriate authorities to control the transmission of the viral variant.


2021 ◽  
Author(s):  
Sam Abbott ◽  
Adam J. Kucharski ◽  
Sebastian Funk ◽  

AbstractBackgroundLocal estimates of the time-varying effective reproduction number (Rt) of COVID-19 in England became increasingly heterogeneous during April and May 2021. This may have been attributable to the spread of the Delta SARS-CoV-2 variant. This paper documents real-time analysis that aimed to investigate the association between changes in the proportion of positive cases that were S-gene positive, an indicator of the Delta variant against a background of the previously predominant Alpha variant, and the estimated time-varying Rt at the level of upper-tier local authorities (UTLA).MethodWe explored the relationship between the proportion of samples that were S-gene positive and the Rt of test-positive cases over time from the 23 February 2021 to the 25 May 2021. Effective reproduction numbers were estimated using the EpiNow2 R package independently for each local authority using two different estimates of the generation time. We then fit a range of regression models to estimate a multiplicative relationship between S-gene positivity and weekly mean Rt estimate.ResultsWe found evidence of an association between increased mean Rt estimates and the proportion of S-gene positives across all models evaluated with the magnitude of the effect increasing as model flexibility was decreased. Models that adjusted for either national level or NHS region level time-varying residuals were found to fit the data better, suggesting potential unexplained confounding.ConclusionsOur results indicated that even after adjusting for time-varying residuals between NHS regions, S-gene positivity was associated with an increase in the effective reproduction number of COVID-19. These findings were robust across a range of models and generation time assumptions, though the specific effect size was variable depending on the assumptions used. The lower bound of the estimated effect indicated that the reproduction number of Delta was above 1 in almost all local authorities throughout the period of investigation.


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