Sequencing and mutations analysis of the first recorded SARS-CoV-2 Omicron variant during the fourth wave of pandemic in Iraq

The Brazilian Journal of Infectious Diseases, Journal Year: 2022, Volume and Issue: 26(5), P. 102677 - 102677

Published: Aug. 8, 2022

Despite vaccine development and vaccination programs underway around the globe, coronavirus disease 2019 (COVID-19) pandemic has not been controlled as SARS-CoV-2 virus is evolving new variants are emerging. This study was conducted to sequence molecularly characterize representing samples from early fourth wave in Iraq. Here, we have performed next-generation sequencing of whole-genome two country's beginning wave. The were sequenced using Illumina Miseq system, reference sequences retrieved GISAID database. Phylogenetic analysis through Mega software. provides an initial molecular characterization first Omicron variant cases recorded country. Our revealed many mutations on spike glycoprotein, especially receptor binding domain, with potential impact immune escape infectivity. findings suggest considering highly mutated immunogenic epitope a for developing combating ongoing pandemic.

Language: Английский

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Establishing an In Vitro System to Assess How Specific Antibodies Drive the Evolution of Foot-and-Mouth Disease Virus

Viruses, Journal Year: 2022, Volume and Issue: 14(8), P. 1820 - 1820

Published: Aug. 19, 2022

Viruses can evolve to respond immune pressures conferred by specific antibodies generated after vaccination and/or infection. In this study, an in vitro system was developed investigate the impact of serum-neutralising upon evolution a foot-and-mouth disease virus (FMDV) isolate. The presence sub-neutralising dilutions antisera delayed onset virus-induced cytopathic effect (CPE) up 44 h compared untreated control cultures. Continued passage with these sera resulted decrease time complete CPE, suggesting that FMDV cultures adapted escape pressure. These phenotypic changes were associated three separate consensus-level non-synonymous mutations accrued viral RNA-encoding amino acids at positions VP266, VP280 and VP1155, corresponding known epitope sites. High-throughput sequencing also identified further nucleotide substitutions within regions encoding leader (Lpro), VP4, VP2 VP3 proteins. While association later adaptation pressure must be verified, results highlight multiple routes which populations neutralising support application simple approach assess humoral on potentially other viruses.

Language: Английский

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SARS-CoV-2 coinfections with variant genomic lineages identified by multiplex fragment analysis

Frontiers in Genetics, Journal Year: 2022, Volume and Issue: 13

Published: Sept. 26, 2022

Immunocompromised patients can experience prolonged SARS-CoV-2 infections in the setting of a lack protectivity immunity despite vaccination. As circulating strains become more heterogeneous, concomitant infection with multiple variants has an increasing concern. patient populations represent potential reservoirs for emergence novel through mutagenic change or coinfection followed by recombinatory events. Identification coinfections is challenging using traditional next generation sequencing pipelines; however, targeted genotyping approaches facilitate detection. Here we describe five COVID-19 cases caused different (Delta/Omicron BA.1 and Omicron BA.1/BA.2) as identified multiplex fragment analysis.

Language: Английский

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Development of a Method for Detection of SARS-CoV-2 Nucleocapsid Antibodies on Dried Blood Spot by DELFIA Immunoassay

Diagnostics, Journal Year: 2023, Volume and Issue: 13(5), P. 897 - 897

Published: Feb. 27, 2023

Antibodies against the SARS-CoV-2 nucleocapsid protein are produced by immune system in response to infection, but most available vaccines developed fight pandemic spread target spike protein. The aim of this study was improve detection antibodies providing a simple and robust method applicable large population. For purpose, we DELFIA immunoassay on dried blood spots (DBSs) converting commercially IVD ELISA assay. A total forty-seven paired plasma were collected from vaccinated and/or previously SARS-CoV-2-infected subjects. DBS-DELFIA resulted wider dynamic range higher sensitivity for detecting nucleocapsid. Moreover, showed good intra-assay coefficient variability 14.6%. Finally, strong correlation found between detected immunoassays (r = 0.9). Therefore, association sampling with technology may provide an easier, minimally invasive, accurate measurement In conclusion, these results justify further research develop certified assay useful diagnostics as well serosurveillance studies.

Language: Английский

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Clinical and Virological Features of Patients Hospitalized with Different Types of COVID-19 Vaccination in Mexico City

Vaccines, Journal Year: 2022, Volume and Issue: 10(8), P. 1181 - 1181

Published: July 26, 2022

Coronavirus disease 2019 (COVID-19) vaccines effectively protect against severe and death. However, the impact of vaccine used, viral variants, host factors on severity remain poorly understood. This work aimed to compare COVID-19 clinical presentations outcomes in vaccinated unvaccinated patients Mexico City. From March September 2021, clinical, demographic characteristics, variants were obtained from 1014 individuals with a documented SARS-CoV-2 infection. We compared unvaccinated, partially vaccinated, fully patients, stratifying by age groups. also fitted multivariate statistical models evaluate vaccination status, lineages, types, parameters. Most hospitalized unvaccinated. In over 61 years old, mortality was significantly higher individuals. aged 31 60 years, more likely be outpatients (46%) than (6.1%). found immune above old risk factors, while full most protective factor in-hospital study suggests that is essential reduce comorbid population such as Mexico.

Language: Английский

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