Omicron variant (B.1.1.529) and its sublineages: What do we know so far amid the emergence of recombinant variants of SARS-CoV-2?

Biomedicine & Pharmacotherapy, Journal Year: 2022, Volume and Issue: 154, P. 113522 - 113522

Published: Aug. 15, 2022

Since the start of COVID-19 pandemic, numerous variants SARS-CoV-2 have been reported worldwide. The advent concern (VOCs) raises severe concerns amid serious containment efforts against that include physical measures, pharmacological repurposing, immunization, and genomic/community surveillance. Omicron variant (B.1.1.529) has identified as a highly modified, contagious, crucial among five VOCs SARS-CoV-2. increased affinity spike protein (S-protein), host receptor, angiotensin converting enzyme-2 (ACE-2), due to higher number mutations in receptor-binding domain (RBD) S-protein proposed primary reason for decreased efficacy majorly available vaccines transmissible nature variant. Because its significant competitive advantage, sublineages swiftly surpassed other become dominant circulating lineages nations. prevalent strain United Kingdom South Africa. Furthermore, emergence recombinant through conjunction with or by mixing variant's sublineages/subvariants poses major threat humanity. This various issues hazards regarding sublineages, such an breakout susceptible populations fully vaccinated persons. As result, understanding features genetic implications this is crucial. Hence, we explained depth evolution analyzed repercussions on infectiousness, dissemination ability, viral entry mechanism, immune evasion. We also presented viewpoint feasible strategies precluding counteracting any future catastrophic spread omicron could result detrimental wave cases.

Language: Английский

---

Human viral nucleic acids concentrations in wastewater solids from Central and Coastal California USA

Scientific Data, Journal Year: 2023, Volume and Issue: 10(1)

Published: June 22, 2023

Abstract We measured concentrations of SARS-CoV-2, influenza A and B virus, respiratory syncytial virus (RSV), mpox human metapneumovirus, norovirus GII, pepper mild mottle nucleic acids in wastewater solids at twelve treatment plants Central California, USA. Measurements were made daily for up to two years, depending on the plant. using digital droplet (reverse-transcription–) polymerase chain reaction (RT-PCR) following best practices making environmental molecular biology measurements. These data can be used better understand disease occurrence communities contributing wastewater.

Language: Английский

---

Making waves: Wastewater surveillance of SARS-CoV-2 in an endemic future

Water Research, Journal Year: 2022, Volume and Issue: 219, P. 118535 - 118535

Published: May 3, 2022

Language: Английский

---

Tracing COVID-19 Trails in Wastewater: A Systematic Review of SARS-CoV-2 Surveillance with Viral Variants

Water, Journal Year: 2023, Volume and Issue: 15(6), P. 1018 - 1018

Published: March 7, 2023

The emergence of new variants SARS-CoV-2 associated with varying infectivity, pathogenicity, diagnosis, and effectiveness against treatments challenged the overall management COVID-19 pandemic. Wastewater surveillance (WWS), i.e., monitoring infections in communities through detecting viruses wastewater, was applied to track spread globally. However, there is a lack comprehensive understanding use WWS for variants. Here we systematically reviewed published articles reporting different wastewater by following PRISMA guidelines provided current state art this study area. A total 80 studies were found that reported until November 2022. Most these (66 out 80, 82.5%) conducted Europe North America, resource-rich countries. There high variation sampling strategy around world, composite (50/66 studies, 76%) as primary method In contrast, grab more common (8/14 57%) resource-limited Among detection methods, reverse transcriptase polymerase chain reaction (RT-PCR)-based sequencing quantitative RT-PCR commonly used wastewater. variants, B1.1.7 (Alpha) variant appeared earlier pandemic most (48/80 studies), followed B.1.617.2 (Delta), B.1.351 (Beta), P.1 (Gamma), others All same pattern clinical within timeline, demonstrating tracked all timely way when emerged. Thus, may be utilized identify presence or absence follow development transmission existing emerging Routine powerful infectious disease tool implemented

Language: Английский

---

Rapid displacement of SARS-CoV-2 variant Delta by Omicron revealed by allele-specific PCR in wastewater

Water Research, Journal Year: 2022, Volume and Issue: 221, P. 118809 - 118809

Published: July 2, 2022

On November 26, 2021, the B.1.1.529 COVID-19 variant was classified as Omicron of concern (VOC). Reports higher transmissibility and potential immune evasion triggered flight bans heightened health control measures across world to stem its distribution. Wastewater-based surveillance has demonstrated be a useful complement for clinical community-based tracking SARS-CoV-2 variants. Using design principles our previous assays that detect variants (Alpha Delta), we developed an allele-specific RT-qPCR assay which simultaneously targets stretch mutations from Q493R Q498R quantitative detection in wastewater. We report their validation against 10-month longitudinal samples influent wastewater treatment plant Italy. RNA concentrations frequencies determined using these agree with cases, revealing rapid displacement Delta by within three weeks. These trends, when mapped vaccination rates, support studies found emergence being associated infection advantage over vaccinated persons. data reinforce versatility, utility accuracy open-sourced methods dynamics communities through informed public responses.

Language: Английский

---

Wastewater Genomic Surveillance Captures Early Detection of Omicron in Utah

Microbiology Spectrum, Journal Year: 2023, Volume and Issue: 11(3)

Published: May 8, 2023

Wastewater-based epidemiology has emerged as a powerful public health tool to trace new outbreaks, detect trends in infection, and provide an early warning of COVID-19 community spread. Here, we investigated the spread SARS-CoV-2 infections across Utah by characterizing lineages mutations detected wastewater samples. We sequenced over 1,200 samples from 32 sewersheds collected between November 2021 March 2022. Wastewater sequencing confirmed presence Omicron (B.1.1.529) on 19, 2021, up 10 days before its corresponding detection via clinical sequencing. Analysis diversity revealed Delta most frequently lineage during (67.71%), but it started declining December with onset (B.1.1529) sublineage BA.1 (6.79%). The proportion increased ~58% January 4, 2022, completely displaced February 7, genomic surveillance BA.3, that was not identified Utah's surveillance. Interestingly, several Omicron-defining began appear prevalence January, aligning surge cases. Our study highlights importance tracking epidemiologically relevant detecting emerging stages outbreak. provides unbiased representation community-wide infection dynamics is excellent complementary surveillance, potential guiding action policy decisions. IMPORTANCE SARS-CoV-2, virus responsible for pandemic, had significant impact health. Global emergence novel variants, shift at-home tests, reduction tests demonstrate need reliable effective strategy contain Monitoring viruses way establish baseline levels complement efforts. particular, can valuable insights into evolution variants. characterized using whole-genome introduction B.1.1.519 (Omicron) Utah. data showed appeared prior patient samples, indicating signal. findings are important perspective timely identification communities high transmission could help guide interventions.

Language: Английский

---

Monkeypox viral nucleic acids detected using both DNA and RNA extraction workflows

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 890, P. 164289 - 164289

Published: May 20, 2023

Language: Английский

---

Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data

Microbial Genomics, Journal Year: 2024, Volume and Issue: 10(5)

Published: May 24, 2024

Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during SARS-CoV-2 pandemic estimating community infection levels by qPCR. Sequencing pathogen genes genomes from wastewater adds information about genetic diversity, which can be used to identify viral lineages (including variants concern) that are circulating in local population. Capturing diversity sequencing not trivial, as samples often contain diverse mixture with real mutations errors, must deconvoluted computationally short reads. In this study we assess nine different computational tools have recently been developed address challenge. We simulated 100 sequence consisting BA.1, BA.2, Delta lineages, various mixtures, well Delta–Omicron recombinant synthetic ‘novel’ lineage. Most performed identifying true present their relative abundances were generally robust variation depth read length. While many identified down 1 % frequency, results more reliable above 5 threshold. The presence unknown lineage, represents unclassified increases error abundance estimates other but magnitude effect was small most tools. also varied how they labelled novel recombinants. our dataset just one possible use cases these methods, hope it helps users understand potential sources bias analysis appreciate commonalities differences methods.

Language: Английский

---

A scoping review of global SARS-CoV-2 wastewater-based epidemiology in light of COVID-19 pandemic

Heliyon, Journal Year: 2024, Volume and Issue: 10(9), P. e30600 - e30600

Published: May 1, 2024

Recently, wastewater-based epidemiology (WBE) research has experienced a strong impetus during the Coronavirus disease 2019 (COVID-19) pandemic. However, few technical issues related to surveillance strategies, such as standardized procedures ranging from sampling testing protocols, need be resolved in preparation for future infectious outbreaks. This review highlights study characteristics, potential use of WBE and overview methods, well methods utilized detect severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) including its variant wastewater. A literature search was performed electronically PubMed Scopus according PRISMA guidelines relevant peer-reviewed articles published between January 2020 March 2022. The identified 588 articles, out which 221 fulfilled necessary criteria are discussed this review. Most global studies were conducted North America (n=75, 34%), followed by Europe (n=68, 30.8%), Asia (n=43, 19.5%). also showed that most application observed correlate SARS-CoV-2 ribonucleic acid (RNA) trends sewage with epidemiological data (n=90, 40.7%). techniques often used globally sample collection, concentration, preferred matrix recovery control various types discussed. Overall, provided framework researchers specializing apply strategic approaches their questions achieving better functional insights. In addition, areas needed more in-depth analysis, ideas new initiatives identified.

Language: Английский

---

Regional Replacement of SARS-CoV-2 Variant Omicron BA.1 with BA.2 as Observed through Wastewater Surveillance

Environmental Science & Technology Letters, Journal Year: 2022, Volume and Issue: 9(6), P. 575 - 580

Published: May 26, 2022

Greater knowledge of circulating SARS-CoV-2 variants can inform pandemic response, vaccine development, disease epidemiology, and use monoclonal antibody treatments. We developed custom assays targeting characteristic mutations in Omicron BA.1 BA.2 confirmed their sensitivity specificity silico vitro. then applied these to daily wastewater solid samples from eight publicly owned treatment works the greater Bay Area California, United States, over four months obtain a spatially temporally intensive data set. documented regional replacement with agreement with, ahead of, clinical sequencing data. This study highlights utility surveillance for real-time tracking sublineage circulation. The results suggest that concerted efforts design RT-PCR target variant wide-scale monitoring implementation will be informative response.

Language: Английский

---