Into the Cauldron of the Variant Soup: Insights into the Molecular Epidemiology and Transition to Endemicity of SARS-CoV-2 in Cyprus (November 2022–February 2024) DOI Creative Commons
Andreas C. Chrysostomou, Leondios G. Kostrikis

Viruses, Journal Year: 2024, Volume and Issue: 16(11), P. 1686 - 1686

Published: Oct. 29, 2024

The coronavirus disease 2019 (COVID-19) pandemic, driven by the emergence of severe acute respiratory syndrome 2 (SARS-CoV-2), has been characterized virus's ongoing evolution, leading to appearance more transmissible variants that have often triggered infection surges. In this study, we analyzed SARS-CoV-2 epidemic in Cyprus, utilizing 1627 viral sequences from infected individuals between November 2022 and February 2024. Over period, 251 distinct lineages sublineages were identified, predominantly categorized into three groups: Omicron 5, XBB, JN.1 (parental lineage BA.2.86), all which harbor S protein mutations linked enhanced transmissibility immune escape. Despite relatively low numbers new infections during lack any major waves, unlike earlier phases these demonstrated varying periods dominance, with 5 prevailing 2023, XBB March generating a wavelet December 2023 These findings suggest Cyprus reached endemicity, gradually replacing previously circulating irrespective seasonal patterns. This study highlights critical importance surveillance evolution emphasizes role preventive measures limiting virus transmission, providing valuable insights for safeguarding public health.

Language: Английский

Evolution of Omicron lineage towards increased fitness in the upper respiratory tract in the absence of severe lung pathology DOI Creative Commons
Arthur Wickenhagen, Meaghan Flagg, Julia R. Port

et al.

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 11, 2025

Abstract The emergence of the Omicron lineage represented a major genetic drift in SARS-CoV-2 evolution. This was associated with phenotypic changes including evasion pre-existing immunity and decreased disease severity. Continuous evolution within raised concerns potential increased transmissibility and/or To address this, we evaluate fitness pathogenesis contemporary variants XBB.1.5, XBB.1.16, EG.5.1, JN.1 upper (URT) lower respiratory tract (LRT). We compare vivo infection Syrian hamsters primary human nasal lung epithelium cells assess differences transmissibility, antigenicity, innate immune activation. replicate efficiently URT but display limited pathology lungs compared to previous fail organoids. is attenuated both LRT other fails transmit male hamster model. Our data demonstrate that has favored URT.

Language: Английский

Citations

0
Real-Time PCR-Based Test as a Research Tool for the Retrospective Detection and Identification of SARS-CoV-2 Variants of Concern in a Sample DOI Open Access

V A Makarova,

Artem Y. Shelkov, Anna A. Iliukhina

et al.

International Journal of Molecular Sciences, Journal Year: 2025, Volume and Issue: 26(5), P. 1786 - 1786

Published: Feb. 20, 2025

The Severe Acute Respiratory Syndrome-related Coronavirus 2 (SARS-CoV-2), a causative agent of the COVID-19 disease, has been constantly evolving since its first identification. Mutations that are embedded in viral genomic RNA affect properties virus and lead to emergence new variants. During pandemic, World Health Organization identified more than ten variants SARS-CoV-2 virus. Five these-Alpha, Beta, Gamma, Delta, Omicron-were classified as concern (VOCs), they caused significant outbreaks disease. Additionally, two progeny Omicron, designated JN.1 KS.1, still causing waves infections. Due various variants, some cases, it become important identify particular variant sample. Here, we have developed multiplexed probe-based real-time PCR system for identification VOCs (Alpha, Omicron B.1.1.529/BA.1, BA.2), well modern KS.1. sensitivity specificity tested using isolated genomes preparations from human nasopharyngeal swabs. allows rapid coronavirus cryopreserved fresh samples.

Language: Английский

Citations

0
Severity of Omicron Subvariants and Vaccine Impact in Catalonia, Spain DOI Creative Commons
Víctor López de Rioja, Luca Basile, Aida Perramon‐Malavez

et al.

Vaccines, Journal Year: 2024, Volume and Issue: 12(5), P. 466 - 466

Published: April 27, 2024

In the current COVID-19 landscape dominated by Omicron subvariants, understanding timing and efficacy of vaccination against emergent lineages is crucial for planning future campaigns, yet detailed studies stratified subvariant, timing, age groups are scarce. This retrospective study analyzed cases from December 2021 to January 2023 in Catalonia, Spain, focusing on vulnerable populations affected variants BA.1, BA.2, BA.5, BQ.1 including two national booster campaigns. Our database includes information such as dates diagnosis, hospitalization death, last vaccination, cause among others. We evaluated impact disease severity age, variant, status, finding that recent significantly mitigated across all although waned six months post-vaccination, except BQ.1, which showed more stable levels. Unvaccinated individuals had higher mortality rates. results highlight importance periodic reduce severe outcomes, influenced variant timing. Although seasonality uncertain, our analysis suggests potential benefit annual >60 years old, probably early fall, if eventually exhibits a major peak similar other respiratory viruses.

Language: Английский

Citations

3
Evolution of Omicron lineage towards increased fitness in the upper respiratory tract in the absence of severe lung pathology DOI Open Access
Arthur Wickenhagen, Meaghan Flagg, Julia R. Port

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 14, 2024

The emergence of the Omicron lineage represented a major genetic drift in SARS-CoV-2 evolution. This was associated with phenotypic changes including evasion pre-existing immunity and decreased disease severity. Continuous evolution within raised concerns potential increased transmissibility and/or To address this, we evaluated fitness pathogenesis contemporary variants XBB.1.5, XBB.1.16, EG.5.1, JN.1 upper (URT) lower respiratory tract (LRT). We compared vivo infection Syrian hamsters primary human nasal lung epithelium cells assessed differences transmissibility, antigenicity, innate immune activation. replicated efficiently URT but displayed limited pathology lungs to previous failed replicate organoids. attenuated both LRT other transmit hamster model. Our data demonstrate that has favored URT.

Language: Английский

Citations

1
Impact analysis of SARS-CoV-2 vaccination in patients treated with monoclonal antibodies: A monocentric experience DOI Creative Commons
Nicola Perrotta,

Luigi Angelo Fiorito,

Cristiana Leanza

et al.

International Immunopharmacology, Journal Year: 2024, Volume and Issue: 142, P. 113101 - 113101

Published: Sept. 12, 2024

Language: Английский

Citations

1
Genomic epidemiology and evolutionary dynamics of the Omicron variant of SARS-CoV-2 during the fifth wave of COVID-19 in Pakistan DOI Creative Commons

Aroona Razzaq,

Cyrollah Disoma, Sara Iqbal

et al.

Frontiers in Cellular and Infection Microbiology, Journal Year: 2024, Volume and Issue: 14

Published: Oct. 22, 2024

Introduction The coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome 2 (SARS-CoV-2), has posed extraordinary challenges to global health systems and economies. virus’s rapid evolution resulted in several variants of concern (VOCs), including the highly transmissible Omicron variant, characterized extensive mutations. In this study, we investigated genetic diversity, population differentiation, evolutionary dynamics VOC during fifth wave COVID-19 Pakistan. Methods A total 954 genomes sequenced Pakistan were analyzed. Bayesian framework was employed for phylogenetic reconstructions, molecular dating, analysis. Results Using a genomics approach, analyzed Pakistani samples, revealing low within-population diversity significant structural variation spike (S) protein. Phylogenetic analysis showed that variant originated from two distinct lineages, BA.1 BA.2, which introduced South Africa, Thailand, Spain, Belgium. Omicron-specific mutations, those receptor-binding domain, identified. estimated rate 2.562E-3 mutations per site year (95% HPD interval: 8.8067E-4 4.1462E-3). skyline plot indicated expansion at end 2021, coinciding with outbreak. Comparative other VOCs as divergent, monophyletic group, suggesting unique pathway. Conclusions This study provides comprehensive overview Omicron’s genomic epidemiology, Pakistan, emphasizing need collaboration monitoring enhancing pandemic preparedness.

Language: Английский

Citations

1
Factors Associated with SARS-CoV-2 Infection in Fully Vaccinated Nursing Home Residents and Workers DOI Creative Commons
Jesús Mateos‐Nozal, Mario Rodríguez-Domínguez, Jesús San Román

et al.

Viruses, Journal Year: 2024, Volume and Issue: 16(2), P. 186 - 186

Published: Jan. 25, 2024

Persons living or working in nursing homes faced a higher risk of SARS-CoV-2 infections during the pandemic, resulting heightened morbidity and mortality among older adults despite robust vaccination efforts. This prospective study evaluated humoral cellular immunity fully vaccinated residents workers from two Madrid, Spain, 2020 to 2021. Measurements IgG levels were conducted August (pre-vaccination) June September 2021 (post-vaccination), alongside assessments neutralizing antibodies responses most vulnerable individuals. Follow-up extended until February 2022 identify factors for infection mortality, involving 267 (mean age 87.6 years, 81.3% women) 302 50.7 82.1% women). Residents exhibited significantly likelihood experiencing COVID-19 before compared with staff (OR [95% CI], 7.2 [3.0 17.2], p < 0.01). Participants history previous showed more significant increases 2020, 2021, an increased proportion However, decay remained same between based on status. During Omicron variant wave, similar rate infection. Notably, preceding clinical immunological receiving three doses did not demonstrate associations overall our participant cohort.

Language: Английский

Citations

0
Anomalies in regional and chronological distributions of Omicron BA.1.1 lineage in the United States DOI Creative Commons
Hideki Kakeya

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: Aug. 17, 2024

Abstract This study compares the collection dates and locations of Omicron BA.1 lineage other major SARS-CoV- 2 mutants registered in NCBI GenBank provides a detailed analysis emergence patterns pure reverse mutants, which contain only mutations no surface glycoprotein. The results indicate that BA.1.1 its were widely distributed throughout United States from early days their emergence, showing statistically significant difference compared to variants, spread small number sources. peak BA.1.1.18 occurred few weeks before all collected samples, whereas variants BA.2 coincides with overall sampling peak. Although peaks BA.1.x collections are not synchronous, completely overlap, such declining abruptly after These regional temporal anomalies lineage, especially virtually impossible explain by current theories natural mutation human-to-human infection.

Language: Английский

Citations

0
Into the Cauldron of the Variant Soup: Insights into the Molecular Epidemiology and Transition to Endemicity of SARS-CoV-2 in Cyprus (November 2022–February 2024) DOI Creative Commons
Andreas C. Chrysostomou, Leondios G. Kostrikis

Viruses, Journal Year: 2024, Volume and Issue: 16(11), P. 1686 - 1686

Published: Oct. 29, 2024

The coronavirus disease 2019 (COVID-19) pandemic, driven by the emergence of severe acute respiratory syndrome 2 (SARS-CoV-2), has been characterized virus's ongoing evolution, leading to appearance more transmissible variants that have often triggered infection surges. In this study, we analyzed SARS-CoV-2 epidemic in Cyprus, utilizing 1627 viral sequences from infected individuals between November 2022 and February 2024. Over period, 251 distinct lineages sublineages were identified, predominantly categorized into three groups: Omicron 5, XBB, JN.1 (parental lineage BA.2.86), all which harbor S protein mutations linked enhanced transmissibility immune escape. Despite relatively low numbers new infections during lack any major waves, unlike earlier phases these demonstrated varying periods dominance, with 5 prevailing 2023, XBB March generating a wavelet December 2023 These findings suggest Cyprus reached endemicity, gradually replacing previously circulating irrespective seasonal patterns. This study highlights critical importance surveillance evolution emphasizes role preventive measures limiting virus transmission, providing valuable insights for safeguarding public health.

Language: Английский

Citations

0