Towards Pandemic-Scale Ancestral Recombination Graphs of SARS-CoV-2 DOI Creative Commons
Shing H. Zhan, Anastasia Ignatieva, Yan Wong

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: June 8, 2023

Abstract Recombination is an ongoing and increasingly important feature of circulating lineages SARS-CoV-2, challenging how we represent the evolutionary history this virus giving rise to new variants potential public health concern by combining transmission immune evasion properties different lineages. Detection recombinant strains challenging, with most methods looking for breaks between sets mutations that characterise distinct In addition, many basic approaches fundamental study viral evolution assume recombination negligible, in a single phylogenetic tree can genetic ancestry strains. Here present initial version sc2ts, method automatically detect recombinants real time cohesively integrate them into genealogy form ancestral graph (ARG), which jointly records mutation, inheritance. We infer two ARGs under sampling strategies, their properties. One contains 1.27 million sequences sampled up June 30, 2021, second more sparsely sampled, consisting 657K 2022. find both are highly consistent known features SARS-CoV-2 evolution, recovering backbone phylogeny, mutational spectra, recapitulating details on majority Using well-established feature-rich tskit library, also be stored concisely processed efficiently using standard Python tools. For example, ARG sequences—encoding inferred reticulate ancestry, variation, extensive metadata—requires 58MB storage, loads less than second. The ability fully effects downstream analyses, quickly recombinants, utilise efficient convenient platform computation based well-engineered technologies makes sc2ts promising approach.

Language: Английский

Nanotechnology in the COVID-19 era: Carbon-based nanomaterials as a promising solution DOI Creative Commons
Massimiliano Papi, Marco De Spirito, Valentina Palmieri

et al.

Carbon, Journal Year: 2023, Volume and Issue: 210, P. 118058 - 118058

Published: April 29, 2023

The Coronavirus Disease 2019 (COVID-19) pandemic has led to collaboration between nanotechnology scientists, industry stakeholders, and clinicians develop solutions for diagnostics, prevention, treatment of Severe Acute Respiratory Syndrome 2 (SARS-CoV-2) infections. Nanomaterials, including carbon-based materials (CBM) such as graphene carbon nanotubes, have been studied their potential in viral research. CBM unique effects on microorganisms, immune interaction, sensitivity diagnostics made them a promising subject SARS-CoV-2 This review discusses the interaction with applicability, physical chemical properties, known interactions components, proposed treatment, uses.

Language: Английский

Citations

11

Genetic and Evolutionary Analysis of Porcine Deltacoronavirus in Guangxi Province, Southern China, from 2020 to 2023 DOI Creative Commons
Biao Li,

Yeheng Gao,

Ma Yan

et al.

Microorganisms, Journal Year: 2024, Volume and Issue: 12(2), P. 416 - 416

Published: Feb. 19, 2024

Porcine deltacoronavirus (PDCoV) has shown large-scale global spread since its discovery in Hong Kong 2012. In this study, a total of 4897 diarrheal fecal samples were collected from the Guangxi province China 2020 to 2023 and tested using RT-qPCR. total, 362 (362/4897, 7.39%) positive for PDCoV. The S, M, N gene sequences obtained 34 after amplification sequencing. These PDCoV sequences, together with other S reference countries, analyzed. Phylogenetic analysis revealed that Chinese strains have diverged recent years. Bayesian new 1.3 lineage began diverge Comparing amino acids those lineages, showed variations mutations, deletions, insertions, some demonstrated same as or similar 1.2 lineage. addition, recombination interlineage CHGX-MT505459-2019 CHGX-MT505449-2017 province. summary, results provide information on prevalence evolution southern China, which will facilitate better comprehension prevention

Language: Английский

Citations

4

SARS-CoV-2 Vaccination and the Bridge between First and Fourth Dose: Where Are We? DOI Creative Commons
Cristina Stasi, Barbara Meoni, Fabio Voller

et al.

Vaccines, Journal Year: 2022, Volume and Issue: 10(3), P. 444 - 444

Published: March 14, 2022

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has induced the explosion of vaccine research. Currently, according to data World Health Organization, there are several vaccines in clinical (145) and preclinical (195) stages, while at least 10 already phase 4 (post-marketing). Vaccines have proven be safe, effective, able reduce spread SARS-CoV-2 infection its variants, as well consequences development disease-19 (COVID-19). In two-dose primary vaccination, different time intervals between two doses been used. Recently, special attention paid assessing immunogenicity following booster administration. third dose against COVID-19 may administered 8 weeks after second dose. Israel, a fourth approved immunocompromised groups. main objective this review is describe principal results studies on effectiveness first-to-fourth vaccination reinfection by variants incidence disease/death caused COVID-19. shown high level protection from symptomatic Accelerating mass third-dose could potentially induce variants.

Language: Английский

Citations

18

Diversity of gammacoronaviruses and deltacoronaviruses in wild birds and poultry in Russia DOI Creative Commons
V. Yu. Marchenko,

Alexey V. Danilenko,

Natalia Kolosova

et al.

Scientific Reports, Journal Year: 2022, Volume and Issue: 12(1)

Published: Nov. 12, 2022

Abstract Coronaviruses of the genera Gammacoronavirus and Deltacoronavirus are globally widespread circulate primarily in wild domestic birds. Prior studies have established frequently occurring crossover events from avian to mammalian reservoirs. However, there is limited understanding diversity geographical distribution coronaviruses among In this study, surveillance birds Russia during 2020 revealed presence 12% samples Targeted NGS approach was used for evaluation genetic based on RdRp gene. While gammacoronviruses were found both poultry, deltacoronaviruses only represent first detections Russia. A number cases with simultaneous detection gamma- one bird reported. The results study highlight importance further research concerning spread within migrating throughout territory across globe.

Language: Английский

Citations

18

Towards Pandemic-Scale Ancestral Recombination Graphs of SARS-CoV-2 DOI Creative Commons
Shing H. Zhan, Anastasia Ignatieva, Yan Wong

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: June 8, 2023

Abstract Recombination is an ongoing and increasingly important feature of circulating lineages SARS-CoV-2, challenging how we represent the evolutionary history this virus giving rise to new variants potential public health concern by combining transmission immune evasion properties different lineages. Detection recombinant strains challenging, with most methods looking for breaks between sets mutations that characterise distinct In addition, many basic approaches fundamental study viral evolution assume recombination negligible, in a single phylogenetic tree can genetic ancestry strains. Here present initial version sc2ts, method automatically detect recombinants real time cohesively integrate them into genealogy form ancestral graph (ARG), which jointly records mutation, inheritance. We infer two ARGs under sampling strategies, their properties. One contains 1.27 million sequences sampled up June 30, 2021, second more sparsely sampled, consisting 657K 2022. find both are highly consistent known features SARS-CoV-2 evolution, recovering backbone phylogeny, mutational spectra, recapitulating details on majority Using well-established feature-rich tskit library, also be stored concisely processed efficiently using standard Python tools. For example, ARG sequences—encoding inferred reticulate ancestry, variation, extensive metadata—requires 58MB storage, loads less than second. The ability fully effects downstream analyses, quickly recombinants, utilise efficient convenient platform computation based well-engineered technologies makes sc2ts promising approach.

Language: Английский

Citations

10