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

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Июнь 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.

Язык: Английский

SARS-CoV-2 biology and host interactions DOI
Silvio Steiner, Annika Kratzel, G. Tuba Barut

и другие.

Nature Reviews Microbiology, Год журнала: 2024, Номер 22(4), С. 206 - 225

Опубликована: Янв. 15, 2024

Язык: Английский

Процитировано

83
Impact of novel microbial secondary metabolites on the pharma industry DOI Creative Commons

Dulce Ramírez-Rendón,

Ajit Kumar Passari, Beatriz Ruiz‐Villafán

и другие.

Applied Microbiology and Biotechnology, Год журнала: 2022, Номер 106(5-6), С. 1855 - 1878

Опубликована: Фев. 21, 2022

Microorganisms are remarkable producers of a wide diversity natural products that significantly improve human health and well-being. Currently, these comprise half all the pharmaceuticals on market. After discovery penicillin by Alexander Fleming 85 years ago, search for study antibiotics began to gain relevance as drugs. Since then, have played valuable role in treating infectious diseases saved many lives. New molecules with anticancer, hypocholesterolemic, immunosuppressive activity now been introduced treat other relevant diseases. Smaller biotechnology companies academic laboratories generate novel secondary metabolites big pharmaceutical no longer develop. The purpose this review is illustrate some recent developments show potential modern technologies like metagenomics genome mining offer development new molecules, different functions therapeutic alternatives needed overcome current severe problems, such SARS-CoV-2 pandemic, antibiotic resistance, emerging • Novel treatment infections caused bacteria, fungi, viruses. Second wave efforts microbial origin against related variants. Microbial drugs used clinical practice hypocholesterolemic agents, immunosuppressants, anticancer therapy.

Язык: Английский

Процитировано

59
Recent review of COVID-19 management: diagnosis, treatment and vaccination DOI Open Access
Vivek P. Chavda, Suneetha Vuppu, Toshika Mishra

и другие.

Pharmacological Reports, Год журнала: 2022, Номер 74(6), С. 1120 - 1148

Опубликована: Окт. 10, 2022

Язык: Английский

Процитировано

55
Comparative Analysis of SARS-CoV-2 Variants of Concern, Including Omicron, Highlights Their Common and Distinctive Amino Acid Substitution Patterns, Especially at the Spike ORF DOI Creative Commons
Marios Nikolaidis, Athanasios Papakyriakou, Katerina Chlichlia

и другие.

Viruses, Год журнала: 2022, Номер 14(4), С. 707 - 707

Опубликована: Март 29, 2022

In order to gain a deeper understanding of the recently emerged and highly divergent Omicron variant concern (VoC), study amino acid substitution (AAS) patterns was performed compared with those other four successful variants (Alpha, Beta, Gamma, Delta) one closely related interest (VoI-Lambda). The Spike ORF consistently emerges as an AAS hotspot in all six lineages, but this enrichment is significantly higher. progenitors each these VoC/VoI lineages underwent positive selection ORF. However, once they were established, their ORFs have been undergoing purifying selection, despite application global vaccination schemes from 2021 onwards. Our analyses reject hypothesis that heavily mutated receptor binding domain (RBD) introduced via recombination another Sarbecovirus. Thus, successive point mutations appear most parsimonious scenario. Intriguingly, we observed significant number wherein new residue not present at any homologous site among known Sarbecoviruses. Such should be further investigated potential adaptations human host. By studying phylogenetic distribution shared between (BA.1) lineage had highest (8/10) recurrent mutations.

Язык: Английский

Процитировано

40
Insights into monkeypox pathophysiology, global prevalence, clinical manifestation and treatments DOI Creative Commons

Liyan Niu,

Dingfa Liang,

Ling Qin

и другие.

Frontiers in Immunology, Год журнала: 2023, Номер 14

Опубликована: Март 21, 2023

On 23rd July 2022, the World Health Organization (WHO) recognized ongoing monkeypox outbreak as a public medical crisis. Monkeypox virus (MPV), etiological agent of monkeypox, is zoonotic, linear, double-stranded DNA virus. In 1970, Democratic Republic Congo reported first case MPV infection. Human-to-human transmission can happen through sexual contact, inhaled droplets, or skin-to-skin contact. Once inoculated, viruses multiply rapidly and spread into bloodstream to cause viremia, which then affect multiple organs, including skin, gastrointestinal tract, genitals, lungs, liver. By September 9, more than 57,000 cases had been in 103 locations, especially Europe United States. Infected patients are characterized by physical symptoms such red rash, fatigue, backache, muscle aches, headache, fever. A variety strategies available for orthopoxviruses, monkeypox. prevention following smallpox vaccine has shown up 85% efficacy, several antiviral drugs, Cidofovir Brincidofovir, may slow viral spread. this article, we review origin, pathophysiology, global epidemiology, clinical manifestation, possible treatments prevent propagation provide cues generate specific drugs.

Язык: Английский

Процитировано

28
Effect of SARS-CoV-2 prior infection and mRNA vaccination on contagiousness and susceptibility to infection DOI Creative Commons
Denis Mongin, Nils Bürgisser,

Gustavo Laurie

и другие.

Nature Communications, Год журнала: 2023, Номер 14(1)

Опубликована: Сен. 6, 2023

The immunity conferred by SARS-CoV-2 vaccines and infections reduces the transmission of virus. To answer how effect is shared between a reduction infectiousness an increased protection against infection, we examined >50,000 positive cases >110,000 contacts from Geneva, Switzerland (June 2020 to March 2022). We assessed association secondary attack rate (i.e. proportion new among contacts) natural infection and/or vaccination, stratifying per four variants adjusting for index contacts' socio-demographic characteristics propensity be tested. Here show that protected rather than reducing cases. Natural strongest immunity. Hybrid did not surpass recent infection. Although smaller amplitude, in due vaccination was less affected time emergence susceptibility These findings support role vaccine underscore complementary interventions propagation, such as mask use or indoor ventilation.

Язык: Английский

Процитировано

26
Deep mining of the Sequence Read Archive reveals major genetic innovations in coronaviruses and other nidoviruses of aquatic vertebrates DOI Creative Commons
Chris Lauber, Xiaoyu Zhang,

Josef Vaas

и другие.

PLoS Pathogens, Год журнала: 2024, Номер 20(4), С. e1012163 - e1012163

Опубликована: Апрель 22, 2024

Virus discovery by genomics and metagenomics empowered studies of viromes, facilitated characterization pathogen epidemiology, redefined our understanding the natural genetic diversity viruses with profound functional structural implications. Here we employed a data-driven virus approach that directly queries unprocessed sequencing data in highly parallelized way involves targeted viral genome assembly strategy wide range sequence similarity. By screening more than 269,000 datasets numerous authors from Sequence Read Archive using two metrics quantitatively assess quality, discovered 40 nidoviruses six families whose members infect vertebrate hosts. They form 13 32 putative subfamilies genera, respectively, include 11 coronaviruses bisegmented genomes fishes amphibians, giant 36.1 kilobase coronavirus duplicated spike glycoprotein (S) gene, tobaniviruses 17 additional corona-, arteri-, cremega-, nanhypo- nangoshaviruses. Genome segmentation emerged single evolutionary event monophyletic lineage encompassing subfamily Pitovirinae . We recovered sequences RNA samples 69 infected validated presence poly(A) tails at both segments 3’RACE PCR subsequent Sanger sequencing. report linkage between accessory proteins phylogenetic relationships distances are incongruent phylogeny replicase proteins. rationalize these observations model inter-family S recombination involving least five ancestral corona- aquatic In support this model, describe an individual fish co-infected Coronaviridae Tobaniviridae Our results expand scale known extraordinary plasticity nidoviral architecture call for revisiting fundamentals expression, particle biology, host ecology nidoviruses.

Язык: Английский

Процитировано

12
Characterization of SARS-CoV-2 Evasion: Interferon Pathway and Therapeutic Options DOI Creative Commons

Mariem Znaidia,

Caroline Demeret, Sylvie van der Werf

и другие.

Viruses, Год журнала: 2022, Номер 14(6), С. 1247 - 1247

Опубликована: Июнь 8, 2022

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is responsible for the current COVID-19 pandemic. SARS-CoV-2 characterized by an important capacity to circumvent innate immune response. The early interferon (IFN) response necessary establish a robust antiviral state. However, this weak and delayed in patients, along with massive pro-inflammatory cytokine production. This dysregulated contributes pathogenicity some individuals leads critical Characterizing interplay between viral factors host immunity crucial better understand how manage disease. Moreover, constant emergence of new variants challenges efficacy existing vaccines. Thus, control virus readjust therapy currently used treat COVID-19, studies should constantly be re-evaluated further decipher mechanisms leading pathogenesis. Regarding role IFN infection, review we summarize which evades recognition. More specifically, explain inhibits signaling pathways (IFN-I/IFN-III) controls interferon-stimulated gene (ISG) expression. We also discuss development use IFNs potential drugs controlling SARS-CoV-2, helping clear infection.

Язык: Английский

Процитировано

37
Simultaneous determination of nirmatrelvir and ritonavir in human plasma using LC–MS/MS and its pharmacokinetic application in healthy Chinese volunteers DOI
Chenxi Liu,

Miqun Zhu,

Liyun Cao

и другие.

Biomedical Chromatography, Год журнала: 2022, Номер 36(11)

Опубликована: Июль 26, 2022

Abstract Paxlovid, a copackaged medication of nirmatrelvir tablets (150 mg) and ritonavir (100 developed by Pfizer, is one the first orally accessible COVID‐19 antiviral medicines to be approved for emergency usage. In this research, an efficient LC–MS/MS method simultaneous determination in human plasma was established validated with remdesivir as internal standard. Chromatographic separations were carried out on Thermo BDS Hypersil C18 column (4.6 × 100 mm, 2.4 μm) using deionized water methanol mobile phase, both added 0.1% (v/v) formic acid. Based positive electrospray ionization mode, analyzed selective reaction monitoring. Excellent precision, accuracy, recovery, linearity demonstrated, covering range 50–5000 ng/mL 10–1000 ritonavir. Then, used determining pharmacokinetic profile Paxlovid healthy Chinese volunteers. The parameters, including C max , T t 1/2 AUC 0 − ∞ Western volunteers, correspond well results investigation.

Язык: Английский

Процитировано

32
The Deltacron conundrum: Its origin and potential health risks DOI
Saria Farheen, Yusha Araf, Yan‐Dong Tang

и другие.

Journal of Medical Virology, Год журнала: 2022, Номер 94(11), С. 5096 - 5102

Опубликована: Июль 11, 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), since its outbreak in December 2019, has been capable of continuing the pandemic by mutating itself into different variants. Mass vaccinations, antibiotic treatment therapy, herd immunity, and preventive measures have reduced disease's severity from emerging However, virus is undergoing recombination among current two variants: Delta Omicron, resulting a new variant, informally known as "Deltacron," which was controversial it might be product lab contamination between Omicron samples. proclamation proved wrong, experts are putting more effort better understanding variant's epidemiological characteristics to control potential outbreaks. This review discussed mutations novel variant prospective risk factors therapeutic options context this variant. study could used guide for implementing appropriate controls sudden

Язык: Английский

Процитировано

31