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

New RT-PCR Assay for the Detection of Current and Future SARS-CoV-2 Variants DOI Creative Commons
Antonio Marchini, Mauro Petrillo, Amy Parrish

et al.

Viruses, Journal Year: 2023, Volume and Issue: 15(1), P. 206 - 206

Published: Jan. 11, 2023

Multiple lineages of SARS-CoV-2 have been identified featuring distinct sets genetic changes that confer to the virus higher transmissibility and ability evade existing immunity. The continuous evolution may pose challenges for current treatment options diagnostic tools. In this study, we first evaluated performance 14 WHO-recommended real-time reverse transcription (RT)-PCR assays currently in use detection found only one assay has reduced against Omicron. We then developed a new duplex RT-PCR based on amplification two ultra-conserved elements present within genome. successfully detects all tested variants concern (including Omicron sub-lineages BA.4 BA.5) from both clinical wastewater samples with high sensitivity specificity. also functions as one-step droplet digital assay. This assay, addition testing, could be adopted surveillance programs routine monitoring SARS-CoV-2's presence population samples. Positive results our conjunction negative an Omicron-specific provide timely indication emergence novel variant certain community thereby aid public health interventions.

Language: Английский

Citations

21
Harnessing three-dimensional (3D) cell culture models for pulmonary infections: State of the art and future directions DOI Open Access
Disha D. Shah, Neha R. Raghani, Mehul R. Chorawala

et al.

Naunyn-Schmiedeberg s Archives of Pharmacology, Journal Year: 2023, Volume and Issue: 396(11), P. 2861 - 2880

Published: June 2, 2023

Language: Английский

Citations

19
Developing an appropriate evolutionary baseline model for the study of SARS-CoV-2 patient samples DOI Creative Commons
John W. Terbot, Parul Johri, Schuyler Liphardt

et al.

PLoS Pathogens, Journal Year: 2023, Volume and Issue: 19(4), P. e1011265 - e1011265

Published: April 5, 2023

Over the past 3 years, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread through human populations in several waves, resulting a global health crisis. In response, genomic surveillance efforts have proliferated hopes of tracking and anticipating evolution this virus, millions patient isolates now being available public databases. Yet, while there is tremendous focus on identifying newly emerging adaptive viral variants, quantification far from trivial. Specifically, multiple co-occurring interacting evolutionary processes are constantly operation must be jointly considered modeled order to perform accurate inference. We here outline critical individual components such an baseline model—mutation rates, recombination distribution fitness effects, infection dynamics, compartmentalization—and describe current state knowledge pertaining related parameters each SARS-CoV-2. close with series recommendations for future clinical sampling, model construction, statistical analysis.

Language: Английский

Citations

18
Discovery and characterization of a pan-betacoronavirus S2-binding antibody DOI
Nicole V. Johnson, Steven C. Wall, Kevin J. Kramer

et al.

Structure, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 1, 2024

Language: Английский

Citations

6
In Silico Evaluation of Antifungal Compounds from Marine Sponges against COVID-19-Associated Mucormycosis DOI Creative Commons
Omkar Pokharkar,

Hariharan Lakshmanan,

Grigory V. Zyryanov

et al.

Marine Drugs, Journal Year: 2022, Volume and Issue: 20(3), P. 215 - 215

Published: March 20, 2022

The world is already facing the devastating effects of SARS-CoV-2 pandemic. A disseminated mucormycosis epidemic emerged to worsen this situation, causing havoc, especially in India. This research aimed perform a multitargeted docking study marine-sponge-origin bioactive compounds against mucormycosis. Information on proven drug targets and marine sponge was obtained via literature search. total seven different were selected. Thirty-five chosen using PASS online program. For homology modeling molecular docking, FASTA sequences 3D structures for protein retrieved from NCBI PDB databases. Autodock Vina PyRx 0.8 used studies. Further, dynamics simulations performed IMODS server top-ranked docked complexes. Moreover, drug-like properties toxicity analyses Lipinski parameters Swiss-ADME, OSIRIS, ProTox-II, pkCSM, StopTox servers. results indicated that naamine D, latrunculin S, (+)-curcudiol, (+)-curcuphenol, aurantoside I, hyrtimomine had highest binding affinity values -8.8, -8.6, -9.8, -11.4, -8.0, -9.0 kcal/mol, respectively. In sum, all MNPs included are good candidates (+)-curcudiol (+)-curcuphenol promising due their broad-spectrum target inhibition potential.

Language: Английский

Citations

28
SARS-CoV-2: tracing the origin, tracking the evolution DOI Creative Commons
Konstantinos Voskarides

BMC Medical Genomics, Journal Year: 2022, Volume and Issue: 15(1)

Published: March 18, 2022

Abstract The origin of SARS-CoV-2 is uncertain. Findings support a “bat origin” but results are not highly convincing. Studies found evidence that was around for many years before the pandemic outbreak. Evidence has been published progenitor already had capability to bind strongly human ACE2 receptor. This may be an indication other animal viruses capable jump humans, having affinity quite worrying since current ecosystems’ collapse brings people high proximity with animals, increasing probabilities random viral transitions. On hand, future adaptation great concern. Virus-host interactions complicated and unfortunately, we still do have accurate tools predicting viruses’ evolution. Viral multifactorial process probably will become soon, as wish, harmless infection. However, humanity currently under largest vaccination program it’s interest see if vaccinations change evolutionary game against virus.

Language: Английский

Citations

27
Digital Health Dashboards for Decision-Making to Enable Rapid Responses During Public Health Crises: Replicable and Scalable Methodology DOI Creative Commons
Tarun Reddy Katapally, Sheriff Tolulope Ibrahim

JMIR Research Protocols, Journal Year: 2023, Volume and Issue: 12, P. e46810 - e46810

Published: June 6, 2023

The COVID-19 pandemic has reiterated the need for cohesive, collective, and deliberate societal efforts to address inherent inefficiencies in our health systems overcome decision-making gaps using real-time data analytics. To achieve this, decision makers independent secure digital platforms that engage citizens ethically obtain big data, analyze convert into evidence, finally, visualize this evidence inform rapid decision-making.The objective of study is develop replicable scalable jurisdiction-specific dashboards monitor, mitigate, manage public crises via integration beyond care.The primary approach development dashboard was use global citizen science tackle pandemics like COVID-19. first step process establish an 8-member Citizen Scientist Advisory Council Digital Epidemiology Population Health Laboratory's community partnerships. Based on consultation with council, three critical needs were prioritized: (1) management household risk COVID-19, (2) facilitation food security, (3) understanding accessibility services. Thereafter, a progressive web application (PWA) developed provide daily services these needs. generated from access PWA are set up be anonymized, aggregated, linked decision-making, is, displays anonymized aggregated obtained devices PWA. hosted Amazon Elastic Compute Cloud server. dashboard's interactive statistical navigation designed Microsoft Power Business Intelligence tool, which creates connection Relational Database server regularly update visualization jurisdiction-specific, data.The resulted decision-making. relayed real time reflect usage provides households ability their request when need, report difficulties issues accessing also delegated alert system risks time, bidirectional engagement allows respond queries, enhanced security.Digital can transform policy by prioritizing as well enable directly communicate mitigate existing emerging crises, paradigm-changing approach, inverting innovation needs, advancing equity.RR1-10.2196/46810.

Language: Английский

Citations

15
The End or a New Era of Development of SARS-CoV-2 Virus: Genetic Variants Responsible for Severe COVID-19 and Clinical Efficacy of the Most Commonly Used Vaccines in Clinical Practice DOI Creative Commons
Dimitrina Miteva, Meglena Kitanova, Hristiana Batselova

et al.

Vaccines, Journal Year: 2023, Volume and Issue: 11(7), P. 1181 - 1181

Published: June 30, 2023

Although the chief of World Health Organization (WHO) has declared end coronavirus disease 2019 (COVID-19) as a global health emergency, is still threat. To be able to manage such pandemics in future, it necessary develop proper strategies and opportunities protect human life. The data on SARS-CoV-2 virus must continuously analyzed, possibilities mutation emergence new, more infectious variants anticipated, well options using different preventive therapeutic techniques. This because fast development severe acute 2 syndrome (SARS-CoV-2) concern have posed significant problem for COVID-19 pandemic control presently available vaccinations. review summarizes that are responsible clinical efficacy most commonly used vaccines practice. consequences after (long COVID or post-COVID conditions) continue subject studies research, affect social economic life worldwide.

Language: Английский

Citations

13
Evolution of Responses to COVID-19 and Epidemiological Characteristics in South Korea DOI Open Access

Junhwi Jeon,

Chang Yong Han,

Tobhin Kim

et al.

International Journal of Environmental Research and Public Health, Journal Year: 2022, Volume and Issue: 19(7), P. 4056 - 4056

Published: March 29, 2022

The characteristics of COVID-19 have evolved at an accelerated rate over the last two years since first SARS-CoV-2 case was discovered in December 2019. This evolution is due to complex interplay among virus, humans, vaccines, and environments, which makes elucidation clinical epidemiological essential assess ongoing policy responses. In this study, we carry out extensive retrospective analysis on infection clusters South Korea from January 2020 September 2021 uncover important social factors associated with age regional patterns through sophisticated large-scale investigation using data provided by Disease Control Prevention Agency (KDCA). Epidemiological include daily confirmed cases, gender, age, city residence, date symptom onset, diagnosis, route infection. We divide time span into six major periods based according various events such as rise new variants, vaccine rollout, change distancing levels, other intervention measures. explore key features relationship unlinked, asymptomatic, serial intervals, infector-infectee interactions, age/region-specific variations. Our results highlight significant impact temporal interventions implemented transmission, particular, that a high level vaccination coverage senior-aged group dramatic reduction cases.

Language: Английский

Citations

21
The Omicron Lineages BA.1 and BA.2 (Betacoronavirus SARS-CoV-2) Have Repeatedly Entered Brazil through a Single Dispersal Hub DOI Creative Commons
Alessandra P. Lamarca, Ueric José Borges de Souza, Filipe Romero Rebello Moreira

et al.

Viruses, Journal Year: 2023, Volume and Issue: 15(4), P. 888 - 888

Published: March 30, 2023

Brazil currently ranks second in absolute deaths by COVID-19, even though most of its population has completed the vaccination protocol. With introduction Omicron late 2021, number COVID-19 cases soared once again country. We investigated this work how lineages BA.1 and BA.2 entered spread country sequencing 2173 new SARS-CoV-2 genomes collected between October 2021 April 2022 analyzing them addition to more than 18,000 publicly available sequences with phylodynamic methods. registered that was present as early 16 November January already 99% samples. More importantly, we detected been mostly imported through state São Paulo, which turn dispersed other states regions Brazil. This knowledge can be used implement efficient non-pharmaceutical interventions against SARS-CoV variants focused on surveillance airports ground transportation.

Language: Английский

Citations

11