Effects of Spike Mutations in SARS-CoV-2 Variants of Concern on Human or Animal ACE2-Mediated Virus Entry and Neutralization DOI
Yunjeong Kim, Natasha N. Gaudreault, David A. Meekins

et al.

Microbiology Spectrum, Journal Year: 2022, Volume and Issue: 10(3)

Published: May 31, 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a zoonotic agent capable of infecting humans and wide range animal species. Over the duration pandemic, mutations in SARS-CoV-2 spike (S) protein have arisen, culminating spread several variants concern (VOCs) with various degrees altered virulence, transmissibility, neutralizing antibody escape. In this study, we used pseudoviruses that express specific S substitutions cell lines angiotensin-converting enzyme (ACE2) from nine different species to gain insights into effects VOC on viral entry neutralization capability. All ACE2 receptors tested, except mink, support for expressing ancestral prototype at levels comparable human ACE2. Most single did not significantly change virus entry, although 614G 484K resulted decreased efficiency. Conversely, combinatorial were associated increased pseudoviruses. Neutralizing titers sera reduced against proteins Beta, Delta, or Omicron VOCs compared parental protein. Especially, variant sera. This study reveals important host effect recently emergent replication, antibody-mediated neutralization.

Language: Английский

Vaccine nationalism and the dynamics and control of SARS-CoV-2 DOI Creative Commons
Caroline E. Wagner, Chadi M. Saad-Roy, Sinead E. Morris

et al.

Science, Journal Year: 2021, Volume and Issue: 373(6562)

Published: Aug. 17, 2021

Stockpiling and control A triumph that has emerged from the catastrophe of severe acute respiratory syndrome coronavirus 2 pandemic been rapid development several potent vaccines. However, 18 months into more than 6 after vaccine approval, wealthy countries remain major beneficiaries. Wagner et al . model consequences stockpiling in affluent on disease rates lower- middle-income for eruption new variants could jeopardize early success For can readily access vaccines, it would be better to share vaccines equitably lower burdens with less access, reduce cost having constantly vigilant case imports, minimize virus evolution. —CA

Language: Английский

Citations

99
Updated picture of SARS-CoV-2 variants and mutations DOI Open Access
Giuseppe Lippi, Camilla Mattiuzzi, Brandon Michael Henry

et al.

Diagnosis, Journal Year: 2021, Volume and Issue: 9(1), P. 11 - 17

Published: Dec. 23, 2021

Abstract The worldwide burden of coronavirus disease 2019 (COVID-19) is still unremittingly prosecuting, with nearly 300 million infections and over 5.3 deaths recorded so far since the origin SARS-CoV-2 (severe acute respiratory syndrome 2) pandemic at end year 2019. fight against this new highly virulent beta appears one most strenuous long challenges that humanity has ever faced, a definitive treatment not been identified far. adoption potentially useful physical preventive measures such as lockdowns, social distancing face masking seems only partially effective for mitigating viral spread, though efficacy continuation on term questionable, due to many economic reasons. Many COVID-19 vaccines have developed are now widely used, their effectiveness challenged by several aspects low uptake limited in some specific populations, well continuous emergence mutations genome, accompanying spread variants, which turn may contribute further decrease current treatments. This article hence aimed provide an updated picture variants emerged from November present time (i.e., early December 2021).

Language: Английский

Citations

73
Targeting COVID Vaccine Hesitancy in Rural Communities in Tennessee: Implications for Extending the COVID-19 Pandemic in the South DOI Creative Commons
Donald J. Alcendor

Vaccines, Journal Year: 2021, Volume and Issue: 9(11), P. 1279 - 1279

Published: Nov. 4, 2021

Approximately 40% of Tennesseans are vaccinated fully, due mainly to higher vaccination levels within urban counties. Significantly lower rates observed in rural Surveys suggest COVID-19 vaccine hesitancy is entrenched mostly among individuals identifying as white, rural, Republican, and evangelical Christian. Rural counties represent 70 the total 95 Tennessee, signifies an immediate public health crisis likely extend pandemic. Tennessee a microcosm pandemic's condition Southern U.S. Unvaccinated communities greatest contributors new infections, hospitalizations, deaths. have long history cultural conservatism, poor literacy, distrust government medical establishments more susceptible misinformation conspiracy theories. Development novel strategies increase acceptance essential. Here, I examine basis following SARS-CoV-2 infection summarize extent South, current efforts across underlying factors contributing hesitancy. Finally, discuss specific combat We must develop that go beyond financial incentives, proven ineffective toward vaccinations. Successful for could unvaccinated populations.

Language: Английский

Citations

59
B.1.617.2 (Delta) Variant of SARS-CoV-2: features, transmission and potential strategies DOI Creative Commons
Yan Zhan, Hui Yin, Ji‐Ye Yin

et al.

International Journal of Biological Sciences, Journal Year: 2022, Volume and Issue: 18(5), P. 1844 - 1851

Published: Jan. 1, 2022

Coronavirus disease 2019 caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has become a pandemic.With continuous evolution of viral genome, SARS-CoV-2 evolved many variants.B.1.617.2, also called Delta, is one most concerned variants.The Delta variant was first reported in India at end 2020 but spread globally, now, to 135 countries and not stand still.Delta shared some mutations with other variants, owned its special on spike proteins, which may be responsible for strong transmission increasing virulence.Under these circumstances, systematic summary necessary.This review will focus variant.We describe all characteristics (including biological features clinical characteristics), analyze potential reasons transmission, provide protective ways combating Delta.

Language: Английский

Citations

57
COVID-19 endgame: From pandemic to endemic? Vaccination, reopening and evolution in low- and high-vaccinated populations DOI
Elisha B. Are,

Yexuan Song,

Jessica E. Stockdale

et al.

Journal of Theoretical Biology, Journal Year: 2022, Volume and Issue: 559, P. 111368 - 111368

Published: Nov. 24, 2022

Language: Английский

Citations

50
SARS-CoV-2 evolved variants optimize binding to cellular glycocalyx DOI Creative Commons
Sang Hoon Kim, Fiona L. Kearns, Mia A. Rosenfeld

et al.

Cell Reports Physical Science, Journal Year: 2023, Volume and Issue: 4(4), P. 101346 - 101346

Published: April 1, 2023

Viral variants of concern continue to arise for SARS-CoV-2, potentially impacting both methods detection and mechanisms action. Here, we investigate the effect an evolving spike positive charge in SARS-CoV-2 subsequent interactions with heparan sulfate angiotensin converting enzyme 2 (ACE2) glycocalyx. We show that positively charged Omicron variant evolved enhanced binding rates negatively Moreover, discover while spike-ACE2 affinity is comparable Delta variant, are significantly enhanced, giving rise a ternary complex spike-heparan sulfate-ACE2 large proportion double-bound triple-bound ACE2. Our findings suggest evolve be more dependent on viral attachment infection. This discovery enables us engineer second-generation lateral-flow test strip harnesses heparin ACE2 reliably detect all concern, including Omicron.

Language: Английский

Citations

41
Fitness, growth and transmissibility of SARS-CoV-2 genetic variants DOI
Erik Volz

Nature Reviews Genetics, Journal Year: 2023, Volume and Issue: 24(10), P. 724 - 734

Published: June 16, 2023

Language: Английский

Citations

37
GenSLMs: Genome-scale language models reveal SARS-CoV-2 evolutionary dynamics DOI

Maxim Zvyagin,

Alexander Brace, Kyle Hippe

et al.

The International Journal of High Performance Computing Applications, Journal Year: 2023, Volume and Issue: 37(6), P. 683 - 705

Published: Oct. 27, 2023

We seek to transform how new and emergent variants of pandemic-causing viruses, specifically SARS-CoV-2, are identified classified. By adapting large language models (LLMs) for genomic data, we build genome-scale (GenSLMs) which can learn the evolutionary landscape SARS-CoV-2 genomes. pre-training on over 110 million prokaryotic gene sequences fine-tuning a SARS-CoV-2-specific model 1.5 genomes, show that GenSLMs accurately rapidly identify concern. Thus, our knowledge, represents one first whole-genome scale foundation generalize other prediction tasks. demonstrate scaling GPU-based supercomputers AI-hardware accelerators utilizing 1.63 Zettaflops in training runs with sustained performance 121 PFLOPS mixed precision peak 850 PFLOPS. present initial scientific insights from examining tracking dynamics paving path realizing this biological data.

Language: Английский

Citations

35
Using big sequencing data to identify chronic SARS-Coronavirus-2 infections DOI Creative Commons
Sheri Harari, Danielle Miller,

Shay Fleishon

et al.

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 20, 2024

Language: Английский

Citations

13
A framework for automated scalable designation of viral pathogen lineages from genomic data DOI Creative Commons
Jakob McBroome, Adriano de Bernardi Schneider, Cornelius Roemer

et al.

Nature Microbiology, Journal Year: 2024, Volume and Issue: 9(2), P. 550 - 560

Published: Feb. 5, 2024

Abstract Pathogen lineage nomenclature systems are a key component of effective communication and collaboration for researchers public health workers. Since February 2021, the Pango dynamic SARS-CoV-2 has been sustained by crowdsourced proposals as new isolates were sequenced. This approach is vulnerable to time-critical delays well regional personal bias. Here we developed simple heuristic dividing phylogenetic trees into lineages, including prioritization mutations or genes. Our implementation efficient on extremely large consisting millions sequences produces similar results existing manually curated designations when applied other viruses chikungunya virus, Venezuelan equine encephalitis virus complex Zika virus. method offers simple, automated consistent pathogen that can assist in developing maintaining phylogeny-based classifications face ever-increasing genomic datasets.

Language: Английский

Citations

10