Browse
Submit Data
Databases
API
Help

Dataset Information

25 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Monophyletic relationship between severe acute respiratory syndrome coronavirus and group 2 coronaviruses.

ABSTRACT: Although primary genomic analysis has revealed that severe acute respiratory syndrome coronavirus (SARS CoV) is a new type of coronavirus, the different protein trees published in previous reports have provided no conclusive evidence indicating the phylogenetic position of SARS CoV. To clarify the phylogenetic relationship between SARS CoV and other coronaviruses, we compiled a large data set composed of 7 concatenated protein sequences and performed comprehensive analyses, using the maximum-likelihood, Bayesian-inference, and maximum-parsimony methods. All resulting phylogenetic trees displayed an identical topology and supported the hypothesis that the relationship between SARS CoV and group 2 CoVs is monophyletic. Relationships among all major groups were well resolved and were supported by all statistical analyses.

SUBMITTER: Zhu G

PROVIDER: S-EPMC7109970 | biostudies-literature | 2004 May

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Monophyletic relationship between severe acute respiratory syndrome coronavirus and group 2 coronaviruses.

Zhu Guan G Chen Hsuan-Wien HW

The Journal of infectious diseases 20040419 9

Although primary genomic analysis has revealed that severe acute respiratory syndrome coronavirus (SARS CoV) is a new type of coronavirus, the different protein trees published in previous reports have provided no conclusive evidence indicating the phylogenetic position of SARS CoV. To clarify the phylogenetic relationship between SARS CoV and other coronaviruses, we compiled a large data set composed of 7 concatenated protein sequences and performed comprehensive analyses, using the maximum-lik ...[more]

PMID: 15116304

Similar Datasets

Severe Acute Respiratory Syndrome Coronavirus 2 Vaccination Boosts Neutralizing Activity Against Seasonal Human Coronaviruses.

Project description:BackgroundMost of the millions of people that are vaccinated against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of coronavirus disease 2019 (COVID-19), have previously been infected by related circulating human coronaviruses (hCoVs) causing common colds and will experience further encounters with these viruses in the future. Whether COVID-19 vaccinations impact neutralization of seasonal coronaviruses is largely unknown.MethodsWe analyzed the capacity of sera derived from 24 individuals before and after heterologous ChAdOx1 nCoV-19 BNT162b2 prime-boost vaccination to neutralize genuine OC43, NL63, and 229E hCoVs, as well as viral pseudoparticles carrying the SARS-CoV-1, SARS-CoV-2, Middle East Respiratory Syndrome (MERS)-CoV, and hCoV-OC43, hCoV-NL63, and hCoV-229E spike proteins. Genuine hCoVs or spike containing pseudovirions were incubated with different concentrations of sera and neutralization efficiencies were determined by measuring viral RNA yields, intracellular viral nucleocapsid expression, or reporter gene expression in Huh-7 cells.ResultsAll individuals showed strong preexisting immunity against hCoV-OC43. Neutralization of hCoV-NL63 was more variable and all sera showed only modest inhibitory activity against genuine hCoV-229E. SARS-CoV-2 vaccination resulted in efficient cross-neutralization of SARS-CoV-1 but not of MERS-CoV. On average, vaccination significantly increased the neutralizing activity against genuine hCoV-OC43, hCoV-NL63, and hCoV-229E.ConclusionsHeterologous COVID-19 vaccination may confer some cross-protection against endemic seasonal coronaviruses.

| S-EPMC8807272 | biostudies-literature

Relationship Between Anxiety, Depression, and Susceptibility to Severe Acute Respiratory Syndrome Coronavirus 2 Infection: Proof of Concept.

Project description:BackgroundPsychological factors can influence susceptibility to viral infections. We examined whether such influences are evident in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection.MethodsParticipants (n = 102) completed measures of anxiety, depression, positive mood, and loneliness and provided a blood sample for the measurement of antibodies to the SARS-CoV-2 spike and nucleocapsid proteins.ResultsSARS-CoV-2 was significantly negatively associated with anxiety and depression. The model remained significant after adjustment for age and gender, although anxiety and depression were no longer significant independent predictors.ConclusionsThese findings offer early support for the hypothesis that psychological factors may influence susceptibility to SARS-CoV-2 infection.

| S-EPMC8807218 | biostudies-literature

Severe acute respiratory syndrome-associated coronavirus infection.

Project description:Whether severe acute respiratory syndrome-associated coronavirus (SARS-CoV) infection can be asymptomatic is unclear. We examined the seroprevalence of SARS-CoV among 674 healthcare workers from a hospital in which a SARS outbreak had occurred. A total of 353 (52%) experienced mild self-limiting illnesses, and 321 (48%) were asymptomatic throughout the course of these observations. None of these healthcare workers had antibody to SARS CoV, indicating that subclinical or mild infection attributable to SARS-CoV in adults is rare.

| S-EPMC3035556 | biostudies-literature

Exploring Noncovalent Protease Inhibitors for the Treatment of Severe Acute Respiratory Syndrome and Severe Acute Respiratory Syndrome-Like Coronaviruses.

Project description:Over the last 20 years, both severe acute respiratory syndrome coronavirus-1 and severe acute respiratory syndrome coronavirus-2 have transmitted from animal hosts to humans causing zoonotic outbreaks of severe disease. Both viruses originate from a group of betacoronaviruses known as subgroup 2b. The emergence of two dangerous human pathogens from this group along with previous studies illustrating the potential of other subgroup 2b members to transmit to humans has underscored the need for antiviral development against them. Coronaviruses modify the host innate immune response in part through the reversal of ubiquitination and ISGylation with their papain-like protease (PLpro). To identify unique or overarching subgroup 2b structural features or enzymatic biases, the PLpro from a subgroup 2b bat coronavirus, BtSCoV-Rf1.2004, was biochemically and structurally evaluated. This evaluation revealed that PLpros from subgroup 2b coronaviruses have narrow substrate specificity for K48 polyubiquitin and ISG15 originating from certain species. The PLpro of BtSCoV-Rf1.2004 was used as a tool alongside PLpro of CoV-1 and CoV-2 to design 30 novel noncovalent drug-like pan subgroup 2b PLpro inhibitors that included determining the effects of using previously unexplored core linkers within these compounds. Two crystal structures of BtSCoV-Rf1.2004 PLpro bound to these inhibitors aided in compound design as well as shared structural features among subgroup 2b proteases. Screening of these three subgroup 2b PLpros against this novel set of inhibitors along with cytotoxicity studies provide new directions for pan-coronavirus subgroup 2b antiviral development of PLpro inhibitors.

| S-EPMC8887654 | biostudies-literature

Fractal signature of coronaviruses related to severe acute respiratory syndrome

Project description:Purpose The aim of this work was to investigate the genome of SARS-CoV, MERS-CoV, and SARS-CoV-2 by the paradigm of chaos theory and fractal geometry. Coronavirus is the agent that causes the severe acute respiratory syndrome (SARS) and Middle East respiratory syndrome (MERS) and emergent infections such as the present pandemic of COVID-19. Understanding its genome pattern is important for developing new and faster ways of testing for identifying the genome of the virus and also for better understanding of its origin and evolution. Methods For that, it was calculated the alpha coefficient by detrended fluctuation analysis (DFA) for the sequences of these genomes converted to binary numbers in order to determine if it is a chaotic or a random series of data. Also, it applied the random walking for obtaining a fractal map of the whole genome and calculated the fractal dimension (FD) by box-counting of this map by two different software. Results With this, it was found that the alpha coefficient of the first SARS viruses was > 0.5, indicating that the series is chaotic or fractal, and has a persistent long-range memory or self-similarity along its sequence. This is not the case for MERS virus, which showed to have a completely random sequence (α < 0.5). For the fractal dimension, SARS viruses presented a FD around 1.5, and for MERS the fractal dimension decreases (FD < 1.5). Conclusion The images generated by random walking of the entire RNA genome are by itself a fractal signature of the virus, which may be applied for studying its origin and for faster diagnostic of COVID-19.

| S-EPMC7320653 | biostudies-literature

Severe acute respiratory syndrome coronavirus 2

Project description:Severe acute respiratory syndrome coronavirus 2 Raw sequence reads

| PRJNA610248 | ENA

Severe acute respiratory syndrome coronavirus 2

Project description:SARS-CoV-2 genomic data and descriptive metadata from primary specimens collected in Nova Scotia, Canada during the COVID-19 outbreak.

| PRJNA669513 | ENA

Severe acute respiratory syndrome coronavirus 2

Project description:Severe acute respiratory syndrome coronavirus 2 with intra-host recombination during superinfection with Alpha and Epsilon variants

| PRJNA800356 | ENA

Severe acute respiratory syndrome coronavirus 2

Project description:Severe acute respiratory syndrome coronavirus 2 Genome sequencing

| PRJNA647448 | ENA

Severe acute respiratory syndrome coronavirus 2

Project description:NYC SARS-CoV-2 Genome sequencing and assembly

| PRJNA704697 | ENA