Dataset Information

Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission

ABSTRACT: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the ongoing coronavirus disease 2019 (COVID-19) pandemic. Understanding the influence of mutations in the SARS-CoV-2 gene on clinical outcomes is critical for treatment and prevention. Here, we analyzed all high-coverage complete SARS-CoV-2 sequences from GISAID database from January 1, 2020, to January 1, 2021, to mine the mutation hotspots associated with clinical outcome and developed a model to predict the clinical outcome in different epidemic strains. Exploring the cause of mutation based on RNA-dependent RNA polymerase (RdRp) and RNA-editing enzyme, mutation was more likely to occur in severe and mild cases than in asymptomatic cases, especially A > G, C > T, and G > A mutations. The mutations associated with asymptomatic outcome were mainly in open reading frame 1ab (ORF1ab) and N genes; especially R6997P and V30L mutations occurred together and were correlated with asymptomatic outcome with high prevalence. D614G, Q57H, and S194L mutations were correlated with mild and severe outcome with high prevalence. Interestingly, the single-nucleotide variant (SNV) frequency was higher with high percentage of nt14408 mutation in RdRp in severe cases. The expression of ADAR and APOBEC was associated with clinical outcome. The model has shown that the asymptomatic percentage has increased over time, while there is high symptomatic percentage in Alpha, Beta, and Gamma. These findings suggest that mutation in the SARS-CoV-2 genome may have a direct association with clinical outcomes and pandemic. Our result and model are helpful to predict the prevalence of epidemic strains and to further study the mechanism of mutation causing severe disease.

SUBMITTER: Pang X

PROVIDER: S-EPMC8558435 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:IntroductionThe evidence for vertical transmission of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is not well established. Therefore, the objective of this review is to summarize emerging evidence on the vertical transmission of Severe Acute Respiratory Syndrome Coronavirus 2.MethodsWe conducted a systematic search in PubMed, CINAHL, Web of Science, SCOPUS, and CENTRAL. Likewise, a search for preprint publications was conducted using MedRxiv and Research Square. Studies that addressed vertical transmission of SARS-CoV-2 (concept) among pregnant women infected by Covid-19 (population) in any setting (community, hospital, or home) in any country or context were considered for inclusion. Any types of studies or reports published between December 2019 and September 2020 addressing the effects of SARS-CoV-2 on pregnant women and their newborn babies were included. Studies were screened for eligibility against the inclusion criteria for the review by two reviewers.ResultsWe identified 51 studies reporting 336 newborns screened for COVID-19. From the 336 newborns screened for COVID-19, only 15 (4.4%) were positive for throat swab RT-PCR. All neonates with positive throat swab RT-PCR were delivered by cesarean section. Among neonates with throat swab SARS-CoV-2 positive only five (33.3%) had concomitant placenta, amniotic fluid, and cord blood samples tested, of which only one amniotic fluid sample is positive for RT PCR. Five neonates had elevated IgG and IgM but without intrauterine tissue tested. Four neonates had chest imaging suggestive of COVID-19 pneumonia.ConclusionCurrently there is not enough evidence on vertical virologic transmission of COVID-19 infection during the third trimester of pregnancy. Additionally, there is no evidence to support cesarean delivery, abstaining from breast feeding nor mother and infant separation. Further research involving an adequate sample size of breast milk, placenta, amniotic fluid, and cord blood to ascertain the possibility of vertical transmission and breast milk transfer is needed.

Dataset Information

Emerging Severe Acute Respiratory Syndrome Coronavirus 2 Mutation Hotspots Associated With Clinical Outcomes and Transmission

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets