Genomic variation, origin tracing, and vaccine development of SARS-CoV-2: A systematic review.
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ABSTRACT:
SUBMITTER: Li T
PROVIDER: S-EPMC8110321 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Amid the COVID-19 outbreak, several bioinformatic analyses have been conducted on SARS-CoV-2 virus genome. Numerous studies rushed to fill the gap about this novel virus. Comparison with other related sequences, structural predictions of the produced proteins, determination of variations in amino acid residues and depiction of possible drug and vaccine targets have been the focus of scientific research from the beginning of this year. In addition to discussing the viral taxonomy, clinical features, life cycle, and genome organization, this review will focus on the recent updates in genome and viral proteins characterization and potential therapeutic and vaccine candidates developed so far. Comparative studies with related genomes and proteins provide understanding for the viral molecular mechanisms and suggest targets for therapeutics and vaccinology trials to stop the escalation of this new virus. This pandemic, with its resulting social and economic afflictions, will definitely have significant marks on our lives in the following years.
| S-EPMC7910145 | biostudies-literature
Project description:ObjectiveTo systematically review evidence on effectiveness of contact tracing apps (CTAs) for SARS-CoV-2 on epidemiological and clinical outcomes.DesignRapid systematic review.Data sourcesEMBASE (OVID), MEDLINE (PubMed), BioRxiv and MedRxiv were searched up to 28 October 2020.Study selectionStudies, both empirical and model-based, assessing effect of CTAs for SARS-CoV-2 on reproduction number (R), total number of infections, hospitalisation rate, mortality rate, and other epidemiologically and clinically relevant outcomes, were eligible for inclusion.Data extractionEmpirical and model-based studies were critically appraised using separate checklists. Data on type of study (ie, empirical or model-based), sample size, (simulated) time horizon, study population, CTA type (and associated interventions), comparator and outcomes assessed, were extracted. The most important findings were extracted and narratively summarised. Specifically for model-based studies, characteristics and values of important model parameters were collected.Results2140 studies were identified, of which 17 studies (2 empirical, 15 model-based studies) were eligible and included in this review. Both empirical studies were observational (non-randomised) studies and at high risk of bias, most importantly due to risk of confounding. Risk of bias of model-based studies was considered low for 12 out of 15 studies. Most studies demonstrated beneficial effects of CTAs on R, total number of infections and mortality rate. No studies assessed effect on hospitalisation. Effect size was dependent on model parameters values used, but in general, a beneficial effect was observed at CTA adoption rates of 20% or higher.ConclusionsCTAs have the potential to be effective in reducing SARS-CoV-2 related epidemiological and clinical outcomes, though effect size depends on other model parameters (eg, proportion of asymptomatic individuals, or testing delays), and interventions after CTA notification. Methodologically sound comparative empirical studies on effectiveness of CTAs are required to confirm findings from model-based studies.
| S-EPMC8277487 | biostudies-literature
Project description:The year 2020 started with the emergence of novel coronavirus, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), which causes COVID-19 infection. Soon after the first evidence was reported in Wuhan, China, the World Health Organization declared global public health emergency and imminent need to understand the pathogenicity of the virus was required in limited time. Once the genome sequence of the virus was delineated, scientists across the world started working on the development of vaccines. Although, some laboratories have been using previously developed vaccine platforms from severe acute respiratory syndrome coronavirus (SARS) and middle east respiratory syndrome-related coronavirus and apply them in COVID-19 vaccines due to genetic similarities between coronaviruses. We have conducted a literature review to assess the background and current status of COVID-19 vaccines. The worldwide implementation and strategies for COVID-19 vaccine development are summarized from studies reported in years 2015-2020. While discussing the vaccine candidates, we have also explained interpretative immune responses of SARS-CoV-2 infection. There are several vaccine candidates at preclinical and clinical stages; however, only 42 vaccines are under clinical trials. Therefore, more industry collaborations and financial supports to COVID-19 studies are needed for mass-scale vaccine development. To develop effective vaccine platforms against SARS-CoV-2, the genetic resemblance with other coronaviruses are being evaluated which may further promote fast-track trials on previously developed SARS-CoV vaccines.
| S-EPMC7753271 | biostudies-literature
Project description:BackgroundSARS-CoV-2 vaccine has been recommended to pregnant women, but survey studies showed contrasting findings worldwide in relation to the willingness to accept vaccination during pregnancy.ObjectiveTo evaluate the evidence from the literature regarding the acceptance rate of the SARS-CoV-2 vaccine in pregnant and breastfeeding women.Study designWe performed a systematic review on the main databases (MEDLINE (PubMed), Scopus, ISI Web of Science) searching for all the peer-reviewed survey studies analyzing the eventual acceptance rate of the SARS-CoV-2 vaccine among pregnant and breastfeeding women. To combine data meta-analyses of proportions and pooled proportions with their 95% confidence intervals (CI) were calculated.Results15 studies including 25,839 women were included in the analysis. The proportion of women actually willing to be vaccinated during pregnancy is 49.1% (95% CI, 42.3-56.0), and the proportion of breastfeeding women is 61.6% (95% CI, 50.0-75.0).ConclusionThe cumulative SARS-CoV-2 vaccine acceptance rate among pregnant women appears still low. Vaccinal campaign are urgently needed to drive more confidence into the vaccine to help reducing the spread of the infection and the possible consequences during pregnancy.
| S-EPMC8648617 | biostudies-literature
Project description:In the midst of the severe acute respiratory syndrome coronavirus 2 pandemic and its attendant morbidity and mortality, safe and efficacious vaccines are needed that induce protective and long-lived immune responses. More than 120 vaccine candidates worldwide are in various preclinical and phase 1 to 3 clinical trials that include inactivated, live-attenuated, viral-vectored replicating and nonreplicating, protein- and peptide-based, and nucleic acid approaches. Vaccines will be necessary both for individual protection and for the safe development of population-level herd immunity. Public-private partnership collaborative efforts, such as the Accelerating COVID-19 Therapeutic Interventions and Vaccines mechanism, are key to rapidly identifying safe and effective vaccine candidates as quickly and efficiently as possible. In this article, we review the major vaccine approaches being taken and issues that must be resolved in the quest for vaccines to prevent coronavirus disease 2019. For this study, we scanned the PubMed database from 1963 to 2020 for all publications using the following search terms in various combinations: SARS, MERS, COVID-19, SARS-CoV-2, vaccine, clinical trial, coronavirus, pandemic, and vaccine development. We also did a Web search for these same terms. In addition, we examined the World Health Organization, Centers for Disease Control and Prevention, and other public health authority websites. We excluded abstracts and all articles that were not written in English.
| S-EPMC7392072 | biostudies-literature
Project description:SARS-CoV-2 (CoV) is the etiological agent of the COVID-19 pandemic and evolves to evade both host immune systems and intervention strategies. We divided the CoV genome into 29 constituent regions and applied novel analytical approaches to identify associations between CoV genomic features and epidemiological metadata. Our results show that nonstructural protein 3 (nsp3) and Spike protein (S) have the highest variation and greatest correlation with the viral whole-genome variation. S protein variation is correlated with nsp3, nsp6, and 3'-to-5' exonuclease variation. Country of origin and time since the start of the pandemic were the most influential metadata associated with genomic variation, while host sex and age were the least influential. We define a novel statistic-coherence-and show its utility in identifying geographic regions (populations) with unusually high (many new variants) or low (isolated) viral phylogenetic diversity. Interestingly, at both global and regional scales, we identify geographic locations with high coherence neighboring regions of low coherence; this emphasizes the utility of this metric to inform public health measures for disease spread. Our results provide a direction to prioritize genes associated with outcome predictors (e.g., health, therapeutic, and vaccine outcomes) and to improve DNA tests for predicting disease status.
| S-EPMC8626494 | biostudies-literature
Project description:Vaccination against SARS-CoV-2 has greatly mitigated the impact of the COVID-19 pandemic. However, concerns have been raised about the degree to which vaccination might drive the emergence and selection of immune escape mutations that will hamper the efficacy of the vaccines. In this study, we investigate whether vaccination impacted the micro-scale adaptive evolution of SARS-CoV-2 in the Oslo region of Norway, during the first nine months of 2021, a period in which the population went from near-zero to almost 90 per cent vaccine coverage in the population over 50 years old. Weekly aggregated data stratified by age on vaccine uptake and number of SARS-CoV-2 cases in the area were obtained from the National Immunization Registry and the Norwegian Surveillance System for Communicable Diseases, respectively. A total of 6,438 virus sequences (7.5 per cent of the registered cases) along with metadata were available. We used a causal-driven approach to investigate the relationship between vaccination progress and changes in the frequency of 362 mutations present in at least ten samples, conditioned on the emergence of new lineages, time, and population vaccination coverage. After validating our approach, we identified 21 positive and 12 negative connections between vaccination progress and mutation prevalence, and most of them were outside the Spike protein. We observed a tendency for the mutations that we identified as positively connected with vaccination to decrease as the vaccinated population increased. After modelling the fitness of different competing mutations in a population, we found that our observations could be explained by a clonal interference phenomenon in which high fitness mutations would be outcompeted by the emergence or introduction of other high-fitness mutations.
| S-EPMC10776306 | biostudies-literature
Project description:SARS-CoV-2 is a new human coronavirus (CoV), which emerged in China in late 2019 and is responsible for the global COVID-19 pandemic that caused more than 97 million infections and 2 million deaths in 12 months. Understanding the origin of this virus is an important issue, and it is necessary to determine the mechanisms of viral dissemination in order to contain future epidemics. Based on phylogenetic inferences, sequence analysis and structure-function relationships of coronavirus proteins, informed by the knowledge currently available on the virus, we discuss the different scenarios on the origin-natural or synthetic-of the virus. The data currently available are not sufficient to firmly assert whether SARS-CoV2 results from a zoonotic emergence or from an accidental escape of a laboratory strain. This question needs to be solved because it has important consequences on the risk/benefit balance of our interactions with ecosystems, on intensive breeding of wild and domestic animals, on some laboratory practices and on scientific policy and biosafety regulations. Regardless of COVID-19 origin, studying the evolution of the molecular mechanisms involved in the emergence of pandemic viruses is essential to develop therapeutic and vaccine strategies and to prevent future zoonoses. This article is a translation and update of a French article published in Médecine/Sciences, August/September 2020 (10.1051/medsci/2020123).Supplementary informationThe online version of this article (10.1007/s10311-020-01151-1) contains supplementary material, which is available to authorized users.
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Project description:The COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still spreading globally. The scientific community is attempting to procure an effective treatment and prevention strategy for COVID-19. A rising number of vaccines for COVID-19 are being developed at an unprecedented speed. Development platforms include traditional inactivated or live attenuated virus vaccines, DNA or RNA vaccines, recombinant viral vector vaccines, and protein or peptide subunit vaccines. There are 23 vaccines in the clinical evaluation stage and at least 140 candidate vaccines in preclinical evaluation. In this review, we describe research regarding basic knowledge on the virus, updates on the animal models, current landscape of vaccines in clinical evaluation and updated research results on vaccine development. Safe and effective COVID-19 vaccines require further investigation.
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Project description:The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the only zoonotic-origin coronavirus (CoV) that has reached the pandemic stage. The virus uses its spike (S) glycoprotein to attach to the host cells and initiate a cascade of events that leads to infection. It has sternly affected public health, economy, education, and social behavior around the world. Several scientific and medical communities have mounted concerted efforts to limit this pandemic and the subsequent wave of viral spread by developing preventative and potential vaccines. So far, no medicine or vaccine has been approved to prevent or treat coronavirus disease 2019 (COVID-19). This review describes the latest advances in the development of SARS-CoV-2 vaccines for humans, mainly focusing on the lead candidates in clinical trials. Moreover, we seek to provide both the advantages and the disadvantages of the leading platforms used in current vaccine development, based on past vaccine delivery efforts for non-SARS CoV-2 infections. We also highlight the population groups who should receive a vaccine against COVID-19 in a timely manner to eradicate the pandemic rapidly.
| S-EPMC7824029 | biostudies-literature