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Emergence of SARS-CoV-2 variant B.1.575.2 containing the E484K mutation in the spike protein in Pamplona (Spain) May-June 2021
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| With the emergence of new SARS-CoV-2 variants and the acquisition of novel mutations in exiting lineages, the need to implement methods capable of monitoring viral dynamics arises. We report the emergence and spread of a new SARS-CoV-2 variant within B.1.575 lineage containing the E484K mutation in the spike protein (n... |
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Genetic Characteristics and Phylogeny of 969-bp S Gene Sequence of SARS-CoV-2 from Hawai'i Reveals the Worldwide Emerging P681H Mutation.
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| The COVID-19 pandemic has ravaged the world, caused over 1.8 million deaths in its first year, and severely affected the global economy. Hawai'i has not been spared from the transmission of SARS-CoV-2 in the local population, including high infection rates in racial and ethnic minorities. Early in the pandemic, we desc... |
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Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data
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| Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost, exemplified by well over a half of million ONT SARS-COV-2 datasets. Tracking low frequency intra-host variants has provided important insights with respect to elucidating within host viral populatio... |
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Genome-wide analysis of 10664 SARS-CoV-2 genomes to identify virus strains in 73 countries based on single nucleotide polymorphism
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| Since the onslaught of SARS-CoV-2, the research community has been searching for a vaccine to fight against this virus. However, during this period, the virus has mutated to adapt to the different environmental conditions in the world and made the task of vaccine design more challenging. In this situation, the identifi... |
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GenBank
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| GenBank® (https://www.ncbi.nlm.nih.gov/genbank/) is a comprehensive, public database that contains 9.9 trillion base pairs from over 2.1 billion nucleotide sequences for 478 000 formally described species. Daily data exchange with the European Nucleotide Archive and the DNA Data Bank of Japan ensures worldwide coverage... |
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The 501Y.V2 SARS-CoV-2 variant has an intermediate viral load between the 501Y.V1 and the historical variants in nasopharyngeal samples from newly diagnosed COVID-19 patients
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| The 501Y.V2 and the 501Y.V1 SARS-CoV-2 variants emerged and spread rapidly into the world. We analysed the RT-PCR cycle threshold values of 643 nasopharyngeal samples of COVID-19 patients at diagnosis and found that the 501Y.V2 variant presented an intermediate viral load between the 501Y.V1 and the historical variants... |
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Stability of SARS-CoV-2 Spike G614 Variant Surpasses That of the D614 Variant after Cold Storage
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| Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) carrying the D614G mutation on the spike protein is the predominant circulating variant and is associated with enhanced infectivity. However, whether this dominant variant can potentially spread through the cold chain and whether the spike protein affects vir... |
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Computational Prediction of N6-methyladenosine (m6A) RNA Methylation in SARS-CoV-2 Viral Transcripts
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| SARS-CoV-2 caused atypical pneumonia (COVID-19) is an ongoing pandemic that seriously threat the global public health. Many people die from this disease with severe symptoms. The most prevalent m6A RNA modification may be involved in by assisting the virus escaping from the host cell immune system attack. We provided h... |
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On spatial molecular arrangements of SARS-CoV2 genomes of Indian patients
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| A pandemic caused by the SARS-CoV2 is being experienced by the whole world since December, 2019. A thorough understanding beyond just sequential similarities among the protein coding genes of SARS-CoV2 is important in order to differentiate or relate to the other known CoVs of the same genus. In this study, we compare ... |
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Combining genomic and epidemiological data to compare the transmissibility of SARS-CoV-2 lineages
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| Emerging SARS-CoV-2 variants have shaped the second year of the COVID-19 pandemic and the public health discourse around effective control measures. Evaluating the public health threat posed by a new variant is essential for appropriately adapting response efforts when community transmission is detected. However, this ... |
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Intra-protein interactions of SARS-CoV-2 and SARS: a bioinformatic analysis for plausible explanation regarding stability, divergency, and severity
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| The current nightmare for the whole world is COVID-19. The occurrence of concentrated pneumonia cases in Wuhan city, Hubei province of China, was first reported on December 30, 2019. SARS-CoV first disclosed in 2002 but had not outspread worldwide. After 18 years, in 2020, it reemerged and outspread worldwide as SARS-C... |
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The Variant Gambit: COVID’s Next Move
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| Over a year after its emergence, COVID-19, the disease caused by SARS-CoV-2, continues to plague the world and dominate our daily lives. Even with the development of effective vaccines, this coronavirus pandemic continues to cause a fervor with the identification of major new variants hailing from the United Kingdom, S... |
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Advancing genomic epidemiology by addressing the bioinformatics bottleneck: Challenges, design principles, and a Swiss example
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| The SARS-CoV-2 pandemic led to a huge increase in global pathogen genome sequencing efforts, and the resulting data are becoming increasingly important to detect variants of concern, monitor outbreaks, and quantify transmission dynamics. However, this rapid up-scaling in data generation brought with it many IT infrastr... |
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Comparative insight into the genomic landscape of SARS-CoV-2 and identification of mutations associated with the origin of infection and diversity
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| The analyses of 2325 severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genomes revealed 107, 162, and 65 nucleotide substitutions in the coding region of SARS-CoV-2 from the three continents America, Europe, and Asia, respectively. Of these nucleotide substitutions 58, 94, and 37 were nonsynonymous types mos... |
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Identification of B.1.346 lineage of SARS-CoV-2 in Japan: Genomic evidence of re-entry of Clade 20C
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| Objectives Whole SARS-CoV-2 genome sequencing from COVID-19 patients is useful for infection control and regional trends evaluation. We report a lineage data collected from hospitals in the Kanto region of Japan. Methods We performed whole genome sequencing in specimens of 198 COVID-19 patients at 13 collaborating hosp... |
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SARS-CoV-2 genetic variations associated with COVID-19 severity
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| Herein, we performed a genome-wide association study on SARS-CoV-2 genomes to identify genetic variations that might be associated with the COVID-19 severity. 152 full-length genomes of SARS-CoV-2 that were generated from original clinical samples and whose patient status could be determined conclusively as either asym... |
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Mutational analysis and assessment of its impact on proteins of SARS-CoV-2 genomes from India
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| The ongoing global pandemic of SARS-CoV-2 implies a corresponding accumulation of mutations. Herein the mutational status of 611 genomes from India along with their impact on proteins was ascertained. After excluding gaps and ambiguous sequences, a total of 493 variable sites (152 parsimony informative and 341 singleto... |
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Specific allelic discrimination of N501Y and other SARS-CoV-2 mutations by ddPCR detects B.1.1.7 lineage in Washington State
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| Real-time epidemiological tracking of variants of concern (VOCs) can help limit the spread of more contagious forms of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as those containing the N501Y mutation. Typically, genetic sequencing is required to be able to track VOCs in real-time. However, sequ... |
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Recurrent deletions in the SARS-CoV-2 spike glycoprotein drive antibody escape
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| Zoonotic pandemics, such as that caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), can follow the spillover of animal viruses into highly susceptible human populations. The descendants of these viruses have adapted to the human host and evolved to evade immune pressure. Coronaviruses acquire subst... |
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An in vitro and in vivo approach for the isolation of Omicron variant from human clinical specimens
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| Due to failure of virus isolation of Omicron variant in Vero CCL-81 from the clinical specimen’s of COVID-19 cases, we infected Syrian hamsters and then passage into Vero CCL-81 cells. The Omicron sequences were studied to assess if hamster could incorporate any mutation to changes its susceptibility. L212C mutation, T... |
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First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France
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| The SARS-CoV-2 21K/BA.1, 21L/BA.2, and BA.3 Omicron variants have recently emerged worldwide. To date, the 21L/BA.2 Omicron variant has remained very minority globally but became predominant in Denmark instead of the 21K/BA.1 variant. Here we describe the first cases diagnosed with this variant in south-eastern France.... |
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Motif Analysis in k-mer Networks: An Approach towards Understanding SARS-CoV-2 Geographical Shifts
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| With an increasing number of SARS-CoV-2 sequences available day by day, new genomic information is getting revealed to us. As SARS-CoV-2 sequences highlight wide changes across the samples, we aim to explore whether these changes reveal the geographical origin of the corresponding samples. The k-mer distributions, deno... |
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Large-scale analysis of synonymous viral variants reveals global adaptation of the SARS-CoV-2 to the human codon usage
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| Many large national and transnational studies were dedicated to the analysis of SARS-CoV-2 genome. Most studies are focused on missense and nonsense mutations, however approximately 30% of the SARS-CoV-2 variants are synonymous, therefore changing the target codon without affecting the corresponding protein sequence. H... |
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Sequential appearance and isolation of a SARS-CoV-2 recombinant between two major SARS-CoV-2 variants in a chronically infected immunocompromised patient
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| Genetic recombination is a major evolutionary mechanism among RNA viruses, and it is common in coronaviruses, including those infecting humans. A few SARS-CoV-2 recombinants have been reported to date whose genome harbored combinations of mutations from different mutants or variants, but a single patient sample was ana... |
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Characterization of SARS-CoV-2 infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting
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| BACKGROUND: Tracing of SARS-CoV-2 transmission chains is still a major challenge for public health authorities, when incidental contacts are not recalled or are not perceived as potential risk contacts. Viral sequencing can address key questions about SARS-CoV-2 evolution and may support reconstruction of viral transmi... |
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16306 Genomic epidemiology of SARS-CoV-2 across New Mexico and the Mountain West
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| ABSTRACT IMPACT: Genomic data can be used by policy and decision makers to guide, and assess the impact of, public health responses to the COVID-19 pandemic. OBJECTIVES/GOALS: Our objective is to investigate the transmission and population dynamics of SARS-CoV-2 in New Mexico and other Mountain West states using whole ... |
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Ancestry and admixture of a southernmost Chilean population: The reflection of a migratory history.
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| OBJECTIVES Punta Arenas is a Chilean city situated on ancestral Aönikenk territory. The city was founded by 19th- and 20th-century colonists from Chile (Chiloé) and Europe (Croatia). This work uses uniparental and ancestry-informative markers (AIMs) to explore the effects of historic migratory and admixture patterns on... |
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SARS‐CoV‐2, the pandemic coronavirus: Molecular and structural insights
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| The outbreak of a novel coronavirus associated with acute respiratory disease, called COVID‐19, marked the introduction of the third spillover of an animal coronavirus (CoV) to humans in the last two decades. The genome analysis with various bioinformatics tools revealed that the causative pathogen (SARS‐CoV‐2) belongs... |
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SARS-CoV-2 Genome Sequence Obtained from Ethiopia
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| The coding-complete severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome sequences from 15 nasopharyngeal swabs collected in Addis Ababa, Ethiopia, during the period from December 2020 to March 2021 were determined using Illumina MiSeq technology. A sequence analysis identified that the B.1 SARS-CoV-2 li... |
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Superspreading of SARS-CoV-2 infections: A Systematic Review and Meta-analysis
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| Superspreading in transmission is a feature of SARS-CoV-2 transmission. We conducted a systematic review and meta-analysis on globally reported dispersion parameters of SARS-CoV-2. The pooled estimate was 0.55 (95% CI: 0.30, 0.79). The study location and method were found to be important drivers for its diversity. |
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Deep learning-based real-time detection of novel pathogens during sequencing
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| Novel pathogens evolve quickly and may emerge rapidly, causing dangerous outbreaks or even global pandemics. Next-generation sequencing is the state of the art in open-view pathogen detection, and one of the few methods available at the earliest stages of an epidemic, even when the biological threat is unknown. Analyzi... |
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Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie
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| The ability to detect recombination in pathogen genomes is crucial to the accuracy of phylogenetic analysis and consequently to forecasting the spread of infectious diseases and to developing therapeutics and public health policies However, previous methods for detecting recombination and reassortment events cannot han... |
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Subtle differences in the pathogenicity of SARS-CoV-2 variants of concern B.1.1.7 and B.1.351 in rhesus macaques
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| The emergence of several SARS-CoV-2 variants has caused global concerns about increased transmissibility, increased pathogenicity, and decreased efficacy of medical countermeasures. Animal models can be used to assess phenotypical changes in the absence of confounding factors that affect observed pathogenicity and tran... |
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Current mutatome of SARS-CoV-2 in Turkey reveals mutations of interest
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| As the underlying pathogen for the COVID-19 pandemic that has affected tens of millions of lives worldwide, SARS-CoV-2 and its mutations are among the most urgent research topics worldwide. Mutations in the virus genome can complicate attempts at accurate testing or developing a working treatment for the disease. Furth... |
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Profiling of the most reliable mutations from sequenced SARS-CoV-2 genomes scattered in Uzbekistan
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| Due to rapid mutations in the coronavirus genome over time and re-emergence of multiple novel variants of concerns (VOC), there is a continuous need for a periodic genome sequencing of SARS-CoV-2 genotypes of particular region. This is for on-time development of diagnostics, monitoring and therapeutic tools against vir... |
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Comparative analysis of human coronaviruses focusing on nucleotide variability and synonymous codon usage patterns
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| The prevailing COVID-19 pandemic has drawn the attention of the scientific community to study the evolutionary origin of Severe Acute Respiratory Syndrome Corona Virus 2 (SARS-CoV-2). This study is a comprehensive quantitative analysis of the protein-coding sequences of seven human coronaviruses (HCoVs) to decipher the... |
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Independent acquisition of short insertions at the RIR1 site in the spike N-terminal domain of the SARS-CoV-2 BA.2 lineage
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| Although the SARS-CoV-2 variants BA.1 and BA.2 share over 30 non-synonymous substitutions in the spike glycoprotein, they show several unique mutations that were likely acquired after the split between these two major omicron lineages. One of the most intriguing mutations associated with BA.1 is the presence of the ins... |
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Shortcomings of SARS-CoV-2 genomic metadata
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| OBJECTIVE: The SARS-CoV-2 pandemic has prompted one of the most extensive and expeditious genomic sequencing efforts in history. Each viral genome is accompanied by a set of metadata which supplies important information such as the geographic origin of the sample, age of the host, and the lab at which the sample was se... |
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[Clinical and genetic analysis of a novel CHD4 gene variant in a Chinese patient with Sifrim-Hitz-Weiss syndrome].
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| OBJECTIVE To explore the genotype-phenotype correlation of a case with Sifrim-Hitz-Weiss syndrome (SIHIWES) caused by a novel CHD4 gene variant. METHODS Genomic DNA was extracted from peripheral blood samples of the patient and her parents. Whole-exome sequencing (WES) was carried out for the patient.Suspected variant ... |
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COVIDOUTCOME-estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome
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| Numerous studies demonstrate frequent mutations in the genome of SARS-CoV-2. Our goal was to statistically link mutations to severe disease outcome. We used an automated machine learning approach where 1594 viral genomes with available clinical follow-up data were used as the training set (797 'severe' and 797 'mild').... |
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SARS-CoV-2 Origin: An Affair of Codons?
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| The furin cleavage site, with an arginine doublet (RR), is one of the clues of the SARS-CoV-2 origin. This furin-RR is encoded by the CGG-CGG sequence. Because arginine can be encoded by six codons, in a previous work we found that in SARS-CoV-2, CGG was the minority arginine codon (3%). Also, analyzing the RR doublet ... |
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The m6A methylome of SARS-CoV-2 in host cells
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| The newly identified Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has resulted in a global health emergency because of its rapid spread and high mortality The molecular mechanism of interaction between host and viral genomic RNA is yet unclear We demonstrate herein that SARS-CoV-2 genomic RNA, as well a... |
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SARS-CoV-2 genomic surveillance enables the identification of Delta/Omicron co-infections in Argentina
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| Molecular surveillance of SARS-CoV-2 is crucial to early detect new variants and lineages. In addition, detection of coinfections with more than one SARS-CoV-2 lineage have been sporadically reported. In this work, surveillance of SARS-CoV-2 variants was performed on 2067 RNA samples (Ct>30) obtained during December 20... |
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First report on the Latvian SARS-CoV-2 isolate genetic diversity
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| Remaining a major healthcare concern with nearly 27 million confirmed cases worldwide at the time of writing, novel severe acute respiratory syndrome coronavirus - 2 (SARS-CoV-2) has caused more than 880 thousand deaths since its outbreak in China, December 2019. First case of a person testing positive for SARS-CoV-2 i... |
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Novel highly divergent SARS-CoV-2 lineage with the Spike substitutions L249S and E484K
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| COVID-19 pandemics has led to genetic diversification of SARS-CoV-2 and the appearance of variants with potential impact in transmissibility and viral escape from acquired immunity. We report a new lineage containing ten amino acid changes across the genome. Further studies are required for monitoring its epidemiologic... |
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The first three waves of the Covid-19 pandemic hint at a limited genetic repertoire for SARS-CoV-2
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| The genomic diversity of SARS-CoV-2 is the result of a relatively low level of spontaneous mutations introduced during viral replication. With millions of SARS-CoV-2 genome sequences now available, we can begin to assess the overall genetic repertoire of this virus. We find that during 2020, there was a global wave of ... |
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Isolation of Virus from a SARS Patient and Genome-wide Analysis of Genetic Mutations Related to Pathogenesis and Epidemiology from 47 SARS-CoV Isolates
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| Severe acute respiratory syndrome (SARS) caused by SARS-associated coronavirus (SARS-CoV) is a fatal disease. Prevention of future outbreaks is essential and requires understanding pathogenesis and evolution of the virus. We have isolated a SARS-CoV in China and analyzed 47 SARS-CoV genomes with the aims to reveal the ... |
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Impact of natural selection on global patterns of genetic variation and association with clinical phenotypes at genes involved in SARS-CoV-2 infection.
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| Significance Viruses are strong sources of natural selection pressure during human evolutionary history. Investigating genetic diversity and detecting signatures of natural selection at host genes related to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection help to identify functionally important v... |
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Tracking the progressive spread of the SARS-CoV-2 Omicron variant in Italy, December 2021 - January 2022
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| The SARS-CoV-2 variant of concern Omicron was first detected in Italy in November 2021. Data from three genomic surveys conducted in Italy between December 2021 and January 2022 suggest that Omicron became dominant in less than one month (prevalence on January 3: 78.6%-83.8%) with a doubling time of 2.7-3.1 days. The m... |
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Early transmissibility assessment of the N501Y mutant strains of SARS-CoV-2 in the United Kingdom, October to November 2020
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| Two new SARS-CoV-2 lineages with the N501Y mutation in the receptor-binding domain of the spike protein spread rapidly in the United Kingdom. We estimated that the earlier 501Y lineage without amino acid deletion Δ69/Δ70, circulating mainly between early September and mid-November, was 10% (6–13%) more transmissible th... |
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Emergence and Evolution of a Prevalent New SARS-CoV-2 Variant in the United States
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| Genomic surveillance can lead to early identification of novel viral variants and inform pandemic response. Using this approach, we identified a new variant of the SARS-CoV-2 virus that emerged in the United States (U.S.). The earliest sequenced genomes of this variant, referred to as 20C-US, can be traced to Texas in ... |
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From Delta to Omicron: analysing the SARS-CoV-2 epidemic in France using variant-specific screening tests (September 1 to December 18, 2021)
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| We analysed 131,478 SARS-CoV-2 variant screening tests performed in France from September 1st to December 18, 2021. Tests consistent with the presence of the Omicron variant exhibit significantly higher cycle threshold Ct values, which could indicate lower amounts of virus genetic material. We estimate that the transmi... |
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SARS-CoV-2 genome-based severity predictions correspond to lower qPCR values and higher viral load
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| The 2019 coronavirus disease (COVID-19) pandemic has demonstrated the importance of predicting, identifying, and tracking mutations throughout a pandemic event. As the COVID-19 global pandemic surpassed one year, several variants had emerged resulting in increased severity and transmissibility. In order to reduce the i... |
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Proteo-Genomic Analysis of SARS-CoV-2: A Clinical Landscape of Single-Nucleotide Polymorphisms, COVID-19 Proteome, and Host Responses
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| [Image: see text] A novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of coronavirus disease 2019 (COVID-19) and continues to be a global health challenge. To understand viral disease biology, we have carried out proteo-genomic analysis using next-generation sequencing (NGS) and ... |
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Importation of SARS‐CoV‐2 Variant B.1.1.7 in Pakistan
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| On December 14 2020, a variant of SARS-CoV-2 characterized as VOC-202012/01 (lineage B.1.1.7) emerged in the United Kingdom [1] with rapid expansion to over 64 countries as of January 27, 2021. This article is protected by copyright. All rights reserved. |
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Determination of Risk Groups for the Covid-19 Underlying Deseases
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| For every disease, there is a certain set of genes whose mutations increase the risk of illness development. DNA sequencing of sick and healthy individuals results in the determination of genes related to certain diseases. Efficient procedures are described in order to determine point mutations in gene sequences of the... |
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Clinical and Infection Prevention Applications of Severe Acute Respiratory Syndrome Coronavirus 2 Genotyping: an Infectious Diseases Society of America/American Society for Microbiology Consensus Review Document
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| Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged into a world of maturing pathogen genomics, with more than 2 million genomes sequenced at the time of writing. The rise of more transmissible variants of concern that impact vaccine and therapeutic effectiveness has led to widespread interest in SARS-... |
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Patient-derived mutations impact pathogenicity of SARS-CoV-2
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| The sudden outbreak of the severe acute respiratory syndrome-coronavirus (SARS-CoV-2) has spread globally with more than 1,300,000 patients diagnosed and a death toll of 70,000. Current genomic survey data suggest that single nucleotide variants (SNVs) are abundant. However, no mutation has been directly linked with fu... |
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The prevalent RNA modification on SARS-CoV-2 RNAs may confound the SNP profile and evolutionary patterns revealed by previous studies
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| Background: The recent outbreak of SARS-CoV-2 has caused severe damage to the world. The concomitant papers on the evolutionary patterns of SARS-CoV-2 is continuously emerging. Studies has utilized the publically available RNA-seq data to find out the so-called SNPs in the virus genome and analyzed their selection patt... |
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An Overview of the Genetic Variations of the SARS-CoV-2 Genomes Isolated in Southeast Asian Countries
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| Monitoring the mutation dynamics of human severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical in understanding its infectivity, virulence and pathogenicity for development of a vaccine. In an "age of mobility," the pandemic highlights the importance and vulnerability of regionalization and labor ma... |
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There is still no evidence of SARS‐CoV‐2 laboratory origin: Response to Segreto and Deigin (10.1002/bies.202100137)
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| The causative agent of COVID‐19 SARS‐CoV‐2 has led to over 4 million deaths worldwide. Understanding the origin of this coronavirus is important for the prevention of future outbreaks. The dominant point of view that the virus transferred to humans either directly from bats or through an intermediate mammalian host has... |
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Peptidome Surveillance Across Evolving SARS-CoV-2 Lineages Reveals HLA Binding Conservation in Nucleocapsid Among Variants With Most Potential for T-Cell Epitope Loss In Spike
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| To provide a unique global view of the relative potential for evasion of CD8+ and CD4+ T cells by SARS-CoV-2 lineages as they evolve over time, we performed a comprehensive analysis of predicted HLA-I and HLA-II binding peptides in spike (S) and nucleocapsid (N) protein sequences of all available SARS-CoV-2 genomes as ... |
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The specification of observed covid-19 in england: A review of auto-mutation
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| Genomic sequencing helps us understand COVID-19 and its spread. It can also help guide treatments in the future and see the impact of interventions. In epidemics, genome structure is important for recognizing any small change in the COVID-19 behavior at any population scale to understand the spreading mechanism and whe... |
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Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch.
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| Late in 2020, two genetically-distinct clusters of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with mutations of biological concern were reported, one in the United Kingdom and one in South Africa. Using a combination of data from routine surveillance, genomic sequencing and international travel we tra... |
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Clinical features, isolation, and complete genome sequence of severe acute respiratory syndrome coronavirus 2 from the first two patients in Vietnam
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| In January 2020, we identified two SARS‐CoV‐2 infections in a familial cluster with one person coming from Wuhan, China. The complete genome sequences of two SARS‐CoV‐2 strains isolated from these patients were identical and 99.98% similar to strains isolated in Wuhan. This is genetically suggestive of human‐to‐human t... |
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Are we moving toward ending SARS‐CoV‐2?
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| The SARS-CoV-2 is a highly transmissible pathogen that has caused a global health crisis and a socioeconomic emergency. The emergence of the Omicron variant, with the highest number of mutations in its genome, has raised considerable concern. Currently, there is a crucial gap in our knowledge in understanding how these... |
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High-Throughput Adaptable SARS-CoV-2 Screening for Rapid Identification of Dominant and Emerging Regional Variants
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| OBJECTIVES: Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variant strains can be associated with increased transmissibility, more severe disease, and reduced effectiveness of treatments. To improve the availability of regional variant surveillance, we describe a variant genotyping system that is... |
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Evolution of SARS-CoV-2 Envelope, Membrane, Nucleocapsid, and Spike Structural Proteins from the Beginning of the Pandemic to September 2020: A Global and Regional Approach by Epidemiological Week
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| Monitoring acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genetic diversity and emerging mutations in this ongoing pandemic is crucial for understanding its evolution and assuring the performance of diagnostic tests, vaccines, and therapies against coronavirus disease (COVID-19). This study reports on the amino ... |
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Betacoronaviruses genome analysis reveals evolution toward specific codons usage: Implications for SARS-CoV-2 mitigation strategies
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| Since the start of the coronavirus disease 2019 (COVID-19) pandemic, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly widespread worldwide becoming one of the major global public health issues of the last centuries. Currently, COVID-19 vaccine rollouts are finally upon us carrying the hope o... |
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Real-time SARS-CoV-2 diagnostic and variants tracking over multiple candidates using nanopore DNA sequencing
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| Since December 2019, a novel coronavirus responsible for a severe acute respiratory syndrome (SARS-CoV-2) is accountable for a major pandemic situation. The emergence of the B.1.1.7 strain, as a highly transmissible variant has accelerated the world-wide interest in tracking SARS-CoV-2 variants’ occurrence. Similarly, ... |
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The Genetic Variant of SARS-CoV-2: would It Matter for Controlling the Devastating Pandemic?
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| The pandemic of COVID-19, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is far from being controlled despite the great effort that have been taken throughout the world. Herd immunity through vaccination is our major expectation to rein the virus. However, the emergence of widespread genetic va... |
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Protein Coding of Variations on SARS-CoV-2 Genomes in Various Regions
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| In this paper, COVID-19 cases in different regions are used for comparison. The related genomes of SARS-CoV-2 are segmented and replaced with sequence operations under protein coding scheme on the A3 module of the MAS. Using protein coding schemes, genomes are transformed and projected as measuring sequences as a vecto... |
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Mutational hotspots and conserved domains of SARS-CoV-2 genome in African population
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| BACKGROUND: Since outbreak in December 2019, the highly infectious and pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over a million deaths globally. With increasing burden, the novel coronavirus has posed a dire threat to public health, social interaction, and global economy. Mutati... |
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Coding-complete genome sequences of two SARS-CoV-2 isolates from Egypt
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| This report announces the complete genome sequences of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolates detected in Egypt. The isolates were obtained from oropharyngeal swab specimens from two Egyptians in Upper and Lower Egypt. Sequence analysis showed mutations that differentiate Egyptian str... |
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Development of highly specific singleplex and multiplex real-time reverse transcription PCR assays for the identification of SARS-CoV-2 Omicron BA.1, BA.2 and Delta variants
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| The Omicron variant of SARS-CoV-2 (B.1.1.529), first identified during November 2021, is rapidly spreading throughout the world, replacing the previously dominant Delta variant. Omicron has a high number of mutations in the spike gene, some of which are associated with greatly increased transmissibility and immune evas... |
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First Phylogenetic Analysis of Malian SARS-CoV-2 Sequences Provides Molecular Insights into the Genomic Diversity of the Sahel Region
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| We are currently facing a pandemic of COVID-19, caused by a spillover from an animal-originating coronavirus to humans occurring in the Wuhan region of China in December 2019. From China, the virus has spread to 188 countries and regions worldwide, reaching the Sahel region on March 2, 2020. Since whole genome sequenci... |
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Whole Genome Sequencing of SARS-CoV-2: Adapting Illumina Protocols for Quick and Accurate Outbreak Investigation during a Pandemic
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| The COVID-19 pandemic has spread very fast around the world. A few days after the first detected case in South Africa, an infection started in a large hospital outbreak in Durban, KwaZulu-Natal (KZN). Phylogenetic analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes can be used to trace the ... |
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SARS-CoV-2 Genomic Surveillance in Northeast Brazil: Timing of Emergence of the Brazilian Variant of Concern P1
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| Since March 2020, 11 lineages of SARS-CoV-2 have been identified in Sergipe state, Northeast Brazil. During the first six months of COVID-19 outbreak, there was a higher frequency of B.1 (58.5%) and B.1.1.33 (17.1%) lineages. During the second wave of COVID-19, there was an increased frequency of P.1 (55.6%), the new B... |
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A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations
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| The infective SARS-CoV-2 is more prone to immune escape. Presently, the significant variants of SARS-CoV-2 are emerging in due course of time with substantial mutations, having the immune escape property. Simultaneously, the vaccination drive against this virus is in progress worldwide. However, vaccine evasion has bee... |
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Rapid detection of the widely circulating B.1.617.2 (Delta) SARS-CoV-2 variant
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| The emergence of the B.1.617.2 (Delta) variant of the severe acute syndrome coronavirus (SARS-CoV-2) that emerged in 2019 (COVID-19), resulted in a surge of cases in India and has expanded and been detected across the world, including in the United States. The B.1.617.2 (Delta) variant has been seen to be twice more tr... |
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Human Alphacoronavirus Universal Primers for Genome Amplification and Sequencing
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| Rapid and accurate sequencing covering the entire genome is essential to identify genetic variations of viral pathogens. However, due to the low viral titers in clinical samples, certain amplification steps are required for viral genome sequencing. At present, there are no universal primers available for alphacoronavir... |
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Identification of site-specific evolutionary trajectories shared across human betacoronaviruses
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| Comparison of evolution among related viruses can provide insights into shared adaptive processes, for example following host switching to a mutual host species. Whilst phylogenetic methods can help identify mutations that may be important for evolutionary processes such as adaptation to a new host, these can be enhanc... |
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COVID-profiler: a webserver for the analysis of SARS-CoV-2 sequencing data
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| BACKGROUND: SARS-CoV-2 virus sequencing has been applied to track the COVID-19 pandemic spread and assist the development of PCR-based diagnostics, serological assays, and vaccines. With sequencing becoming routine globally, bioinformatic tools are needed to assist in the robust processing of resulting genomic data. RE... |
### Instruction:
Please summerize the given abstract to a title
### Response:
SARS-CoV-2 Genomic Surveillance in Northeast Brazil: Timing of Emergence of the Brazilian Variant of Concern P1
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| Since March 2020, 11 lineages of SARS-CoV-2 have been identified in Sergipe state, Northeast Brazil. During the first six months of COVID-19 outbreak, there was a higher frequency of B.1 (58.5%) and B.1.1.33 (17.1%) lineages. During the second wave of COVID-19, there was an increased frequency of P.1 (55.6%), the new B... |
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Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: An endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations
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| Accumulation of mutations within the genome is the primary driving force for viral evolution within an endemic setting. This inherent feature often leads to altered virulence, infectivity and transmissibility as well as antigenic shift to escape host immunity, which might compromise the efficacy of vaccines and antivir... |
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The B.1.427/1.429 (epsilon) SARS-CoV-2 variants are more virulent than ancestral B.1 (614G) in Syrian hamsters
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| As novel SARS-CoV-2 variants continue to emerge, it is critical that their potential to cause severe disease and evade vaccine-induced immunity is rapidly assessed in humans and studied in animal models. In early January 2021, a novel SARS-CoV-2 variant designated B.1.429 comprising 2 lineages, B.1.427 and B.1.429, was... |
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### Response:
An Updated Investigation Prior To COVID-19 Vaccination Program In Indonesia: Full-Length Genome Mutation Analysis Of SARS-CoV-2
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| Introduction Indonesia kick-started the big project of COVID-19 vaccination program in January 2021 by employed vaccine to the president of Indonesia. The outbreak and rapid transmission of COVID-19 have endangered the global health and economy. This study aimed to investigate the full-length genome mutation analysis o... |
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Introductions and early spread of SARS-CoV-2 in the New York City area
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| New York City (NYC) has emerged as one of the epicenters of the current SARS-CoV-2 pandemic. To identify the early transmission events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus causing COVID-19 in patients seeking care at the Mount Sinai Health System. Phylogenetic an... |
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Global variation in SARS-CoV-2 proteome and its implication in pre-lockdown emergence and dissemination of 5 dominant SARS-CoV-2 clades
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| SARS-CoV-2 is currently causing major havoc worldwide with its efficient transmission and propagation. To track the emergence as well as the persistence of mutations during the early stage of the pandemic, a comparative analysis of SARS-CoV-2 whole proteome sequences has been performed by considering manually curated 3... |
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### Response:
SARS-CoV-2 variant evolution in the United States: High accumulation of viral mutations over time likely through serial Founder Events and mutational bursts
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| Since the first case of COVID-19 in December 2019 in Wuhan, China, SARS-CoV-2 has spread worldwide and within a year has caused 2.29 million deaths globally. With dramatically increasing infection numbers, and the arrival of new variants with increased infectivity, tracking the evolution of its genome is crucial for ef... |
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### Response:
A comparative phylogenomic analysis of SARS-CoV-2 strains reported from non-human mammalian species and environmental samples
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| Coronaviruses (CoVs) infect a wide range of domestic and wild mammals. These viruses have a potential and tendency to cross-species barriers and infect humans. Novel human coronavirus 2019-nCoV (hCoV-19) emerged from Wuhan, China, and has caused a global pandemic. Genomic features of SARS-CoV-2 may attribute inter-spec... |
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### Response:
Understanding the possible origin and genotyping of the first Bangladeshi SARS-CoV-2 strain
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| The novel coronavirus, SARS-CoV-2, has caused the most unfathomable pandemic in the history of humankind. Bangladesh is also a victim of this critical situation. To investigate the genomic features of the pathogen from Bangladesh, the first complete genome of the virus has very recently been published. Therefore, long-... |
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### Response:
Profiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies
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| BACKGROUND: The genome of SARS-CoV-2 is susceptible to mutations during viral replication due to the errors generated by RNA-dependent RNA polymerases. These mutations enable the SARS-CoV-2 to evolve into new strains. Viral quasispecies emerge from de novo mutations that occur in individual patients. In combination, th... |
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### Response:
An insight into sars-cov-2 phylogenetics and genomics for sixty isolates occurring in india
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| Introduction: Analysis of genome sequences to search for encoded proteins and motifs is a most widely used technique for the prediction of new drug and vaccine targets. It can effectively leverage computational techniques to deliver effective and pragmatic advantages in the search of new drug and vaccines. Materials an... |
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Please summerize the given abstract to a title
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Multi-branch cooperation on SARS-CoV-2 omicron capture: a case report
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| Shortly after the WHOs first notice a suspected case of omicron SARS-CoV-2 was reported in Liberec, Czech Republic. The primary goal of the following actions was to test the presence of the variant and stop the spread of the virus variant. On November 25 a sixty-year-old lady, who had recently returned from Namibia, vi... |
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### Response:
Molecular Evolution of Human Coronavirus 229E in Hong Kong and a Fatal COVID-19 Case Involving Coinfection with a Novel Human Coronavirus 229E Genogroup
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| Compared to other human coronaviruses, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) are relatively understudied. We report a fatal case of COVID-19 pneumonia coinfected with HCoV-229E in Hong Kong. Genome sequencing of SARS-CoV-2 and HCoV-229E from a nasopharyngeal sample of the patient sho... |
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### Response:
SARS-CoV-2 genomic surveillance in Rondônia, Brazilian Western Amazon
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| SARS-CoV-2 has spread rapidly around the world, with Brazil currently considered an epicenter of the pandemic. The Northern region has the second highest incidence coefficient, as well as the third highest mortality rate in the country. This study aimed to investigate information about the evolutionary history of epide... |
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### Response:
SARS-CoV-2 variants: Subversion of antibody response and predicted impact on T cell recognition
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| COVID-19 variants of concern, including B.1.1.7, B.1.351, and P.1, encompass mutations facilitating immune evasion. Neutralizing antibody recognition and function may be variably impaired. We considered the impact of mutations on T cell responses. Mutations could be neutral or result in either loss or gain of predicted... |
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### Response:
A Genomic Snapshot of the SARS-CoV-2 Pandemic in the Balearic Islands
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| Objective: To analyze the SARS-CoV-2 genomic epidemiology in the Balearic Islands, a unique setting in which the course of the pandemic has been influenced by a complex interplay between insularity, severe social restrictions and tourism travels. Methods: Since the onset of the pandemic, more than 2,700 SARS-CoV-2 posi... |
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### Response:
COVID‐19: emergence and mutational diversification of SARS‐CoV‐2
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| The origin of the SARS‐CoV‐2 virus is not yet defined, but a viral zoonosis from bats – with or without an alternative animal as an intermediate host – is still the most likely hypothesis. The intensive virological and epidemiological research combined with massive sequencing efforts of whole viral genomes allowed an u... |
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