scholarly journals Genome Recombination between Delta and Alpha Variants of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

2021 ◽  
Author(s):  
Tsuyoshi Sekizuka ◽  
Kentaro Itokawa ◽  
Masumichi Saito ◽  
Michitsugu Shimatani ◽  
Shutoku Matsuyama ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Genetic Variations ◽  
Clinical Specimens ◽  
Genome Recombination ◽  
Genomic Recombination

Prominent genomic recombination has been observed between the Delta and Alpha variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) isolated from clinical specimens in Japan. It is necessary to intensively study such marked genetic variations and characterize the emerging variants after careful verification of their lineage and clade assignment.

scholarly journals Mutation Profile of SARS-CoV-2 Genome Sequences Originating from Eight Israeli Patient Isolates

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Galia Zaide ◽  
Inbar Cohen-Gihon ◽  
Ofir Israeli ◽  
Dana Stein ◽  
Ohad Shifman ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Nonsynonymous Substitution ◽  
Genetic Variations ◽  
Open Reading Frame ◽  
Care Homes ◽  
Clinical Samples ◽  
Genome Sequences ◽  
Reading Frame ◽  
Mutation Profile ◽  
Asymptomatic Individuals

ABSTRACT We report the genome sequences and the identification of genetic variations in eight clinical samples of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Samples were collected from nasopharyngeal swabs of symptomatic and asymptomatic individuals from five care homes for elderly and infirm persons in Israel. The sequences obtained are valuable, as they carry a newly reported nonsynonymous substitution located within the nucleoprotein open reading frame.

scholarly journals Identification of eight SARS-CoV-2 ORF7a deletion variants in 2,726 clinical specimens

2020 ◽  
Author(s):  
Sun Hee Rosenthal ◽  
Ron M. Kagan ◽  
Anna Gerasimova ◽  
Ben Anderson ◽  
David Grover ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Transmembrane Protein ◽  
Type I ◽  
Clinical Specimens ◽  
Host Interactions

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ORF7a, the ortholog of SARS-CoV ORF7a, is a type I transmembrane protein and plays an important role in virus-host interactions. Deletion variants in ORF7a may influence virulence, but only a few such isolates have been reported. Here, we report 8 unique ORF7a deletion variants of 6 to 96 nucleotides in length identified from 2,726 clinical specimens collected in March of 2020.

scholarly journals Genetic variations in the human severe acute respiratory syndrome coronavirus receptor ACE2 and serine protease TMPRSS2

2020 ◽  
pp. jclinpath-2020-206867
Author(s):  
Kohei Fujikura ◽  
Kazuma Uesaka
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Genetic Variations ◽  
Single Nucleotide ◽  
S Protein ◽  
Angiotensin Converting Enzyme 2 ◽  
Coding Regions ◽  
Recent Emergence ◽  
Contact Residues ◽  
Host Cell Surface ◽  
Host Genetic

AimsThe recent emergence of novel, pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a global health emergency. The coronaviral entry requires the spike (S)-protein for attachment to the host cell surface, and employs human angiotensin-converting enzyme 2 (hACE2) for entry and transmembrane protease serine 2 (TMPRSS2) for S-protein priming. Although coronaviruses undergo evolution by mutating themselves, it is also essential to know the host genetic factors. Here, we describe the single nucleotide variations (SNVs) in human ACE2 and TMPRSS2.MethodsThe genetic variants derived from five population-sequencing projects were classified by variant type, allele frequency (AF), ethnic group and estimated pathogenicity. The SNVs in SARS-CoV-2/hACE2 contact residues were investigated. The genetic variability was normalised using non-linear regression and the total number of SNVs was estimated by the derived formulas.ResultsWe detected 349 and 551 SNVs in ACE2 and TMPRSS2, respectively, in a total of 156 513 individuals. The vast majority (>97%) of the SNVs were very rare (AF <0.1%) and population-specific, and were computationally estimated to be more frequently deleterious than the SNVs with high AF. These SNVs were distributed throughout the coding regions; some ACE2 variants were located in the SARS-CoV-2/hACE2 contact residues, with a hemizygous state occurring in males. Using regression analysis, the total numbers of genetic variations in ACE2 and TMPRSS2 were 1.1×103 and 1.5×103, respectively, for a population of one million people.ConclusionThe majority of SNVs in ACE2 and TMPRSS2 are rare, population-specific and deleterious, and a multitude of very rare SNVs may explain different susceptibility to SARS-CoV-2.

scholarly journals Report of SARS-CoV-2 B1.1.7 Lineage in Morocco

2021 ◽  
Vol 10 (16) ◽  
Author(s):  
Mouna Ouadghiri ◽  
Tarik Aanniz ◽  
Abdelomunim Essabbar ◽  
Myriam Seffar ◽  
Hakima Kabbaj ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Female Patient ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Clinical Sample ◽  
Genetic Variations ◽  
Nasopharyngeal Swab

ABSTRACT Here, we report the near-complete genome sequence and the genetic variations of a clinical sample of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) harboring the N501Y mutation assigned to the B.1.1.7 lineage. The sample was collected from a nasopharyngeal swab of a female patient from Temara, Morocco, and the sequencing was done using Ion S5 technology.

scholarly journals Evaluation of a quantitative RT-PCR assay for the detection of the emerging coronavirus SARS-CoV-2 using a high throughput system

2020 ◽  
Vol 25 (9) ◽  
Author(s):  
Susanne Pfefferle ◽  
Svenja Reucher ◽  
Dominic Nörz ◽  
Marc Lütgehetmann
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
High Throughput ◽  
Open Channel ◽  
High Volume ◽  
Analytical Performance ◽  
Molecular Assay ◽  
Rt Pcr ◽  
Pcr Assay ◽  
Clinical Specimens ◽  
Hands On

Facing the emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), high-volume respiratory testing is demanded in laboratories worldwide. We evaluated the performance of a molecular assay for the detection of SARS-CoV-2 on a high-throughput platform, the cobas 6800, using the ‘open channel’ for integration of a laboratory-developed assay. We observed good analytical performance in clinical specimens. The fully automated workflow enables high-throughput testing with minimal hands-on time, while offering fast and reliable results.

scholarly journals A Zoonotic Adenoviral Human Pathogen Emerged through Genomic Recombination among Human and Nonhuman Simian Hosts

2019 ◽  
Vol 93 (18) ◽  
Author(s):  
Shoaleh Dehghan ◽  
Jason Seto ◽  
Elizabeth B. Liu ◽  
Ashrafali M. Ismail ◽  
Ramana Madupu ◽  
...  
Keyword(s):  
Immune Responses ◽  
Human Adenovirus ◽  
Human Pathogen ◽  
Host Immune Responses ◽  
Genome Recombination ◽  
Gene Delivery Vectors ◽  
Ping Pong ◽  
Genomic Recombination ◽  
Recombinant Genome ◽  
Insight Into

ABSTRACTGenomics analysis of a historically intriguing and predicted emergent human adenovirus (HAdV) pathogen, which caused pneumonia and death, provides insight into a novel molecular evolution pathway involving “ping-pong” zoonosis and anthroponosis. The genome of this promiscuous pathogen is embedded with evidence of unprecedented multiple, multidirectional, stable, and reciprocal cross-species infections of hosts from three species (human, chimpanzee, and bonobo). This recombinant genome, typed as HAdV-B76, is identical to two recently reported simian AdV (SAdV) genomes isolated from chimpanzees and bonobos. Additionally, the presence of a critical adenoviral replication element found in HAdV genomes, in addition to genes that are highly similar to counterparts in other HAdVs, reinforces its potential as a human pathogen. Reservoirs in nonhuman hosts may explain periods of apparent absence and then reemergence of human adenoviral pathogens, as well as present pathways for the genesis of those thought to be newly emergent. The nature of the HAdV-D76 genome has implications for the use of SAdVs as gene delivery vectors in human gene therapy and vaccines, selected to avoid preexisting and potentially fatal host immune responses to HAdV.IMPORTANCEAn emergent adenoviral human pathogen, HAdV-B76, associated with a fatality in 1965, shows a remarkable degree of genome identity with two recently isolated simian adenoviruses that contain cross-species genome recombination events from three hosts: human, chimpanzee, and bonobo. Zoonosis (nonhuman-to-human transmission) and anthroponosis (human to nonhuman transmission) may play significant roles in the emergence of human adenoviral pathogens.

scholarly journals Haplotype networks of SARS-CoV-2 infections in theDiamond Princesscruise ship outbreak

2020 ◽  
Vol 117 (33) ◽  
pp. 20198-20201 ◽  
Author(s):  
Tsuyoshi Sekizuka ◽  
Kentaro Itokawa ◽  
Tsutomu Kageyama ◽  
Shinji Saito ◽  
Ikuyo Takayama ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Severe Acute Respiratory Syndrome ◽  
Haplotype Network ◽  
Whole Genome ◽  
Mass Gathering ◽  
Cruise Ship ◽  
Direct Transmission ◽  
Clinical Specimens ◽  
Phylogeny Analysis ◽  
Haplotype Networks

TheDiamond Princesscruise ship was put under quarantine offshore Yokohama, Japan, after a passenger who disembarked in Hong Kong was confirmed as a coronavirus disease 2019 case. We performed whole-genome sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) directly from PCR+clinical specimens and conducted a phylogenetic analysis of the outbreak. All tested isolates exhibited a transversion at G11083T, suggesting that SARS-CoV-2 dissemination on theDiamond Princessoriginated from a single introduction event before the quarantine started. Although further spreading might have been prevented by quarantine, some progeny clusters could be linked to transmission through mass-gathering events in the recreational areas and direct transmission among passengers who shared cabins during the quarantine. This study demonstrates the usefulness of haplotype network/phylogeny analysis in identifying potential infection routes.

scholarly journals Effective Heat Inactivation of SARS-CoV-2

2020 ◽  
Author(s):  
Tony Wang ◽  
Christopher Lien ◽  
Shufeng Liu ◽  
Prabhuanand Selveraj
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Healthcare Professionals ◽  
Infectious Virus ◽  
Heat Inactivation ◽  
Clinical Specimens ◽  
Global Pandemic ◽  
Human Sera ◽  
Laboratory Workers ◽  
Stool Samples ◽  
The Stability

The outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2 or 2019-nCoV) has quickly turned into a global pandemic. Infectious viruses had been isolated from oro- or naso-pharyngeal swabs, sputum and possibly stool samples of infected individuals. Handling these clinical specimens therefore poses a biosafety risk to both healthcare professionals and laboratory workers. In this study, we aimed to evaluate the stability of SARS-CoV-2 under different heat conditions and report that the virus is stable at 37 C for at least 24 hours. Heating at 56 C for 30 minutes, however, effectively inactivated the virus while preserved the stability of viral RNA in both human sera and sputum samples. These findings provide critical information regarding the biology of the virus as well as a practical way to inactivate infectious virus that is potentially found in clinical specimens.

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