SARS-CoV-2 genomes from Oklahoma, USA

Genomic sequencing has played a major role in understanding the pathogenicity of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). With the current pandemic, it is essential that SARS-CoV-2 viruses are sequenced regularly to determine mutations and genomic modifications in different geographical locations. In this study, we sequenced SARS-CoV-2 from five clinical samples obtained in Oklahoma, United States during different time points of pandemic presence in the state. One sample from the initial days of the pandemic in the state and four during the peak in Oklahoma were sequenced. Previously reported mutations including D614G in S gene, P4715L in ORF1ab, S194L, R203K, and G204R in N gene were identified in the genomes sequenced in this study. Possible novel mutations were also detected in the S gene (G1167V), ORF1ab (A6269S and P3371S), ORF7b (T28I), and ORF8 (G96R). Phylogenetic analysis of the genomes showed similarity to other SARS-CoV-2 viruses reported from across the globe. Structural characterization indicates that the mutations in S gene possibly influences conformational flexibility and motion of the spike protein, and the mutations in N gene are associated with disordered linker region within the nucleocapsid protein.

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Analysis of human coronavirus 229E spike and nucleoprotein genes demonstrates genetic drift between chronologically distinct strains

Journal of General Virology ◽

10.1099/vir.0.81662-0 ◽

2006 ◽

Vol 87 (5) ◽

pp. 1203-1208 ◽

Cited By ~ 32

Author(s):

Doris Chibo ◽

Chris Birch

Keyword(s):

Phylogenetic Analysis ◽

Respiratory Infections ◽

N Gene ◽

Human Coronavirus ◽

S Gene ◽

Limited Variation ◽

Contrast Analysis ◽

Human Coronaviruses ◽

Human Coronavirus 229E ◽

S Genes

Historically, coronaviruses have been recognized as a cause of minor respiratory infections in humans. However, the recent identification of three novel human coronaviruses, one causing severe acute respiratory syndrome (SARS), has prompted further examination of these viruses. Previous studies of geographically and chronologically distinct Human coronavirus 229E (HCoV-229E) isolates have found only limited variation within S gene nucleotide sequences. In contrast, analysis of the S genes of contemporary Human coronavirus OC43 variants identified in Belgium revealed two distinct viruses circulating during 2003 and 2004. Here, the S and N gene sequences of 25 HCoV-229E variants identified in Victoria, Australia, between 1979 and 2004 in patients with symptomatic infections were determined. Phylogenetic analysis showed clustering of the isolates into four groups, with evidence of increasing divergence with time. Evidence of positive selection in the S gene was also established.

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Phylogenetic analysis of variable and conserved genomic regions in severe acute respiratory syndrome coronavirus 2 (COVID-19)

10.21203/rs.3.rs-88200/v1 ◽

2020 ◽

Author(s):

Abeer F. El Nahas ◽

Nasema M. Elkatatny ◽

Haitham G. Abo-Al-Ela

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Reference Sequence ◽

N Gene ◽

Conserved Regions ◽

S Gene ◽

Genomic Regions ◽

Conserved Genomic Regions

Abstract SARS-CoV-2 has rapidly spread around the world. Several mutations have been detected in its genome, but they do not seem to affect the abilities of the virus to spread or infect. We aimed to explore the conserved genomic regions in coronavirus that could contain the key strengths of the virus. SARS-CoV-2 sequence data were retrieved from Genbank from the period of December 2019 to March 2020. Phylogenetic analyses were conducted for 207 sequences using MEGAX compared with the reference sequence (MN908947.3- CHN-Wuhan Dec-2019). The analysis included seven important genomic regions, the ORF1ab gene (21,290 bp), S gene (3,822 bp), Orf3a gene (827 bp), E gene (227 bp), M gene (669 bp), and N gene (1,259 bp), which play critical roles in virus invasion and replication. Furthermore, the variant nucleotides and amino acids were detected by MEGAX and BLAST. Through the phylogenetic analysis and amino acid substitution, the ORF1ab gene showed 11 conserved regions and also several variable sites. The E and M genes were mainly conserved, and all sequences were included in one clade, with one or two amino acid variants. Orf3a and the N gene have four conserved sites distributed along the genes. The S gene has 12 mutations and four main large conserved regionsWe conclude that the favored occurrence of mutations at the ORFab and Orf3a genes during the SARS-CoV epidemic is an important mechanism for virus pathogenesis. The E and M proteins have an almost conserved structure, whereas the S and N genes have many conserved regions, which could serve as possible targets for vaccine design for SARS-CoV.

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S-variant SARS-CoV-2 is associated with significantly higher viral loads in samples tested by ThermoFisher TaqPath RT-QPCR

10.1101/2020.12.24.20248834 ◽

2020 ◽

Cited By ~ 2

Author(s):

Michael Kidd ◽

Alex Richter ◽

Angus Best ◽

Jeremy Mirza ◽

Benita Percival ◽

...

Keyword(s):

Viral Load ◽

N Gene ◽

Clinical Samples ◽

Published Data ◽

List Type ◽

Recent Information ◽

Viral Loads ◽

S Gene ◽

Viral Genes ◽

The Uk

AbstractBirmingham University Turnkey laboratory is part of the Lighthouse network responsible for testing clinical samples under the UK government ‘Test & Trace’ scheme. Samples are analysed for the presence of SARS-CoV-2 in respiratory samples using the Thermofisher TaqPath RT-QPCR test, which is designed to co-amplify sections of three SARS-CoV-2 viral genes.Since more recent information became available regarding the presence of SARS-CoV-2 variants of concern (S-VoC), which can show a suboptimal profile in RT-QPCR tests such as the ThermoFisher TaqPath used at the majority of Lighthouse laboratories, we analysed recently published data for trends and significance of the S-gene ‘dropout’ variant.Results showed that:the population of S-gene dropout samples had significantly lower median Ct values of ORF and N-gene targets compared to samples where S-gene was detectedon a population basis, S-gene dropout samples clustered around very low Ct values for ORF and N targetslinked Ct values for individual samples showed that a low Ct for ORF and N were clearly associated with an S-dropout characteristicwhen conservatively inferring relative viral load from Ct values, approximately 35% of S-dropout samples had high viral loads between 10 and 10,000-fold greater than 1 × 106, compared to 10% of S-positive samples.This analysis suggests that patients whose samples exhibit the S-dropout profile in the TaqPath test are more likely to have high viral loads at the time of sampling. The relevance of this to epidemiological reports of fast spread of the SARS-CoV-2 in regions of the UK is discussed.

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Phylogenetic analysis of variable and conserved genomic regions in severe acute respiratory syndrome coronavirus 2 (COVID-19)

10.21203/rs.3.rs-88200/v2 ◽

2020 ◽

Author(s):

Abeer F. El Nahas ◽

Nasema M. Elkatatny ◽

Haitham G. Abo-Al-Ela

Keyword(s):

Phylogenetic Analysis ◽

Amino Acid ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Reference Sequence ◽

N Gene ◽

Conserved Regions ◽

S Gene ◽

Genomic Regions ◽

Conserved Genomic Regions

Abstract SARS-CoV-2 has rapidly spread around the world. Several mutations have been detected in its genome, but they do not seem to affect the abilities of the virus to spread or infect. We aimed to explore the conserved genomic regions in coronavirus that could contain the key strengths of the virus. SARS-CoV-2 sequence data were retrieved from Genbank from the period of December 2019 to March 2020. Phylogenetic analyses were conducted for 207 sequences using MEGAX compared with the reference sequence (MN908947.3- CHN-Wuhan Dec-2019). The analysis included seven important genomic regions, the ORF1ab gene (21,290 bp), S gene (3,822 bp), Orf3a gene (827 bp), E gene (227 bp), M gene (669 bp), and N gene (1,259 bp), which play critical roles in virus invasion and replication. Furthermore, the variant nucleotides and amino acids were detected by MEGAX and BLAST. Through the phylogenetic analysis and amino acid substitution, the ORF1ab gene showed 11 conserved regions and also several variable sites. The E and M genes were mainly conserved, and all sequences were included in one clade, with one or two amino acid variants. Orf3a and the N gene have four conserved sites distributed along the genes. The S gene has 12 mutations and four main large conserved regionsWe conclude that the favored occurrence of mutations at the ORFab and Orf3a genes during the SARS-CoV epidemic is an important mechanism for virus pathogenesis. The E and M proteins have an almost conserved structure, whereas the S and N genes have many conserved regions, which could serve as possible targets for vaccine design for SARS-CoV.

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SARS-CoV-2 genome sequences from Lucknow, Uttar Pradesh, India by Nanopore Sequencing

10.1101/2021.10.05.463185 ◽

2021 ◽

Author(s):

Biswajit Sahoo ◽

Pramod Kumar Maurya ◽

Ratnesh Kumar Tripathi ◽

Jyotsana Agarwal ◽

Swasti Tiwari

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Genome Sequencing ◽

Genome Analysis ◽

Uttar Pradesh ◽

The State ◽

N Gene ◽

Nanopore Sequencing ◽

Genome Sequences ◽

Novel Mutations ◽

Severity Of The Disease

A new challenge has immerged in the form of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in worldwide. Rapid genome sequencing of SARS-CoV-2 has been a powerful tool to study the pathogenicity of severe acute respiratory syndrome coronavirus 2. During this pandemic situation more genome sequencing of SARS-CoV-2 should be done in order to detect the mutations and genomic modifications across the globe. Here, in this study we have sequenced 23 SARS-CoV-2 positive samples from the state of Uttar Pradesh, India collected during the first pandemic. A range of 2-22 mutations were observed including D614G, L452R, Q613H, Q677H, T1027I in S gene, S194L in N gene, Q57H, L106F, T175I in ORF3a gene as reported previously and also possible novel mutations like P309S in ORF1ab gene, T379I in N gene and L52F, V77I in ORF3a gene were detected. Phylogenetic genome analysis has shown similarity with other SARS-CoV-2 viruses reported in Uttar Pradesh. Mutations in these genes have the potential to affect the severity of the disease. Therefore, identify the mutation is very important to know the pathogenicity of SARS-CoV-2 virus.

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Phylogeny of 2019-nCoVs and SARS-like CoVs of Human, Bat and Pangolin Origin

International Journal of Veterinary Science ◽

10.37422/ijvs/20.078 ◽

2020 ◽

Keyword(s):

N Gene ◽

Whole Genome ◽

Human Origin ◽

Gene Sequences ◽

M Gene ◽

S Gene ◽

Shared Identity ◽

Novel Coronavirus ◽

S Genes

A novel coronavirus first broke out in Wuhan, China in December, 2019 has been declared a pandemic by WHO on March, 2020. This work aimed to search for probable ancestor of the virus, phylogeny of 2019-nCoVs and similar SL-CoVs based on the whole genome, M, N, ORF1ab, orf3a, and S gene sequences (n=84) obtained from GenBank using BLASTn software in the NCBI was done. Nucleotides of ORF3a and S-genes among 2019-nCoVs are identical, whereas its similar on the whole genome (99.9-100%), M-gene (99.7-100%), N-gene (99.9-100%) and ORF1ab-gene (99.7-100%). nCoVs are similar to bat CoV/RaTG13 on the whole genome (96.2%), M-gene (95.0%), N-gene (97%), ORF1ab-gene (95.3%), ORF3a-gene (99.1%) and S-gene (90.7%). Likewise, nCoVs exhibited homology to bat-CoVZXC21 on M-gene (93.2%), N-gene (91.5%), ORF1ab-gene (93.1%) and ORF3a-gene (94.4%). The emergent viruses shared identity to bat-CoVZC45 on N-gene (91.3%), ORF1ab-gene (92.8%) and ORF3a-gene (94.0%). In addition, pangolin-CoV/MP789 exhibited common sequences on M-gene (91.0%), N-gene (96.3%) and ORF3a-gene (93.3%) to nCoV. Furthermore, pangolin-CoV/MP789 is analogous to bat CoV/RaTG13 (91.3%) and bat-SL-CoVZXC21 (92.2%) on M-gene and to bat CoV/RaTG13 (94.8%) on N-gene. Nevertheless, nCoVs are distinct from the previously identified SL-CoVs of human origin. The present analysis indicates that nCoVs may have transmitted from bats, pangolin and/or unidentified hosts.

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Molecular Characterisation and Phylogenetic Analysis of Dermatophytic Fungi Isolated from Tinea Capitis in Northwest Nigeria Using Sequence of the 28S rRNA

Microbiology Research ◽

10.3390/microbiolres12030046 ◽

2021 ◽

Vol 12 (3) ◽

pp. 646-655

Author(s):

Hussain Yahaya Ungo-kore ◽

Joseph Olorunmola Ehinmidu ◽

Josiah Ademola Onaolapo ◽

Olayeni Stephen Olonitola

Keyword(s):

Phylogenetic Analysis ◽

Tinea Capitis ◽

28S Rdna ◽

Clinical Samples ◽

28S Rrna ◽

Trichophyton Tonsurans ◽

Detection And Identification ◽

Microsporum Audouinii ◽

Trichophyton Simii ◽

Dermatophyte Species

The detection and identification of fungal DNA from clinical samples is one of the fundamental approaches in biomedicine. The incidence, distribution, and control of dermatophytes has progress significantly and the use of phylogenetic species concepts based on rRNA regions have enhanced the taxonomy of dermatophyte species; however, the use of 28S rDNA genes has certain limitations. This gene has been used in dermatophyte taxonomy with limited enumeration; we appraised the sequence disparity within and among groups of the species, the gene ranking in identification, phylogenetic analysis, and taxonomy of 32 strains of eight dermatophyte species. In this study, a set of primers was adopted to amplify the target followed by a partial sequencing of the rDNA. The utilization of a pairwise nucleotide differentiation, an affinity was observed among eight dermatophyte species, with disparity among species ranging from 0 to 197 base pair (bp). Intra-species bp differences were found within strains of Trichophyton eriotrephon, Trichophyton bullosum, Trichophyton simii (Trichophyton genus), Microsporum audouinii, and Trichophyton tonsurans (Microsporum and Trichophyton genus, respectively); however, only some strains of Trichophyton eriotrephon were found to be invariant having three genotypes. Trichophyton tonsurans exhibited most intra-species variability. The characterization and construction of a phylogenetic tree of 28S rDNA gene on dermatophyte species provide a bedrock of an additional finding of connections between species. However, 28S rRNA capture provides a novel method of effective and sensitive detection of dermatophytes lodged in human skin scale. We report for the first time the emergence of T. eriotrephon, T. bullosum, T. simii, T. benhamiae, and Ctenomyces serratus dermatophytes from Tinea capitis in Nigeria.

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Pediatric Oncologists’ Experiences Returning and Incorporating Genomic Sequencing Results into Cancer Care

Journal of Personalized Medicine ◽

10.3390/jpm11060570 ◽

2021 ◽

Vol 11 (6) ◽

pp. 570

Author(s):

Rebecca L. Hsu ◽

Amanda M. Gutierrez ◽

Sophie K. Schellhammer ◽

Jill O. Robinson ◽

Sarah Scollon ◽

...

Keyword(s):

Cancer Care ◽

Cancer Genomics ◽

Emotional Responses ◽

Genetic Counselors ◽

Genomic Sequencing ◽

Uncertain Information ◽

Time Points ◽

Genomic Results

Pediatric oncologists’ perspectives around returning and incorporating tumor and germline genomic sequencing (GS) results into cancer care are not well-described. To inform optimization of cancer genomics communication, we assessed oncologists’ experiences with return of genomic results (ROR), including their preparation/readiness for ROR, collaboration with genetic counselors (GCs) during ROR, and perceived challenges. The BASIC3 study paired pediatric oncologists with GCs to return results to patients’ families. We thematically analyzed 24 interviews with 12 oncologists at two post-ROR time points. Oncologists found pre-ROR meetings with GCs and geneticists essential to interpreting patients’ reports and communicating results to families. Most oncologists took a collaborative ROR approach where they discussed tumor findings and GCs discussed germline findings. Oncologists perceived many roles for GCs during ROR, including answering families’ questions and describing information in lay language. Challenges identified included conveying uncertain information in accessible language, limits of oncologists’ genetics expertise, and navigating families’ emotional responses. Oncologists emphasized how GCs’ and geneticists’ support was essential to ROR, especially for germline findings. GS can be successfully integrated into cancer care, but to account for the GC shortage, alternative ROR models and access to genetics resources will be needed to better support families and avoid burdening oncologists.

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Developing Adaptive Change Capabilities Through Client-Centred Therapy

Behaviour Change ◽

10.1017/bec.2012.24 ◽

2012 ◽

Vol 29 (4) ◽

pp. 258-271 ◽

Cited By ~ 4

Author(s):

Terry Bowles

Keyword(s):

Gender Differences ◽

Therapeutic Alliance ◽

Adaptive Change ◽

The State ◽

Residual Effects ◽

Clinical Group ◽

Therapeutic Experience ◽

Time Points ◽

Insight Into

Clients undergo change as a function of engaging in a therapeutic experience. To date, little research into the residual effects of therapy have been completed using client-centred therapy. Some therapies provide didactic experiences to gain and practise skills and understandings so they can be recalled after the conclusion of therapy. Other therapies preclude such interventions and instead emphasise the insights of the client and the transformative therapeutic alliance to facilitate change. This research is an investigation of the possibility that client-centred therapy provides clients with experiences to allow insight into, and understanding of processes to optimally facilitate change through therapy. The aims of the research were to establish: whether factors known to enhance change in therapy increased for clients from the beginning to the end of therapy; whether the clinical group (n = 28; intervention) scores differed from a nonclinical group at both time points (n = 22; control); and establish whether gender differences were present. Analyses showed that nonclinical respondents’ scores at Times 1 and 2 were consistently higher on all factors compared with clinical respondents. The findings indicated that scores did not vary significantly between Time 1 and 2 for either the clinical or the nonclinical groups of respondents. The state/trait-like characteristics of the factors are discussed in reference to their application in therapeutic and applied settings.

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