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

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.

scholarly journals In silico Molecular Characterization and Phylogenetic Analyses of SARS-CoV-2 in Mediterranean Basin

2021 ◽  
pp. 34-47
Author(s):  
Ghaleb. M. Adwan
Keyword(s):  
Gene Product ◽  
Mediterranean Basin ◽  
Phylogenetic Analyses ◽  
Virus Transmission ◽  
N Gene ◽  
Local Alignment ◽  
Whole Genome ◽  
M Gene ◽  
S Gene ◽  
The Impact

Background: The novel human coronavirus disease COVID-19 has become the fifth reported pandemic since the global spread of 1918 flu and counted as the first documented coronavirus worldwide spread in the history. The COVID-19 was initially considered as a respiratory disease, but SARS-CoV-2 can lead to cause other serious complications. Purpose: This study aimed to conduct phylogenetic analyses of the whole genome of SARS-CoV-2 strains isolated from infected humans in Mediterranean basin countries, Orf1ab gene, S gene, M gene, N gene and Orf3a gene sequences. In addition, the products of Orf1ab, S, M and N genes were also phylogenetically analyzed. Changes that occurred on the S-gene product of these SARS-CoV-2 strains were also detected. Materials and Methods: The whole genome of SARS-CoV-2 isolates, the genes and the gene products (Accessed July 20, 2020) were recovered in Mediterranean basin countries were retrieved from GenBank Database previously available in National Center for Biotechnology Information (NCBI) using BLAST (Basic Local Alignment Search Tool) system. Analyses of these sequences were carried out using computer program MEGA6 software. Results: The Phylogenetic analyses showed that Bat coronavirus RaTG13 isolate is more closely related to SARS-CoV-2 isolates than Pangolin coronaviruse isolates. The S gene product of this virus mediates entry into the host cell and has S1/S2 cleavage site containing multibasic amino acid sequence (PRRAR) which is not detected in other closely related coronaviruses. Many coronavirus strains that deposited in GenBank, showed that they have PRR sequence in Orf1ab gene product. Conclusion: we conclude that part of multibasic S1/S2 motif acquired by recombination or insertion. Theoretically, any coronavirus strain acquired this sequence becomes highly pathogenic to humans. The dominant mutation (79.3%) at S gene product level was 614D→G. The impact of mutations detected in S gene product on virus transmission, diagnosis, pathogenicity and strategies of antiviral therapy, should be rapidly assessed in further studies.

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

2006 ◽  
Vol 87 (5) ◽  
pp. 1203-1208 ◽  
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.

scholarly journals Discriminatory Weight of SNPs in Spike SARS-CoV-2 Variants: A Technically Rapid, Unambiguous, and Bioinformatically Validated Laboratory Approach

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 123
Author(s):  
Nicolò Musso ◽  
Paolo Giuseppe Bonacci ◽  
Dafne Bongiorno ◽  
Stefano Stracquadanio ◽  
Dalida Angela Bivona ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Sanger Sequencing ◽  
N Gene ◽  
Whole Genome ◽  
S Gene ◽  
Rapid Spread ◽  
Alpha Beta ◽  
Alpha Variant ◽  
Commercial Kits ◽  
Gene Portion

Background: The SARS-CoV-2 virus has assumed considerable importance during the COVID-19 pandemic. Its mutation rate is high, involving the spike (S) gene and thus there has been a rapid spread of new variants. Herein, we describe a rapid, easy, adaptable, and affordable workflow to uniquely identify all currently known variants through as few analyses. Our method only requires two conventional PCRs of the S gene and two Sanger sequencing reactions, and possibly another PCR/sequencing assay on a N gene portion to identify the B.1.160 lineage. Methods: We selected an S gene 1312 bp portion containing a set of SNPs useful for discriminating all variants. Mathematical, statistical, and bioinformatic analyses demonstrated that our choice allowed us to identify all variants even without looking for all related mutations, as some of them are shared by different variants (e.g., N501Y is found in the Alpha, Beta, and Gamma variants) whereas others, that are more informative, are unique (e.g., A57 distinctive to the Alpha variant). Results: A “weight” could be assigned to each mutation that may be present in the selected portion of the S gene. The method’s robustness was confirmed by analyzing 80 SARS-CoV-2-positive samples. Conclusions: Our workflow identified the variants without the need for whole-genome sequencing and with greater reliability than with commercial kits.

scholarly journals Bovine Coronavirus Infections in Turkey: Molecular Analysis of the Full-Length Spike Gene Sequences of Viruses From Digestive and Respiratory Infections

2021 ◽  
Author(s):  
Secil Sevinc Temizkan ◽  
Feray Alkan
Keyword(s):  
Amino Acid ◽  
Genetic Relationships ◽  
Full Length ◽  
N Gene ◽  
Nasal Discharge ◽  
Gene Sequences ◽  
Bovine Coronavirus ◽  
Positive Effects ◽  
S Gene ◽  
Pcr Targeting

Abstract BCoV can be spread by animal activity. Despite the widespread cattle farming in the region, limited studies exist in Turkey about BCoV. The aim of this study was to reveal the latest aspects in Turkey about BCoV and evaluate the data. This is the first study reporting the full-length sequences of S genes of BCoV in Turkey.In this study samples were collected from 119 cattle, presenting clinical signs of respiratory (n=78) or digestive tract infection (n=41) in distinctive farms located in widely different provinces of Turkey. Samples were screened for bovine coronavirus (BCoV) by a RT-nested PCR targeting the N gene. BCoV was found positive in 35 samples (9 faeces and 26 nasal discharge) and RT-PCR analysis of the S gene was performed. The partial/full-length S gene sequences were able to be obtained from 11 samples (8 faeces and 3 nasal discharge). Phylogenetic tree of the S gene sequences was analyzed for the genetic relationships among BCoVs from Turkey and other countries. Results showed that many different amino acid changes exist in local strains and these changes were persistent in faeces and nasal discharge origin. Likewise, some nucleotide and amino acid changes were compatible with previous studies which have critical importance for tropism. These results could represent a novelty in the current literature adding new data on BCoV from Turkey and these data could have potentially positive effects on the vaccination approach and control strategies due to lack of information.

scholarly journals Iterative Variable Gene Discovery from Whole Genome Sequencing with a Bootstrapped Multiresolution Algorithm

2019 ◽  
Vol 2019 ◽  
pp. 1-13 ◽  
Author(s):  
David N. Olivieri ◽  
Francisco Gambón-Deza
Keyword(s):  
Learning Algorithm ◽  
Supervised Machine Learning ◽  
Specific Response ◽  
Whole Genome ◽  
Gene Sequences ◽  
Model Species ◽  
V Genes ◽  
V Gene ◽  
And Function ◽  
Python Programming

In jawed vertebrates, variable (V) genes code for antigen-binding regions of B and T lymphocyte receptors, which generate a specific response to foreign pathogens. Obtaining the detailed repertoire of these genes across the jawed vertebrate kingdom would help to understand their evolution and function. However, annotations of V-genes are known for only a few model species since their extraction is not amenable to standard gene finding algorithms. Also, the more distant evolution of a taxon is from such model species, and there is less homology between their V-gene sequences. Here, we present an iterative supervised machine learning algorithm that begins by training a small set of known and verified V-gene sequences. The algorithm successively discovers homologous unaligned V-exons from a larger set of whole genome shotgun (WGS) datasets from many taxa. Upon each iteration, newly uncovered V-genes are added to the training set for the next predictions. This iterative learning/discovery process terminates when the number of new sequences discovered is negligible. This process is akin to “online” or reinforcement learning and is proven to be useful for discovering homologous V-genes from successively more distant taxa from the original set. Results are demonstrated for 14 primate WGS datasets and validated against Ensembl annotations. This algorithm is implemented in the Python programming language and is freely available at http://vgenerepertoire.org.

scholarly journals Molecular Characterisation of a Rare Reassortant Porcine-Like G5P[6] Rotavirus Strain Detected in an Unvaccinated Child in Kasama, Zambia

Pathogens ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 663
Author(s):  
Wairimu M. Maringa ◽  
Peter N. Mwangi ◽  
Julia Simwaka ◽  
Evans M. Mpabalwani ◽  
Jason M. Mwenda ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
The Other ◽  
Interspecies Transmission ◽  
Whole Genome ◽  
Molecular Characterisation ◽  
Human Origin ◽  
Reassortment Event ◽  
Reassortant Strain ◽  
Unvaccinated Child ◽  
Cognate Gene

A human-porcine reassortant strain, RVA/Human-wt/ZMB/UFS-NGS-MRC-DPRU4723/2014/G5P[6], was identified in a sample collected in 2014 from an unvaccinated 12 month old male hospitalised for gastroenteritis in Zambia. We sequenced and characterised the complete genome of this strain which presented the constellation: G5-P[6]-I1-R1-C1-M1-A8-N1-T1-E1-H1. The genotype A8 is often observed in porcine strains. Phylogenetic analyses showed that VP6, VP7, NSP2, NSP4, and NSP5 genes were closely related to cognate gene sequences of porcine strains (e.g., RVA/Pig-wt/CHN/DZ-2/2013/G5P[X] for VP7) from the NCBI database, while VP1, VP3, VP4, and NSP3 were closely related to porcine-like human strains (e.g., RVA/Human-wt/CHN/E931/2008/G4P[6] for VP1, and VP3). On the other hand, the origin of the VP2 was not clear from our analyses, as it was not only close to both porcine (e.g., RVA/Pig-tc/CHN/SWU-1C/2018/G9P[13]) and porcine-like human strains (e.g., RVA/Human-wt/LKA/R1207/2009/G4P[6]) but also to three human strains (e.g., RVA/Human-wt/USA/1476/1974/G1P[8]). The VP7 gene was located in lineage II that comprised only porcine strains, which suggests the occurrence of independent porcine-to-human reassortment events. The study strain may have collectively been derived through interspecies transmission, or through reassortment event(s) involving strains of porcine and porcine-like human origin. The results of this study underline the importance of whole-genome characterisation of rotavirus strains and provide insights into interspecies transmissions from porcine to humans.

scholarly journals Transcriptome and Network Analyses of Heterostyly in Turnera subulata Provide Mechanistic Insights: Are S-Loci a Red-Light for Pistil Elongation?

Plants ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 713 ◽  
Author(s):  
Paige M. Henning ◽  
Joel S. Shore ◽  
Andrew G. McCubbin
Keyword(s):  
Red Light ◽  
Genetic Networks ◽  
Light Signaling ◽  
Self Incompatibility ◽  
S Locus ◽  
Network Analyses ◽  
S Gene ◽  
Self Fertilization ◽  
Pistil Length ◽  
S Genes

Heterostyly employs distinct hermaphroditic floral morphs to enforce outbreeding. Morphs differ structurally in stigma/anther positioning, promoting cross-pollination, and physiologically blocking self-fertilization. Heterostyly is controlled by a self-incompatibility (S)-locus of a small number of linked S-genes specific to short-styled morph genomes. Turnera possesses three S-genes, namely TsBAHD (controlling pistil characters), TsYUC6, and TsSPH1 (controlling stamen characters). Here, we compare pistil and stamen transcriptomes of floral morphs of T. subulata to investigate hypothesized S-gene function(s) and whether hormonal differences might contribute to physiological incompatibility. We then use network analyses to identify genetic networks underpinning heterostyly. We found a depletion of brassinosteroid-regulated genes in short styled (S)-morph pistils, consistent with hypothesized brassinosteroid-inactivating activity of TsBAHD. In S-morph anthers, auxin-regulated genes were enriched, consistent with hypothesized auxin biosynthesis activity of TsYUC6. Evidence was found for auxin elevation and brassinosteroid reduction in both pistils and stamens of S- relative to long styled (L)-morph flowers, consistent with reciprocal hormonal differences contributing to physiological incompatibility. Additional hormone pathways were also affected, however, suggesting S-gene activities intersect with a signaling hub. Interestingly, distinct S-genes controlling pistil length, from three species with independently evolved heterostyly, potentially intersect with phytochrome interacting factor (PIF) network hubs which mediate red/far-red light signaling. We propose that modification of the activities of PIF hubs by the S-locus could be a common theme in the evolution of heterostyly.

scholarly journals Comparison of M and N gene sequences distinguishes variation amongst equine arteritis virus isolates

1994 ◽  
Vol 75 (6) ◽  
pp. 1491-1497 ◽  
Author(s):  
E. D. Chirnside ◽  
C. M. Wearing ◽  
M. M. Binns ◽  
J. A. Mumford
Keyword(s):  
Equine Arteritis Virus ◽  
N Gene ◽  
Gene Sequences ◽  
Virus Isolates
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