scholarly journals Genetic drift of human coronavirus OC43 spike gene during adaptive evolution

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Lili Ren ◽  
Yue Zhang ◽  
Jianguo Li ◽  
Yan Xiao ◽  
Jing Zhang ◽  
...  
Keyword(s):  
Adaptive Evolution ◽  
Genetic Drift ◽  
Human Coronavirus ◽  
Spike Gene

scholarly journals Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015–16

2020 ◽  
Vol 6 (1) ◽  
Author(s):  
Carol A Abidha ◽  
Joyce Nyiro ◽  
Everlyn Kamau ◽  
Osman Abdullahi ◽  
David James Nokes ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics ◽  
Control Strategies ◽  
Respiratory Illness ◽  
Respiratory Pathogen ◽  
Human Coronavirus ◽  
Spike Gene ◽  
Low Genetic Diversity ◽  
Coastal Kenya ◽  
Close Phylogenetic Relationship

Abstract Human coronavirus OC43 (HCoV-OC43) is a major contributor to seasonal outbreaks of acute respiratory illness (ARI). The origins of locally circulating HCoV-OC43 strains and characteristics of their genetic diversity are unknown for most settings despite significance to effective HCoV control strategies. Between December 2015 and June 2016, we undertook ARI surveillance in coastal Kenya in nine outpatients and one inpatient health facility (HF). Ninety-two patient samples tested HCoV-OC43 positive and forty (43.5%) were successfully sequenced in spike (S) gene region (2,864 long, ∼70%). Phylogenetic analysis confirmed co-circulation of two distinct HCoV-OC43 clades that closely clustered with genotype G (n = 34, 85%) and genotype H (n = 6, 15%) reference strains. Local viruses within the same clade displayed low genetic diversity yielding identical sequences in multiple HF. Furthermore, the newly sequenced Kenyan viruses showed close phylogenetic relationship to other contemporaneous sampled strains (2015–16) including those originating from distant places (e.g. USA and China). Using a genetic similarity threshold of 99.1 per cent at nucleotide level, the HCoV-OC43 strains sampled globally between 1967 and 2019 fell into nine sequence clusters. Notably, some of these clusters appeared to have become extinct, or occurred only sporadically in a few geographical areas while others persisted globally for multiple years. In conclusion, we found that HCoV-OC43 strains spread rapidly both locally and across the globe with limited genetic evolution in the spike gene. Full-genome sequences that are spatio-temporally representative are required to advance understanding of the transmission pathways of this important human respiratory pathogen.

scholarly journals Genie: An interactive real-time simulation for teaching genetic drift

2018 ◽  
Author(s):  
Andreina I. Castillo ◽  
Ben H. Roos ◽  
Michael S. Rosenberg ◽  
Reed A. Cartwright ◽  
Melissa A. Wilson Sayres
Keyword(s):  
Real Time ◽  
Student Performance ◽  
Adaptive Evolution ◽  
Genetic Drift ◽  
Student Development ◽  
Evolutionary Mechanisms ◽  
Before And After ◽  
Teachers And Students ◽  
Evolutionary Concepts ◽  
The Difference

AbstractBackgroundOne of the most challenging topics for students in Evolution courses is that of non-adaptive evolution, particularly genetic drift. Novel teaching techniques and software have been implemented to facilitate student understanding of this and other evolution related topics; nonetheless, some of them still present certain disadvantages. Here we introduce Genie, a web-based application designed to demonstrate population genetics and evolutionary concepts.ResultsWe used Genie as a tool to teach 203 students taking Arizona State University’s Evolution course. Students freely used Genie during recitation session after having learned about genetic drift and other mechanism of non-adaptive evolution during lectures. Student performance and comprehension of genetic drift, and other evolutionary concepts, was tested with the Genetic Drift Inventory before and after using Genie. We found that Genie was an efficient tool for teaching genetic drift, mutation, the effects of barrier formation, and gene flow, across a variety of student demographics. Specifically, we found that with our implementation of Genie, students had significantly improved understanding of concepts such as: changes in alleles frequencies due to genetic drift and the difference between adaptive and non-adaptive evolutionary mechanisms.ConclusionsWe believe that the easy usage, creativity, and real-time nature of Genie makes it an accessible tool for both teachers and students learning non-adaptive evolution, as well as a means for student development of creative and critical thinking. Genie is freely available (https://cartwrig.ht/apps/genie/) and can be easily accessed across different operating systems.

scholarly journals Longitudinal epidemiology of human coronavirus OC43 in Yamagata, Japan, 2010–2017: Two groups based on spike gene appear one after another

2020 ◽  
Vol 93 (2) ◽  
pp. 945-951 ◽  
Author(s):  
Kenichi Komabayashi ◽  
Yohei Matoba ◽  
Shizuka Tanaka ◽  
Junji Seto ◽  
Yoko Aoki ◽  
...  
Keyword(s):  
Human Coronavirus ◽  
Spike Gene ◽  
Longitudinal Epidemiology

scholarly journals A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Simon Pollett ◽  
Matthew A. Conte ◽  
Mark Sanborn ◽  
Richard G. Jarman ◽  
Grace M. Lidl ◽  
...  
Keyword(s):  
Recombination Event ◽  
Temporal Structure ◽  
Structural Genes ◽  
Genome Sequences ◽  
High Confidence ◽  
Human Coronavirus ◽  
Spike Gene ◽  
Free Data ◽  
Human Coronaviruses ◽  
Recombination Breakpoints

AbstractThe SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in the non-ORF1 region of the genome containing structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.

scholarly journals Evolutionary dynamics of bovine coronaviruses: natural selection pattern of the spike gene implies adaptive evolution of the strains

2013 ◽  
Vol 94 (9) ◽  
pp. 2036-2049 ◽  
Author(s):  
Mehdi R. M. Bidokhti ◽  
Madeleine Tråvén ◽  
Neel K. Krishna ◽  
Muhammad Munir ◽  
Sándor Belák ◽  
...  
Keyword(s):  
Amino Acid ◽  
Adaptive Evolution ◽  
Evolutionary Dynamics ◽  
Common Ancestor ◽  
Protein Gene ◽  
Interspecies Transmission ◽  
Amino Acid Residues ◽  
S Protein ◽  
Spike Gene ◽  
Selection Pattern

Coronaviruses demonstrate great potential for interspecies transmission, including zoonotic outbreaks. Although bovine coronavirus (BCoV) strains are frequently circulating in cattle farms worldwide, causing both enteric and respiratory disease, little is known about their genomic evolution. We sequenced and analysed the full-length spike (S) protein gene of 33 BCoV strains from dairy and feedlot farms collected during outbreaks that occurred from 2002 to 2010 in Sweden and Denmark. Amino acid identities were >97 % for the BCoV strains analysed in this work. These strains formed a clade together with Italian BCoV strains and were highly similar to human enteric coronavirus HECV-4408/US/94. A high similarity was observed between BCoV, canine respiratory coronavirus (CRCoV) and human coronavirus OC43 (HCoV-OC43). Molecular clock analysis of the S gene sequences estimated BCoV and CRCoV diverged from a common ancestor in 1951, while the time of divergence from a common ancestor of BCoV and HCoV-OC43 was estimated to be 1899. BCoV strains showed the lowest similarity to equine coronavirus, placing the date of divergence at the end of the eighteenth century. Two strongly positive selection sites were detected along the receptor-binding subunit of the S protein gene: spanning amino acid residues 109–131 and 495–527. By contrast, the fusion subunit was observed to be under negative selection. The selection pattern along the S glycoprotein implies adaptive evolution of BCoVs, suggesting a successful mechanism for BCoV to continuously circulate among cattle and other ruminants without disappearance.

scholarly journals A comparative recombination analysis of human coronaviruses and implications for the SARS-CoV-2 pandemic

2021 ◽  
Author(s):  
Simon Pollett ◽  
Matthew A Conte ◽  
Mark Sanborn ◽  
Richard G Jarman ◽  
Grace M. Lidl ◽  
...  
Keyword(s):  
Recombination Event ◽  
Temporal Structure ◽  
Structural Genes ◽  
Genome Sequences ◽  
High Confidence ◽  
Human Coronavirus ◽  
Spike Gene ◽  
Free Data ◽  
Human Coronaviruses ◽  
Recombination Breakpoints

ABSTRACTThe SARS-CoV-2 pandemic prompts evaluation of recombination in human coronavirus (hCoV) evolution. We undertook recombination analyses of 158,118 public seasonal hCoV, SARS-CoV-1, SARS-CoV-2 and MERS-CoV genome sequences using the RDP4 software. We found moderate evidence for 8 SARS-CoV-2 recombination events, two of which involved the spike gene, and low evidence for one SARS-CoV-1 recombination event. Within MERS-CoV, 229E, OC43, NL63 and HKU1 datasets, we noted 7, 1, 9, 14, and 1 high-confidence recombination events, respectively. There was propensity for recombination breakpoints in structural genes, and recombination severely skewed the temporal structure of these data, especially for NL63 and OC43. Bayesian time-scaled analyses on recombinant-free data indicated the sampled diversity of seasonal CoVs emerged in the last 70 years, with 229E displaying continuous lineage replacements. These findings emphasize the importance of genomic based surveillance to detect recombination in SARS-CoV-2, particularly if recombination may lead to immune evasion.

scholarly journals Adaptive Evolution under Extreme Genetic Drift in Oxidatively Stressed Caenorhabditis elegans

2017 ◽  
Vol 9 (11) ◽  
pp. 3008-3022 ◽  
Author(s):  
Stephen F Christy ◽  
Riana I Wernick ◽  
Michael J Lue ◽  
Griselda Velasco ◽  
Dana K Howe ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Adaptive Evolution ◽  
Genetic Drift
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