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 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 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 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 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.

Deubiquitinase Activity and Regulation of Antiviral Innate Immune Responses by Papain-like Proteases of Human Coronavirus NL63*

2010 ◽  
Vol 37 (8) ◽  
pp. 871-880 ◽  
Author(s):  
Li SUN ◽  
Yu-Dong YANG ◽  
Dian-Bo LIU ◽  
Ya-Ling XING ◽  
Xiao-Juan CHEN ◽  
...  
Keyword(s):  
Immune Responses ◽  
Innate Immune ◽  
Innate Immune Responses ◽  
Human Coronavirus

The Seasonal End of Human Coronavirus Hospital Admissions with Implications for SARS-CoV-2 (Preprint)

2020 ◽  
Author(s):  
Alan T Evangelista
Keyword(s):  
Hospital Admissions ◽  
Disease Incidence ◽  
Influenza Viruses ◽  
Seasonal Effects ◽  
Human Coronavirus ◽  
Enveloped Virus ◽  
Multiplex Pcr Assay ◽  
Contact Transmission ◽  
Human Coronaviruses

UNSTRUCTURED The seasonality of influenza viruses and endemic human coronaviruses was tracked over an 8-year period to assess key epidemiologic reduction points in disease incidence for an urban area in the northeast United States. Patients admitted to a pediatric hospital with worsening respiratory symptoms were tested using a multiplex PCR assay from nasopharyngeal swabs. The additive seasonal effects of outdoor temperatures and indoor relative humidity (RH) were evaluated. The 8-year average peak activity of human coronaviruses occurred in the first week of January, when droplet and contact transmission was enabled by the low indoor RH of 20-30%. Previous studies have shown that an increase in RH to 50% has been associated with markedly reduced viability and transmission of influenza virus and animal coronaviruses. As disease incidence was reduced by 50% in early March, to 75% in early April, to greater than 99% at the end of April, a relationship was observed from colder temperatures in January with a low indoor RH to a gradual increase in outdoor temperatures in April with an indoor RH of 45-50%. As a lipid-bound, enveloped virus with similar size characteristics to endemic human coronaviruses, SARS-CoV-2 should be subject to the same dynamics of reduced viability and transmission with increased humidity. In addition to the major role of social distancing, the transition from lower to higher indoor RH with increasing outdoor temperatures could have an additive effect on the decrease in SARS-CoV-2 cases in May. Over the 8-year period of this study, human coronavirus activity was either zero or >99% reduction in the months of June through September, and the implication would be that SARS-Cov-2 may follow a similar pattern. INTERNATIONAL REGISTERED REPORT RR2-doi.org/10.1101/2020.05.15.20103416

scholarly journals Structural Mapping of Mutations in Spike, RdRp and Orf3a Genes of SARS-CoV-2 in Influenza Like Illness (ILI) Patients

Viruses ◽  
2021 ◽  
Vol 13 (1) ◽  
pp. 136
Author(s):  
Bandar Alosaimi ◽  
Asif Naeem ◽  
Majed F. Alghoribi ◽  
Lilian Okdah ◽  
Maaweya E. Hamed ◽  
...  
Keyword(s):  
Surveillance Systems ◽  
Case Definitions ◽  
Structural Mapping ◽  
Policy Makers ◽  
Influenza Like Illness ◽  
Spike Gene ◽  
Ambulatory Patients ◽  
Community Transmission ◽  
Next Generation Sequencing Ngs ◽  
Epidemiological Link

In December 2019, the emergence of SARS-CoV-2 virus in China led to a pandemic. Since both Influenza Like Illness (ILI) and COVID-19 case definitions overlap, we re-investigated the ILI cases using PCR for the presence of SARS-CoV-2 in 739 nasopharyngeal swabs collected from November 2019 to March 2020. SARS-CoV-2 RNA was found in 37 samples (5%) collected mostly during February 2020. It was followed by confirmation of evolutionary and spatial relationships using next generation sequencing (NGS). We observed that the overall incidence of ILI cases during 2019–2020 influenza season was considerably higher than previous years and was gradually replaced with SARS-CoV-2, which indicated a silent transmission among ambulatory patients. Sequencing of representative isolates confirmed independent introductions and silent transmission earlier than previously thought. Evolutionary and spatial analyses revealed clustering in the GH clade, characterized by three amino acid substitutions in spike gene (D614G), RdRp (P323L) and NS3 (Q57H). P323L causes conformational change near nsp8 binding site that might affect virus replication and transcription. In conclusion, assessment of the community transmission among patients with mild COVID-19 illness, particularly those without epidemiological link for acquiring the virus, is of utmost importance to guide policy makers to optimize public health interventions. The detection of SARS-CoV-2 in ILI cases shows the importance of ILI surveillance systems and warrants its further strengthening to mitigate the ongoing transmission of SARS-CoV-2. The effect of NS3 substitutions on oligomerization or membrane channel function (intra- and extracellular) needs functional validation.

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