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

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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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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A protocol for adding knowledge to Wikidata: aligning resources on human coronaviruses

BMC Biology ◽

10.1186/s12915-020-00940-y ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Andra Waagmeester ◽

Egon L. Willighagen ◽

Andrew I. Su ◽

Martina Kutmon ◽

Jose Emilio Labra Gayo ◽

...

Keyword(s):

Common Ground ◽

Knowledge Bases ◽

Public Knowledge ◽

Medical Problems ◽

Human Coronavirus ◽

Data Schema ◽

Helping Others ◽

Human Coronaviruses ◽

The Right ◽

Human Coronavirus 229E

Abstract Background Pandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a “commons.” Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases. However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modeled with entity schemas represented by Shape Expressions. Results As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable is demonstrated by integrating data from NCBI (National Center for Biotechnology Information) Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. Conclusions Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, human coronavirus NL63, human coronavirus 229E, human coronavirus HKU1, human coronavirus OC4).

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SARS-CoV-2 genomes from Oklahoma, USA

10.1101/2020.09.15.20195420 ◽

2020 ◽

Author(s):

Sai Narayanan ◽

John Corban Ritchey ◽

Girish Patil ◽

Narasaraju Teluguakula ◽

Sunil More ◽

...

Keyword(s):

Phylogenetic Analysis ◽

The State ◽

N Gene ◽

Clinical Samples ◽

Genomic Sequencing ◽

Novel Mutations ◽

Time Points ◽

S Gene ◽

Contagious Nature ◽

Geographical Locations

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 5 clinical samples obtained in Oklahoma, USA during different time points of pandemic presence in the state. One sample from the initial days of the pandemic in the state and 4 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 such as G1167V in S gene, A6269S and P3371S in ORF1ab, T28I in ORF7b, G96R in ORF8. Phylogenetic analysis of the genomes showed similarity to viruses from across the globe. These novel mutations and phylogenetic analysis emphasize the contagious nature of the virus.

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A protocol for adding knowledge to Wikidata, a case report

10.1101/2020.04.05.026336 ◽

2020 ◽

Cited By ~ 2

Author(s):

Andra Waagmeester ◽

Egon L. Willighagen ◽

Andrew I Su ◽

Martina Kutmon ◽

Jose Emilio Labra Gayo ◽

...

Keyword(s):

Common Ground ◽

Knowledge Bases ◽

Public Knowledge ◽

Medical Problems ◽

Human Coronavirus ◽

Data Schema ◽

Helping Others ◽

Human Coronaviruses ◽

The Right ◽

Human Coronavirus 229E

AbstractPandemics, even more than other medical problems, require swift integration of knowledge. When caused by a new virus, understanding the underlying biology may help finding solutions. In a setting where there are a large number of loosely related projects and initiatives, we need common ground, also known as a “commons”. Wikidata, a public knowledge graph aligned with Wikipedia, is such a commons and uses unique identifiers to link knowledge in other knowledge bases However, Wikidata may not always have the right schema for the urgent questions. In this paper, we address this problem by showing how a data schema required for the integration can be modelled with entity schemas represented by Shape Expressions. As a telling example, we describe the process of aligning resources on the genomes and proteomes of the SARS-CoV-2 virus and related viruses as well as how Shape Expressions can be defined for Wikidata to model the knowledge, helping others studying the SARS-CoV-2 pandemic. How this model can be used to make data between various resources interoperable, is demonstrated by integrating data from NCBI Taxonomy, NCBI Genes, UniProt, and WikiPathways. Based on that model, a set of automated applications or bots were written for regular updates of these sources in Wikidata and added to a platform for automatically running these updates. Although this workflow is developed and applied in the context of the COVID-19 pandemic, to demonstrate its broader applicability it was also applied to other human coronaviruses (MERS, SARS, Human Coronavirus NL63, Human coronavirus 229E, Human coronavirus HKU1, Human coronavirus OC4).

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Seroprevalence of human coronaviruses among patients visiting Hospital-Based Sentinel Sites in Uganda

10.21203/rs.3.rs-116084/v1 ◽

2020 ◽

Author(s):

Elijah Mulabbi ◽

Robert Tweyongyere ◽

Fred Wabwire ◽

Edison Mworozi ◽

Jeff Koehlerb ◽

...

Keyword(s):

Odds Ratio ◽

Respiratory Infections ◽

Control Strategies ◽

Cross Reactivity ◽

Serum Samples ◽

Human Coronavirus ◽

Respiratory Illnesses ◽

Significant Difference ◽

Causative Agents ◽

Human Coronaviruses

Abstract Background: Human coronaviruses are causative agents of respiratory infections with several subtypes being prevalent worldwide. They cause respiratory illnesses of varying severity and have been described to be continuously emerging but their prevalence is not well documented in Uganda. This study assessed the seroprevalence of antibodies against the previously known human coronaviruses prior 2019 in Uganda.Methods: A total 377 serum samples collected from volunteers that showed influenza like illness in five hospital-based sentinel sites and archived were analyzed using a commercial Qualitative Human Coronavirus Antibody IgG ELISA kit. Although there is no single kit available that can detect the presence of all the circulating coronaviruses, this kit uses a nucleoprotein, aa 340-390 to coat the wells and since there is significant homology among the various human coronavirus strains with regards to the coded for proteins, there is significant cross reactivity beyond HCoV HKU-39849 2003. This gives the kit a qualitative ability to detect the presence of human coronavirus antibodies in a sample. Results: The overall seroprevalence for all the sites was 87.53% with no significant difference in the seroprevalence between the Hospital based sentinel sites (p=0.8). Of the seropositive, the age group 1-5 years had the highest percentage (46.97), followed by 6-10 years (16.67) and then above 20 (16.36). The volunteers were divided into two broad categories, those below five years and those above five years, to calculate the odds ratio. The odds ratio of those seropositive with an age above 5 years with reference to those below 5 years was 0.62. This shows that those below 5 are more likely to be seropositive compared to those above 5 years. The seropositivity was generally high throughout the year with highest being recorded in March and the lowest in February and December. Conclusions: The seroprevalence of Human coronaviruses is alarmingly high which calls for need to identify and characterize the circulating coronavirus strains so as to guide policy on the control strategies.

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Seroprevalence of human coronaviruses among patients visiting hospital-based sentinel sites in Uganda

BMC Infectious Diseases ◽

10.1186/s12879-021-06258-6 ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Elijah Nicholas Mulabbi ◽

Robert Tweyongyere ◽

Fred Wabwire-Mangen ◽

Edison Mworozi ◽

Jeff Koehlerb ◽

...

Keyword(s):

Respiratory Infections ◽

Control Strategies ◽

Cross Reactivity ◽

Serum Samples ◽

Human Coronavirus ◽

Respiratory Illnesses ◽

Significant Difference ◽

Causative Agents ◽

Human Coronaviruses ◽

Group 1

Abstract Background Human coronaviruses are causative agents of respiratory infections with several subtypes being prevalent worldwide. They cause respiratory illnesses of varying severity and have been described to be continuously emerging but their prevalence is not well documented in Uganda. This study assessed the seroprevalence of antibodies against the previously known human coronaviruses prior 2019 in Uganda. Methods A total 377 serum samples collected from volunteers that showed influenza like illness in five hospital-based sentinel sites and archived were analyzed using a commercial Qualitative Human Coronavirus Antibody IgG ELISA kit. Although there is no single kit available that can detect the presence of all the circulating coronaviruses, this kit uses a nucleoprotein, aa 340–390 to coat the wells and since there is significant homology among the various human coronavirus strains with regards to the coded for proteins, there is significant cross reactivity beyond HCoV HKU-39849 2003. This gives the kit a qualitative ability to detect the presence of human coronavirus antibodies in a sample. Results The overall seroprevalence for all the sites was 87.53% with no significant difference in the seroprevalence between the Hospital based sentinel sites (p = 0.8). Of the seropositive, the age group 1–5 years had the highest percentage (46.97), followed by 6–10 years (16.67) and then above 20 (16.36). An odds ratio of 1.6 (CI 0.863–2.97, p = 0.136) showed that those volunteers below 5 years of age were more likely to be seropositive compared to those above 5 years. The seropositivity was generally high throughout the year with highest being recorded in March and the lowest in February and December. Conclusions The seroprevalence of Human coronaviruses is alarmingly high which calls for need to identify and characterize the circulating coronavirus strains so as to guide policy on the control strategies.

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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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A Novel Two-Step, Direct-to-PCR Method for Virus Detection off Swabs using Human Coronavirus 229E

10.21203/rs.3.rs-40525/v1 ◽

2020 ◽

Author(s):

Zachary P Morehouse ◽

Caleb M Proctor ◽

Gabriella L Ryan ◽

Rodney J Nash

Keyword(s):

Limit Of Detection ◽

Virus Detection ◽

N Gene ◽

Viral Detection ◽

Viral Lysis ◽

Human Coronavirus ◽

Specimen Collection ◽

Extraction And Purification ◽

Human Coronavirus 229E

Abstract Background Currently, one of the most reliable methods for viral infection detection are polymerase chain reaction (PCR) based assays. This process is time and resource heavy, requiring multiple steps of lysis, extraction, purification, and amplification procedures. Herein, we have developed a method to detect virus off swabs using solely shaker-mill based mechanical lysis and the transfer of the viral lysate directly to a PCR assay for virus detection, bypassing the substantial reagent and time investments required for extraction and purification steps.Methods Using Human Coronavirus 229E (HCoV-229E) as a model system, we spiked swabs in vitro for proof-of-concept testing. Swabs were spiked in serial dilutions from 1.2x106 to 1.2x101 copies/mL and then placed in 2mL tubes with viral transport media (VTM) to mimic the specimen collection procedures in the clinic prior to processing via shaker-mill homogenization. After homogenization, 1 µL of lysate was processed using RT-qPCR for amplification of the nucleocapsid (N) gene, qualifying viral detection. Results HCoV-229E in vitro spiked swabs were processed in a novel two-step, direct-to-PCR methodology for viral detection. After running 54 swabs, we confidently determined our limit of detection to be 1.2x103 viral copies/mL with 96.30% sensitivity. Conclusion We have proven that the shaker-mill homogenization-based two-step, direct-to-PCR procedures provides sufficient viral lysis off swabs, where the resulting lysate can be used directly in PCR for the detection of HCoV-229E. This finding allows for reductions in the time and resources required for PCR based virus detection in comparison to the traditional extraction-to-PCR methodology.

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Crystal structure of the post-fusion core of the Human coronavirus 229E spike protein at 1.86 Å resolution

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798318008318 ◽

2018 ◽

Vol 74 (9) ◽

pp. 841-851 ◽

Cited By ~ 6

Author(s):

Lei Yan ◽

Bing Meng ◽

Jiangchao Xiang ◽

Ian A. Wilson ◽

Bei Yang

Keyword(s):

Electrostatic Interactions ◽

Hydrophobic Interactions ◽

Respiratory Infections ◽

Host Cells ◽

Complete Fusion ◽

Viral Fusion ◽

Human Coronavirus ◽

Upper Respiratory ◽

Heptad Repeats ◽

Human Coronavirus 229E

Human coronavirus 229E (HCoV-229E) usually causes mild upper respiratory infections in heathy adults, but may lead to severe complications or mortality in individuals with weakened immune systems. Virus entry of HCoV-229E is mediated by its spike (S) protein, where the S1 domain facilitates attachment to host cells and the S2 domain is involved in subsequent fusion of the virus and host membranes. During the fusion process, two heptad repeats, HR1 and HR2, in the S2 domain assemble into a six-helix membrane-fusion structure termed the fusion core. Here, the complete fusion-core structure of HCoV-229E has been determined at 1.86 Å resolution, representing the most complete post-fusion conformation thus far among published human alphacoronavirus (α-HCoV) fusion-core structures. The overall structure of the HCoV-229E fusion core is similar to those of SARS, MERS and HCoV-NL63, but the packing of its 3HR1 core differs from those of SARS and MERS in that it contains more noncanonical `x' and `da' layers. Side-by-side electrostatic surface comparisons reveal that the electrostatic surface potentials are opposite in α-HCoVs and β-HCoVs at certain positions and that the HCoV-229E surface also appears to be the most hydrophobic among the various HCoVs. In addition to the highly conserved hydrophobic interactions between HR1 and HR2, some polar and electrostatic interactions are also well preserved across different HCoVs. This study adds to the structural profiling of HCoVs to aid in the structure-based design of pan-coronavirus small molecules or peptides to inhibit viral fusion.

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BRIEF FACTS ABOUT COVID-19 (SARS-CoV-2) and DETAILS

10.31219/osf.io/4mfwa ◽

2021 ◽

Author(s):

Sorush Niknamian

Keyword(s):

Respiratory Tract ◽

Common Cold ◽

Respiratory Tract Infections ◽

Human Coronavirus ◽

The Family ◽

The Common ◽

Human Coronaviruses ◽

The 1960S ◽

Tract Infections ◽

Human Coronavirus 229E

Coronaviruses are a group of related viruses that cause diseases in mammals and birds. In humans, coronaviruses cause respiratory tract infections that can range from mild to lethal. Mild illnesses include some cases of the common cold, while more lethal varieties can cause SARS, MERS, and COVID-19. The outbreak was identified in Wuhan, China, in December 2019, declared to be a Public Health Emergency of International Concern on 30 January 2020, and recognized as a pandemic on 11 March 2020. Coronaviruses are the subfamily Orthocoronavirinae, within the family of Coronaviridae, order Nidovirales, and realm Riboviria. They are enveloped viruses with a positive-sense single-stranded RNA genome and a nucleocapsid of helical symmetry. The genome size of coronaviruses is approximately from 26 to 32 kilobases. Coronaviruses were first discovered in the 1930s and Human coronaviruses were discovered in the 1960s. The earliest ones studied were from human patients with the common cold, which were later named human coronavirus 229E and human coronavirus OC43. Other human coronaviruses have since been identified, including SARS-CoV in 2003, HCoV NL63 in 2004, HKU1 in 2005, MERS-CoV in 2012, and SARS-CoV-2 in 2019. Most of these have involved serious respiratory tract infections

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