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1.
J Virol ; 96(4): e0195521, 2022 02 23.
Article in English | MEDLINE | ID: covidwho-1701123

ABSTRACT

The receptor binding domain (RBD) of the coronavirus spike protein (S) has been verified to be the main target for potent neutralizing antibodies (nAbs) in most coronaviruses, and the N-terminal domain (NTD) of some betacoronaviruses has also been indicated to induce nAbs. For alphacoronavirus HCoV-229E, its RBD has been shown to have neutralizing epitopes, and these epitopes could change over time. However, whether neutralizing epitopes exist on the NTD and whether these epitopes change like those of the RBD are still unknown. Here, we verified that neutralizing epitopes exist on the NTD of HCoV-229E. Furthermore, we characterized an NTD targeting nAb 5H10, which could neutralize both pseudotyped and authentic HCoV-229E VR740 in vitro. Epitope mapping indicated that 5H10 targeted motif E1 (147-167 aa) and identified F159 as critical for 5H10 binding. More importantly, our results revealed that motif E1 was highly conserved among clinical isolates except for F159. Further data proved that mutations at position 159 gradually appeared over time and could completely abolish the neutralizing ability of 5H10, supporting the notion that position 159 may be under selective pressure during the human epidemic. In addition, we also found that contemporary clinical serum has a stronger binding capacity for the NTD of contemporary strains than historic strains, proving that the epitope on the NTD could change over time. In summary, these findings define a novel neutralizing epitope on the NTD of HCoV-229E S and provide a theoretical basis for the design of vaccines against HCoV-229E or related coronaviruses. IMPORTANCE Characterization of the neutralizing epitope of the spike (S) protein, the major invasion protein of coronaviruses, can help us better understand the evolutionary characteristics of these viruses and promote vaccine development. To date, the neutralizing epitope distribution of alphacoronaviruses is not well known. Here, we identified a neutralizing antibody that targeted the N-terminal domain (NTD) of the alphacoronavirus HCoV-229E S protein. Epitope mapping revealed a novel epitope that was not previously discovered in HCoV-229E. Further studies identified an important residue, F159. Mutations that gradually appeared over time at this site abolished the neutralizing ability of 5H10, indicating that selective pressure occurred at this position in the spread of HCoV-229E. Furthermore, we found that the epitopes within the NTD also changed over time. Taken together, our findings defined a novel neutralizing epitope and highlighted the role of the NTD in the future prevention and control of HCoV-229E or related coronaviruses.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , Coronavirus 229E, Human , Coronavirus Infections , Epitopes , Spike Glycoprotein, Coronavirus , Amino Acid Motifs , Animals , Coronavirus 229E, Human/genetics , Coronavirus 229E, Human/immunology , Coronavirus Infections/genetics , Coronavirus Infections/immunology , Epitopes/genetics , Epitopes/immunology , Female , Humans , Mice , Mice, Inbred BALB C , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology
3.
Virol J ; 18(1): 166, 2021 08 13.
Article in English | MEDLINE | ID: covidwho-1533268

ABSTRACT

The emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.


Subject(s)
COVID-19 Vaccines , COVID-19/virology , SARS-CoV-2/genetics , Animals , COVID-19/transmission , Coronavirus 229E, Human/genetics , Coronavirus 229E, Human/immunology , Coronavirus 229E, Human/pathogenicity , Coronavirus NL63, Human/genetics , Coronavirus NL63, Human/immunology , Coronavirus NL63, Human/pathogenicity , Coronavirus OC43, Human/genetics , Coronavirus OC43, Human/immunology , Coronavirus OC43, Human/pathogenicity , Humans , Immunity , Mutation , SARS-CoV-2/immunology , SARS-CoV-2/pathogenicity
4.
PLoS Comput Biol ; 17(11): e1009560, 2021 11.
Article in English | MEDLINE | ID: covidwho-1523396

ABSTRACT

Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively.


Subject(s)
COVID-19/genetics , COVID-19/virology , Coronavirus Infections/genetics , Coronavirus Infections/virology , SARS-CoV-2/genetics , Adaptation, Physiological/genetics , Amino Acid Substitution , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/physiology , Animals , CD13 Antigens/genetics , CD13 Antigens/physiology , Common Cold/genetics , Common Cold/virology , Computational Biology , Coronavirus 229E, Human/genetics , Coronavirus 229E, Human/physiology , Evolution, Molecular , Genomics , Host Microbial Interactions/genetics , Host Microbial Interactions/physiology , Host Specificity/genetics , Host Specificity/physiology , Humans , Mammals/genetics , Mammals/virology , Phylogeny , Protein Interaction Domains and Motifs/genetics , Receptors, Virus/genetics , Receptors, Virus/physiology , SARS-CoV-2/physiology , Selection, Genetic , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/physiology , Virus Internalization
5.
Virology ; 564: 33-38, 2021 12.
Article in English | MEDLINE | ID: covidwho-1447220

ABSTRACT

Endemic seasonal coronaviruses cause morbidity and mortality in a subset of patients, but no specific treatment is available. Molnupiravir is a promising pipeline antiviral drug for treating SARS-CoV-2 infection potentially by targeting RNA-dependent RNA polymerase (RdRp). This study aims to evaluate the potential of repurposing molnupiravir for treating seasonal human coronavirus (HCoV) infections. Molecular docking revealed that the active form of molnupiravir, ß-D-N4-hydroxycytidine (NHC), has similar binding affinity to RdRp of SARS-CoV-2 and seasonal HCoV-NL63, HCoV-OC43 and HCoV-229E. In cell culture models, treatment of molnupiravir effectively inhibited viral replication and production of infectious viruses of the three seasonal coronaviruses. A time-of-drug-addition experiment indicates the specificity of molnupiravir in inhibiting viral components. Furthermore, combining molnupiravir with the protease inhibitor GC376 resulted in enhanced antiviral activity. Our findings highlight that the great potential of repurposing molnupiravir for treating seasonal coronavirus infected patients.


Subject(s)
Coronavirus 229E, Human/genetics , Coronavirus Infections/drug therapy , Coronavirus NL63, Human/genetics , Coronavirus OC43, Human/genetics , Cytidine/analogs & derivatives , Hydroxylamines/pharmacology , Antiviral Agents/chemistry , Antiviral Agents/metabolism , Antiviral Agents/pharmacology , Common Cold/drug therapy , Coronavirus 229E, Human/drug effects , Coronavirus 229E, Human/physiology , Coronavirus NL63, Human/drug effects , Coronavirus NL63, Human/physiology , Coronavirus OC43, Human/drug effects , Coronavirus OC43, Human/physiology , Cytidine/pharmacology , Humans , Molecular Docking Simulation , Protein Binding/drug effects , Pyrrolidines/pharmacology , RNA-Dependent RNA Polymerase/chemistry , RNA-Dependent RNA Polymerase/genetics , RNA-Dependent RNA Polymerase/metabolism , Seasons , Sulfonic Acids/pharmacology , Virus Replication/drug effects , Virus Replication/genetics
6.
Sci Rep ; 11(1): 4499, 2021 02 24.
Article in English | MEDLINE | ID: covidwho-1383120

ABSTRACT

The purpose of the study was to compare clinical characteristics and mortality among adults infected with human coronaviruses (HCoV) 229E and OC43. We conducted a retrospective cohort study of adults (≥ 18 years) admitted to the ward of a university teaching hospital for suspected viral infection from October 2012 to December 2017. Multiplex real-time polymerase chain reaction (PCR) was used to test for respiratory viruses. Multivariate logistic regression was used to compare mortality among patients with HCoV 229E and HCoV OC43 infections. The main outcome was 30-day all-cause mortality. Of 8071 patients tested, 1689 were found to have a respiratory virus infection. Of these patients, 133 had HCoV infection, including 12 mixed infections, 44 HCoV 229E infections, and 77 HCoV OC43 infections. HCoV 229E infections peaked in January and February, while HCoV OC43 infections occurred throughout the year. The 30-day all-cause mortality was 25.0% among patients with HCoV 229E infection, and 9.1% among patients with HCoV OC43 infection (adjusted odds ratio: 3.58, 95% confidence interval: 1.19-10.75). Infections with HCoVs 229E and OC43 appear to have different seasonal patterns, and HCoV 229E might be more virulent than HCoV OC43.


Subject(s)
Coronavirus 229E, Human/genetics , Coronavirus Infections/mortality , Coronavirus Infections/virology , Coronavirus OC43, Human/genetics , Aged , Coinfection/mortality , Coinfection/virology , Female , Hospitalization , Humans , Male , Middle Aged , Real-Time Polymerase Chain Reaction/methods , Respiratory Tract Infections/mortality , Respiratory Tract Infections/virology , Retrospective Studies
7.
Nat Commun ; 12(1): 3726, 2021 06 17.
Article in English | MEDLINE | ID: covidwho-1275922

ABSTRACT

High-throughput, high-accuracy detection of emerging viruses allows for the control of disease outbreaks. Currently, reverse transcription-polymerase chain reaction (RT-PCR) is currently the most-widely used technology to diagnose the presence of SARS-CoV-2. However, RT-PCR requires the extraction of viral RNA from clinical specimens to obtain high sensitivity. Here, we report a method for detecting novel coronaviruses with high sensitivity by using nanopores together with artificial intelligence, a relatively simple procedure that does not require RNA extraction. Our final platform, which we call the artificially intelligent nanopore, consists of machine learning software on a server, a portable high-speed and high-precision current measuring instrument, and scalable, cost-effective semiconducting nanopore modules. We show that artificially intelligent nanopores are successful in accurately identifying four types of coronaviruses similar in size, HCoV-229E, SARS-CoV, MERS-CoV, and SARS-CoV-2. Detection of SARS-CoV-2 in saliva specimen is achieved with a sensitivity of 90% and specificity of 96% with a 5-minute measurement.


Subject(s)
Artificial Intelligence , COVID-19 Nucleic Acid Testing/methods , Machine Learning , Nanopores , COVID-19 Nucleic Acid Testing/instrumentation , Coronavirus 229E, Human/genetics , Equipment Design/economics , Humans , Limit of Detection , Middle East Respiratory Syndrome Coronavirus/genetics , Nanoparticles/chemistry , Polymerase Chain Reaction , SARS-CoV-2/genetics , Saliva/virology , Sensitivity and Specificity , Software
8.
Viruses ; 13(6)2021 06 05.
Article in English | MEDLINE | ID: covidwho-1259626

ABSTRACT

Epithelial characteristics underlying the differential susceptibility of chronic asthma to SARS-CoV-2 (COVID-19) and other viral infections are currently unclear. By revisiting transcriptomic data from patients with Th2 low versus Th2 high asthma, as well as mild, moderate, and severe asthmatics, we characterized the changes in expression of human coronavirus and influenza viral entry genes relative to sex, airway location, and disease endotype. We found sexual dimorphism in the expression of SARS-CoV-2-related genes ACE2, TMPRSS2, TMPRSS4, and SLC6A19. ACE2 receptor downregulation occurred specifically in females in Th2 high asthma, while proteases broadly assisting coronavirus and influenza viral entry, TMPRSS2, and TMPRSS4, were highly upregulated in both sexes. Overall, changes in SARS-CoV-2-related gene expression were specific to the Th2 high molecular endotype of asthma and different by asthma severity and airway location. The downregulation of ACE2 (COVID-19, SARS) and ANPEP (HCoV-229E) viral receptors wascorrelated with loss of club and ciliated cells in Th2 high asthma. Meanwhile, the increase in DPP4 (MERS-CoV), ST3GAL4, and ST6GAL1 (influenza) was associated with increased goblet and basal activated cells. Overall, this study elucidates sex, airway location, disease endotype, and changes in epithelial heterogeneity as potential factors underlying asthmatic susceptibility, or lack thereof, to SARS-CoV-2.


Subject(s)
Asthma/immunology , COVID-19/immunology , Coronavirus Infections/immunology , Epithelial Cells/virology , Gene Expression , Host Microbial Interactions , Influenza, Human/immunology , Severity of Illness Index , Asthma/genetics , Asthma/virology , COVID-19/genetics , Coronavirus 229E, Human/genetics , Coronavirus 229E, Human/immunology , Coronavirus Infections/genetics , Epithelial Cells/classification , Female , Gene Expression Profiling , Host Microbial Interactions/genetics , Host Microbial Interactions/immunology , Humans , Influenza, Human/genetics , Male , Middle East Respiratory Syndrome Coronavirus/genetics , Middle East Respiratory Syndrome Coronavirus/immunology , Orthomyxoviridae/genetics , Orthomyxoviridae/immunology , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Sex Characteristics
9.
Virol J ; 18(1): 89, 2021 04 30.
Article in English | MEDLINE | ID: covidwho-1209064

ABSTRACT

BACKGROUND: A novel coronavirus (SARS-CoV-2) emerging has put global public health institutes on high alert. Little is known about the epidemiology and clinical characteristics of human coronaviruses infections in relation to infections with other respiratory viruses. METHODS: From February 2017 to December 2019, 3660 respiratory samples submitted to Zhejiang Children Hospital with acute respiratory symptoms were tested for four human coronaviruses RNA by a novel two-tube multiplex reverse transcription polymerase chain reaction assays. Samples were also screened for the occurrence of SARS-CoV-2 by reverse transcription-PCR analysis. RESULTS: Coronavirus RNAs were detected in 144 (3.93%) specimens: HCoV-HKU1 in 38 specimens, HCoV-NL63 in 62 specimens, HCoV-OC43 in 38 specimens and HCoV-229E in 8 specimens. Genomes for SARS-CoV-2 were absent in all specimens by RT-PCR analysis during the study period. The majority of HCoV infections occurred during fall months. No significant differences in gender, sample type, year were seen across species. 37.5 to 52.6% of coronaviruses detected were in specimens testing positive for other respiratory viruses. Phylogenic analysis identified that Zhejiang coronaviruses belong to multiple lineages of the coronaviruses circulating in other countries and areas. CONCLUSION: Common HCoVs may have annual peaks of circulation in fall months in the Zhejiang province, China. Genetic relatedness to the coronaviruses in other regions suggests further surveillance on human coronaviruses in clinical samples are clearly needed to understand their patterns of activity and role in the emergence of novel coronaviruses.


Subject(s)
COVID-19/diagnosis , Multiplex Polymerase Chain Reaction/methods , Respiratory Tract Infections/virology , SARS-CoV-2/genetics , Adolescent , Betacoronavirus/genetics , Betacoronavirus/isolation & purification , COVID-19/complications , COVID-19/genetics , COVID-19/physiopathology , Child , Child, Preschool , China/epidemiology , Coronavirus/genetics , Coronavirus/isolation & purification , Coronavirus 229E, Human/genetics , Coronavirus 229E, Human/isolation & purification , Coronavirus NL63, Human/genetics , Coronavirus NL63, Human/isolation & purification , Coronavirus OC43, Human/genetics , Coronavirus OC43, Human/isolation & purification , Female , Hospitalization , Humans , Infant , Infant, Newborn , Male , Phylogeny , Respiratory Tract Infections/complications , Respiratory Tract Infections/etiology , SARS-CoV-2/isolation & purification , Spike Glycoprotein, Coronavirus/genetics
10.
Viruses ; 13(4)2021 04 15.
Article in English | MEDLINE | ID: covidwho-1184510

ABSTRACT

Coronaviruses (CoV) are widely distributed pathogens of human and animals and can cause mild or severe respiratory and gastrointestinal disease. Antigenic and genetic similarity of some CoVs within the Betacoronavirus genus is evident. Therefore, for the first time in Slovenia, we investigated the genetic diversity of partial 390-nucleotides of RNA-dependent-RNA polymerase gene (RdRp) for 66 human (HCoV) and 24 bovine CoV (BCoV) positive samples, collected between 2010 and 2016 from human patients and cattle with respiratory disease. The characterized CoV strains belong to four different clusters, in three separate human clusters HCoV-HKU1 (n = 34), HCoV-OC43 (n = 31) and HCoV 229E (n = 1) and bovine grouping only as BCoVs (n = 24). BCoVs from cattle and HCoV-OC43 were genetically the most closely related and share 96.4-97.1% nucleotide and 96.9-98.5% amino acid identity.


Subject(s)
Cattle Diseases/virology , Coronavirus/classification , Coronavirus/genetics , Animals , Cattle , Cattle Diseases/transmission , Coronavirus 229E, Human/genetics , Coronavirus Infections/transmission , Coronavirus OC43, Human/genetics , Coronavirus, Bovine/genetics , Female , Genetic Variation , Humans , Male , Slovenia
11.
PLoS Pathog ; 17(4): e1009453, 2021 04.
Article in English | MEDLINE | ID: covidwho-1172889

ABSTRACT

There is intense interest in antibody immunity to coronaviruses. However, it is unknown if coronaviruses evolve to escape such immunity, and if so, how rapidly. Here we address this question by characterizing the historical evolution of human coronavirus 229E. We identify human sera from the 1980s and 1990s that have neutralizing titers against contemporaneous 229E that are comparable to the anti-SARS-CoV-2 titers induced by SARS-CoV-2 infection or vaccination. We test these sera against 229E strains isolated after sera collection, and find that neutralizing titers are lower against these "future" viruses. In some cases, sera that neutralize contemporaneous 229E viral strains with titers >1:100 do not detectably neutralize strains isolated 8-17 years later. The decreased neutralization of "future" viruses is due to antigenic evolution of the viral spike, especially in the receptor-binding domain. If these results extrapolate to other coronaviruses, then it may be advisable to periodically update SARS-CoV-2 vaccines.


Subject(s)
Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , Coronavirus 229E, Human/genetics , Coronavirus 229E, Human/immunology , Immune Evasion , Humans , SARS-CoV-2/genetics , SARS-CoV-2/immunology
12.
J Clin Invest ; 131(10)2021 05 17.
Article in English | MEDLINE | ID: covidwho-1171752

ABSTRACT

Recent studies have shown T cell cross-recognition of SARS-CoV-2 and common cold coronavirus spike proteins. However, the effect of SARS-CoV-2 vaccines on T cell responses to common cold coronaviruses (CCCs) remains unknown. In this study, we analyzed CD4+ T cell responses to spike peptides from SARS-CoV-2 and 3 CCCs (HCoV-229E, HCoV-NL63, and HCoV-OC43) before and after study participants received Pfizer-BioNTech (BNT162b2) or Moderna (mRNA-1273) mRNA-based COVID-19 vaccines. Vaccine recipients showed broad T cell responses to the SARS-CoV-2 spike protein, and we identified 23 distinct targeted peptides in 9 participants, including 1 peptide that was targeted in 6 individuals. Only 4 of these 23 targeted peptides would potentially be affected by mutations in the UK (B.1.1.7) and South African (B.1.351) variants, and CD4+ T cells from vaccine recipients recognized the 2 variant spike proteins as effectively as they recognized the spike protein from the ancestral virus. Interestingly, we observed a 3-fold increase in the CD4+ T cell responses to HCoV-NL63 spike peptides after vaccination. Our results suggest that T cell responses elicited or enhanced by SARS-CoV-2 mRNA vaccines may be able to control SARS-CoV-2 variants and lead to cross-protection against some endemic coronaviruses.


Subject(s)
CD4-Positive T-Lymphocytes/immunology , COVID-19 Vaccines/immunology , Coronavirus 229E, Human , Coronavirus NL63, Human , Coronavirus OC43, Human , RNA, Messenger , SARS-CoV-2 , Spike Glycoprotein, Coronavirus , Adult , Coronavirus 229E, Human/genetics , Coronavirus 229E, Human/immunology , Coronavirus NL63, Human/genetics , Coronavirus NL63, Human/immunology , Coronavirus OC43, Human/genetics , Coronavirus OC43, Human/immunology , Cross Reactions , Female , Humans , Male , Middle Aged , RNA, Messenger/genetics , RNA, Messenger/immunology , SARS-CoV-2/genetics , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology
13.
Nat Genet ; 53(4): 435-444, 2021 04.
Article in English | MEDLINE | ID: covidwho-1123140

ABSTRACT

The ongoing COVID-19 pandemic has caused a global economic and health crisis. To identify host factors essential for coronavirus infection, we performed genome-wide functional genetic screens with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human coronavirus 229E. These screens uncovered virus-specific as well as shared host factors, including TMEM41B and PI3K type 3. We discovered that SARS-CoV-2 requires the lysosomal protein TMEM106B to infect human cell lines and primary lung cells. TMEM106B overexpression enhanced SARS-CoV-2 infection as well as pseudovirus infection, suggesting a role in viral entry. Furthermore, single-cell RNA-sequencing of airway cells from patients with COVID-19 demonstrated that TMEM106B expression correlates with SARS-CoV-2 infection. The present study uncovered a collection of coronavirus host factors that may be exploited to develop drugs against SARS-CoV-2 infection or future zoonotic coronavirus outbreaks.


Subject(s)
COVID-19/genetics , CRISPR-Cas Systems , Genome, Human/genetics , Genome-Wide Association Study/methods , Membrane Proteins/genetics , Nerve Tissue Proteins/genetics , Bronchoalveolar Lavage Fluid/cytology , COVID-19/epidemiology , COVID-19/virology , Cell Line, Tumor , Cells, Cultured , Coronavirus 229E, Human/genetics , Epidemics , Epithelial Cells/virology , Gene Expression , Host-Pathogen Interactions , Humans , Proviruses/physiology , SARS-CoV-2/physiology , Virus Internalization
14.
mSphere ; 6(1)2021 02 10.
Article in English | MEDLINE | ID: covidwho-1079035

ABSTRACT

Compared to other human coronaviruses, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) are relatively understudied. We report a fatal case of COVID-19 pneumonia coinfected with HCoV-229E in Hong Kong. Genome sequencing of SARS-CoV-2 and HCoV-229E from a nasopharyngeal sample of the patient showed that the SARS-CoV-2 strain HK13 was most closely related to SARS-CoV-2 type strain Wuhan-Hu-1 (99.99% nucleotide identity), compatible with his recent history of travel to Wuhan. The HCoV-229E strain HK20-42 was most closely related to HCoV-229E strain SC0865 from the United States (99.86% nucleotide identity). To investigate if it may represent a newly emerged HCoV-229E genotype in Hong Kong, we retrieved 41 archived respiratory samples that tested positive for HCoV-229E from 2004 to 2019. Pneumonia and exacerbations of chronic airway diseases were common among infected patients. Complete RdRp, S, and N gene sequencing of the 41 HCoV-229E strains revealed that our contemporary HCoV-229E strains have undergone significant genetic drift with clustering of strains in chronological order. Two novel genogroups were identified, in addition to previously described genogroups 1 to 4, with recent circulating strains including strain HK20-42 belonging to novel genogroup 6. Positive selection was detected in the spike protein and receptor-binding domain, which may be important for viral evolution at the receptor-binding interphase. Molecular dating analysis showed that HCoV-229E shared the most recent common ancestor with bat and camel/alpaca 229E-related viruses at ∼1884, while camel/alpaca viruses had a relatively recent common ancestor at ∼1999. Further studies are required to ascertain the evolutionary origin and path of HCoV-229E.IMPORTANCE Since its first appearance in the 1960s, the genetic diversity and evolution of human coronavirus 229E (HCoV-229E) have been relatively understudied. In this study, we report a fatal case of COVID-19 coinfected with HCoV-229E in Hong Kong. Genome sequencing revealed that our SARS-CoV-2 strain is highly identical to the SARS-CoV-2 strain from Wuhan, compatible with the patient's recent travel history, whereas our HCoV-229E strain in this study is highly identical to a recent strain in the United States. We also retrieved 41 archived HCoV-229E strains from 2004 to 2019 in Hong Kong for sequence analysis. Pneumonia and exacerbations of chronic airway diseases were common diagnoses among the 41 patients. The results showed that HCoV-229E was evolving in chronological order. Two novel genogroups were identified in addition to the four preexisting HCoV-229E genogroups, with recent circulating strains belonging to novel genogroup 6. Molecular clock analysis dated bat-to-human and bat-to-camelid transmission to as early as 1884.


Subject(s)
COVID-19/pathology , Common Cold/pathology , Coronavirus 229E, Human/genetics , Genetic Variation/genetics , SARS-CoV-2/genetics , Adolescent , Adult , Aged , Aged, 80 and over , Base Sequence , COVID-19/mortality , Child , Child, Preschool , Coinfection/virology , Evolution, Molecular , Female , Genome, Viral/genetics , Hong Kong , Humans , Infant , Male , Middle Aged , Protein Domains/genetics , Sequence Analysis, RNA , Spike Glycoprotein, Coronavirus/genetics , Young Adult
15.
Arch Virol ; 166(3): 929-933, 2021 Mar.
Article in English | MEDLINE | ID: covidwho-1046769

ABSTRACT

This is the first study of respiratory infections in Córdoba, Argentina, caused by endemic human coronavirus (HCoV)-OC43 and HCOV-229E, which circulated during 2011-2012 at a 3% rate, either as single or multiple infections. They were detected mainly in children, but HCoV-229E was also found in adults. HCoV-229E was detected in five out of 631 samples (0.8%), and HCoV-OC43 was found in 14 out of 631 (2.2%) samples. Clinical manifestations ranged from fever to respiratory distress, and a significant association of HCoV-229E with asthma was observed. Further studies and surveillance are needed to provide better clinical insights, early diagnosis, and medical care of patients, as well as to contribute to epidemiology modeling and prevention.


Subject(s)
Common Cold/epidemiology , Coronavirus 229E, Human/isolation & purification , Coronavirus Infections/epidemiology , Coronavirus OC43, Human/isolation & purification , Adolescent , Adult , Aged , Argentina , Child , Child, Preschool , Common Cold/virology , Coronavirus 229E, Human/genetics , Coronavirus Infections/virology , Coronavirus OC43, Human/genetics , Cross-Sectional Studies , Humans , Infant , Middle Aged , Retrospective Studies , Seasons , Young Adult
16.
Proc Natl Acad Sci U S A ; 118(6)2021 02 09.
Article in English | MEDLINE | ID: covidwho-1039676

ABSTRACT

RNA-dependent RNA polymerases (RdRps) of the Nidovirales (Coronaviridae, Arteriviridae, and 12 other families) are linked to an amino-terminal (N-terminal) domain, called NiRAN, in a nonstructural protein (nsp) that is released from polyprotein 1ab by the viral main protease (Mpro). Previously, self-GMPylation/UMPylation activities were reported for an arterivirus NiRAN-RdRp nsp and suggested to generate a transient state primed for transferring nucleoside monophosphate (NMP) to (currently unknown) viral and/or cellular biopolymers. Here, we show that the coronavirus (human coronavirus [HCoV]-229E and severe acute respiratory syndrome coronavirus 2) nsp12 (NiRAN-RdRp) has Mn2+-dependent NMPylation activity that catalyzes the transfer of a single NMP to the cognate nsp9 by forming a phosphoramidate bond with the primary amine at the nsp9 N terminus (N3825) following Mpro-mediated proteolytic release of nsp9 from N-terminally flanking nsps. Uridine triphosphate was the preferred nucleotide in this reaction, but also adenosine triphosphate, guanosine triphosphate, and cytidine triphosphate were suitable cosubstrates. Mutational studies using recombinant coronavirus nsp9 and nsp12 proteins and genetically engineered HCoV-229E mutants identified residues essential for NiRAN-mediated nsp9 NMPylation and virus replication in cell culture. The data corroborate predictions on NiRAN active-site residues and establish an essential role for the nsp9 N3826 residue in both nsp9 NMPylation in vitro and virus replication. This residue is part of a conserved N-terminal NNE tripeptide sequence and shown to be the only invariant residue in nsp9 and its homologs in viruses of the family Coronaviridae The study provides a solid basis for functional studies of other nidovirus NMPylation activities and suggests a possible target for antiviral drug development.


Subject(s)
Coronavirus 229E, Human/genetics , RNA-Binding Proteins/metabolism , SARS-CoV-2/genetics , Viral Nonstructural Proteins/metabolism , Virus Replication , Amino Acid Sequence , Amino Acid Substitution , Asparagine/genetics , Cell Line , Conserved Sequence , Coronavirus 229E, Human/physiology , Coronavirus RNA-Dependent RNA Polymerase/genetics , Coronavirus RNA-Dependent RNA Polymerase/metabolism , Humans , Manganese/metabolism , Protein Domains , RNA-Binding Proteins/genetics , Recombinant Proteins/genetics , Recombinant Proteins/metabolism , Transcription, Genetic , Viral Nonstructural Proteins/genetics
17.
J Med Virol ; 93(7): 4438-4445, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-986280

ABSTRACT

The hologic panther fusion (PF) platform provides fully automated CE marked diagnostics for respiratory viruses, including the recently discovered severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) by a transcription mediated amplification (TMA) assay, but not for the endemic human coronaviruses (hCoV). Therefore, a laboratory developed test (LDT) comprising a multiplexed reverse transcription polymerase chain reaction (RT-PCR) protocol that detects and differentiates the four hCoV NL63, 229E, HKU1, and OC43 was adapted on the PF. The novel CE marked Aptima SARS-CoV-2 TMA and the LDT for hCoV were validated with 321 diagnostic specimens from the upper and lower respiratory tract in comparison to two SARS-CoV-2 RT-PCRs (PF E-gene RT-PCR and genesig RT-PCR, 157 specimens) or the R-GENE hCoV/hParaFlu RT-PCR (164 specimens), respectively. For the endemic hCoV, results were 96.3% concordant with two specimens discordantly positive in the PF and four specimens discordantly positive in the R-GENE assay. All discordantly positive samples had Ct values between 33 and 39. The PF hCoV LDT identified 23 hCoV positive specimens as NL63, 15 as 229E, 15 as HKU1, and 25 as OC43. The Aptima SARS-CoV-2 TMA gave 99.4% concordant results compared to the consensus results with a single specimen discordantly positive. Moreover, 36 samples from proficiency testing panels were detected and typed correctly by both novel methods. In conclusion, the SARS-CoV-2 TMA and the LDT for hCoV enhanced the diagnostic spectrum of the PF for all coronaviruses circulating globally for a multitude of diagnostic materials from the upper and lower respiratory tract.


Subject(s)
Alphacoronavirus/genetics , COVID-19/diagnosis , Coronavirus 229E, Human/genetics , Coronavirus NL63, Human/genetics , Coronavirus OC43, Human/genetics , SARS-CoV-2/genetics , Humans , Nucleic Acid Amplification Techniques/methods , Respiratory System/virology , Reverse Transcriptase Polymerase Chain Reaction/methods
18.
Cell Host Microbe ; 29(2): 267-280.e5, 2021 02 10.
Article in English | MEDLINE | ID: covidwho-978239

ABSTRACT

The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has devastated the global economy and claimed more than 1.7 million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a focused high-coverage CRISPR-Cas9 library targeting 332 members of a recently published SARS-CoV-2 protein interactome. We leveraged the compact nature of this library to systematically screen SARS-CoV-2 at two physiologically relevant temperatures along with three related coronaviruses (human coronavirus 229E [HCoV-229E], HCoV-NL63, and HCoV-OC43), allowing us to probe this interactome at a much higher resolution than genome-scale studies. This approach yielded several insights, including potential virus-specific differences in Rab GTPase requirements and glycosylphosphatidylinositol (GPI) anchor biosynthesis, as well as identification of multiple pan-coronavirus factors involved in cholesterol homeostasis. This coronavirus essentiality catalog could inform ongoing drug development efforts aimed at intercepting and treating coronavirus disease 2019 (COVID-19) and help prepare for future coronavirus outbreaks.


Subject(s)
COVID-19/virology , SARS-CoV-2/metabolism , CRISPR-Cas Systems , Coronavirus 229E, Human/genetics , Coronavirus 229E, Human/metabolism , Coronavirus NL63, Human/genetics , Coronavirus NL63, Human/metabolism , Coronavirus OC43, Human , Genes, Viral , Host-Pathogen Interactions , Humans , SARS-CoV-2/genetics , Viral Proteins/genetics , Viral Proteins/metabolism
19.
Biosens Bioelectron ; 170: 112656, 2020 Dec 15.
Article in English | MEDLINE | ID: covidwho-797526

ABSTRACT

Point-of-care risk assessment (PCRA) for airborne viruses requires a system that can enrich low-concentration airborne viruses dispersed in field environments into a small volume of liquid. In this study, airborne virus particles were collected to a degree above the limit of detection (LOD) for a real-time quantitative reverse transcription polymerase chain reaction (qRT-PCR). This study employed an electrostatic air sampler to capture aerosolized test viruses (human coronavirus 229E (HCoV-229E), influenza A virus subtype H1N1 (A/H1N1), and influenza A virus subtype H3N2 (A/H3N2)) in a continuously flowing liquid (aerosol-to-hydrosol (ATH) enrichment) and a concanavalin A (ConA)-coated magnetic particles (CMPs)-installed fluidic channel for simultaneous hydrosol-to-hydrosol (HTH) enrichment. The air sampler's ATH enrichment capacity (EC) was evaluated using the aerosol counting method. In contrast, the HTH EC for the ATH-collected sample was evaluated using transmission-electron-microscopy (TEM)-based image analysis and real-time qRT-PCR assay. For example, the ATH EC for HCoV-229E was up to 67,000, resulting in a viral concentration of 0.08 PFU/mL (in a liquid sample) for a viral epidemic scenario of 1.2 PFU/m3 (in air). The real-time qRT-PCR assay result for this liquid sample was "non-detectable" however, subsequent HTH enrichment for 10 min caused the "non-detectable" sample to become "detectable" (cycle threshold (CT) value of 33.8 ± 0.06).


Subject(s)
Biosensing Techniques/instrumentation , Coronavirus 229E, Human/isolation & purification , Coronavirus Infections/virology , Influenza A Virus, H1N1 Subtype/isolation & purification , Influenza A Virus, H3N2 Subtype/isolation & purification , Influenza, Human/virology , Aerosols/analysis , Air Microbiology , Biosensing Techniques/economics , Coronavirus 229E, Human/genetics , Environmental Monitoring/economics , Environmental Monitoring/instrumentation , Equipment Design , Humans , Influenza A Virus, H1N1 Subtype/genetics , Influenza A Virus, H3N2 Subtype/genetics , Reverse Transcriptase Polymerase Chain Reaction/instrumentation , Time Factors
20.
Infect Genet Evol ; 84: 104440, 2020 Oct.
Article in English | MEDLINE | ID: covidwho-621792

ABSTRACT

SARS-CoV-2, a new coronavirus strain responsible for COVID-19, has emerged in Wuhan City, China, and continuing its global pandemic nature. The availability of the complete gene sequences of the virus helps to know about the origin and molecular characteristics of this virus. In the present study, we performed bioinformatic analysis of the available gene sequence data of SARS-CoV-2 for the understanding of evolution and molecular characteristics and immunogenic resemblance of the circulating viruses. Phylogenetic analysis was performed for four types of representative viral proteins (spike, membrane, envelope and nucleoprotein) of SARS-CoV-2, HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1, MERS-CoV, HKU4, HKU5 and BufCoV-HKU26. The findings demonstrated that SARS-CoV-2 exhibited convergent evolutionary relation with previously reported SARS-CoV. It was also depicted that SARS-CoV-2 proteins were highly similar and identical to SARS-CoV proteins, though proteins from other coronaviruses showed a lower level of resemblance. The cross-checked conservancy analysis of SARS-CoV-2 antigenic epitopes showed significant conservancy with antigenic epitopes derived from SARS-CoV. Descriptive epidemiological analysis on several epidemiological indices was performed on available epidemiological outbreak information from several open databases on COVID-19 (SARS-CoV-2). Satellite-derived imaging data have been employed to understand the role of temperature in the environmental persistence of the virus. Findings of the descriptive analysis were used to describe the global impact of newly emerged SARS-CoV-2, and the risk of an epidemic in Bangladesh.


Subject(s)
Antigens, Viral/genetics , Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Genome, Viral , Pandemics , Pneumonia, Viral/epidemiology , SARS Virus/genetics , Spike Glycoprotein, Coronavirus/chemistry , Alphacoronavirus/classification , Alphacoronavirus/genetics , Alphacoronavirus/metabolism , Amino Acid Sequence , Animals , Antigens, Viral/chemistry , Antigens, Viral/metabolism , Bangladesh/epidemiology , Base Sequence , Betacoronavirus/classification , Betacoronavirus/metabolism , Binding Sites , COVID-19 , Chiroptera/virology , Computational Biology , Coronavirus 229E, Human/classification , Coronavirus 229E, Human/genetics , Coronavirus 229E, Human/metabolism , Coronavirus Infections/virology , Coronavirus NL63, Human/classification , Coronavirus NL63, Human/genetics , Coronavirus NL63, Human/metabolism , Coronavirus OC43, Human/classification , Coronavirus OC43, Human/genetics , Coronavirus OC43, Human/metabolism , Humans , Middle East Respiratory Syndrome Coronavirus/classification , Middle East Respiratory Syndrome Coronavirus/genetics , Middle East Respiratory Syndrome Coronavirus/metabolism , Models, Molecular , Mutation , Nucleoproteins/chemistry , Nucleoproteins/genetics , Nucleoproteins/metabolism , Phylogeny , Pneumonia, Viral/virology , Protein Binding , Protein Interaction Domains and Motifs , SARS Virus/classification , SARS Virus/metabolism , SARS-CoV-2 , Sequence Alignment , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/metabolism , Viral Envelope Proteins/chemistry , Viral Envelope Proteins/genetics , Viral Envelope Proteins/metabolism
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