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1.
Virol J ; 19(1): 67, 2022 Apr 11.
Article in English | MEDLINE | ID: covidwho-1785162

ABSTRACT

BACKGROUND: The newly discovered severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and four seasonal human coronaviruses (HCoVs) (HCoV-229E, HCoV-OC43, HCoV-NL63 and HCoV-HKU1) still circulate worldwide. The early clinical symptoms of SARS-CoV-2 and seasonal HCoV infections are similar, so rapid and accurate identification of the subtypes of HCoVs is crucial for early diagnosis, early treatment, prevention and control of these infections. However, current multiplex molecular diagnostic techniques for HCoV subtypes including SARS-CoV-2 are limited. METHODS: We designed primers and probes specific for the S and N genes of SARS-CoV-2, the N gene of severe acute respiratory syndrome coronavirus (SARS-CoV), and the ORF1ab gene of four seasonal HCoVs, as well as the human B2M gene product. We developed and optimized a quadruple quantitative real-time PCR assay (qq-PCR) for simultaneous detection of SARS-CoV-2, SARS-CoV and four seasonal HCoVs. This assay was further tested for specificity and sensitivity, and validated using 184 clinical samples. RESULTS: The limit of detection of the qq-PCR assay was in the range 2.5 × 101 to 6.5 × 101 copies/µL for each gene and no cross-reactivity with other common respiratory viruses was observed. The intra-assay and inter-assay coefficients of variation were 0.5-2%. The qq-PCR assay had a 91.9% sensitivity and 100.0% specificity for SARS-CoV-2 and a 95.7% sensitivity and 100% specificity for seasonal HCoVs, using the approved commercial kits as the reference. Compared to the commercial kits, total detection consistency was 98.4% (181/184) for SARS-CoV-2 and 98.6% (142/144) for seasonal HCoVs. CONCLUSION: With the advantages of sensitivity, specificity, rapid detection, cost-effectiveness, and convenience, this qq-PCR assay has potential for clinical use for rapid discrimination between SARS-CoV-2, SARS-CoV and seasonal HCoVs.


Subject(s)
COVID-19 , Coronavirus NL63, Human , Coronavirus OC43, Human , COVID-19/diagnosis , Coronavirus NL63, Human/genetics , Coronavirus OC43, Human/genetics , Humans , Real-Time Polymerase Chain Reaction/methods , SARS-CoV-2/genetics
2.
Jpn J Infect Dis ; 75(2): 121-126, 2022 Mar 24.
Article in English | MEDLINE | ID: covidwho-1756480

ABSTRACT

Human coronaviruses (HCoVs) are distributed globally and they cause a range of respiratory symptoms. Since HCoV infection usually causes mild upper respiratory tract disease and currently has no specific therapy, there are limited reports on its features, especially in adults. We aimed to evaluate the features of HCoV infections in clinical settings. Adult patients with respiratory symptoms from October 2014 to September 2019 at Nagasaki Genbaku Isahaya Hospital were enrolled. Multiplex reverse transcription-polymerase chain reaction as performed for 15 viruses, including HCoVs, and eight bacterial species on the patients' respiratory specimens. A total of 121 cases were recruited with HKU1, OC43, 229E, and NL63 strains in 80, 21, 12, and 11 cases, respectively. The percentage of HCoV-infected patients peaked in winter (47.5%). Symptoms of fever (69.4%), cough (47.9%), and comorbidities of asthma/cough variant asthma (34.7%) were frequently observed. Lymphocytopenia and increased C-reactive protein levels were observed in laboratory tests. Co-infection with other viruses was identified in 38.8% of the cases. In the repeat-positive cases, 42% were repeat positive within 100 days. HCoV-infected patients showed winter seasonality with a high frequency of comorbidity with asthma and co-infections. Re-infection within an early period was suspected, but further consideration is required.


Subject(s)
Coronavirus 229E, Human , Coronavirus Infections , Coronavirus OC43, Human , Coronavirus , Respiratory Tract Infections , Adult , Coronavirus/genetics , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Coronavirus OC43, Human/genetics , Humans
3.
Int J Mol Sci ; 23(6)2022 Mar 10.
Article in English | MEDLINE | ID: covidwho-1742485

ABSTRACT

The B and T lymphocytes of the adaptive immune system are important for the control of most viral infections, including COVID-19. Identification of epitopes recognized by these cells is fundamental for understanding how the immune system detects and removes pathogens, and for antiviral vaccine design. Intriguingly, several cross-reactive T lymphocyte epitopes from SARS-CoV-2 with other betacoronaviruses responsible for the common cold have been identified. In addition, antibodies that cross-recognize the spike protein, but not the nucleoprotein (N protein), from different betacoronavirus have also been reported. Using a consensus of eight bioinformatic methods for predicting B-cell epitopes and the collection of experimentally detected epitopes for SARS-CoV and SARS-CoV-2, we identified four surface-exposed, conserved, and hypothetical antigenic regions that are exclusive of the N protein. These regions were analyzed using ELISA assays with two cohorts: SARS-CoV-2 infected patients and pre-COVID-19 samples. Here we describe four epitopes from SARS-CoV-2 N protein that are recognized by the humoral response from multiple individuals infected with COVID-19, and are conserved in other human coronaviruses. Three of these linear surface-exposed sequences and their peptide homologs in SARS-CoV-2 and HCoV-OC43 were also recognized by antibodies from pre-COVID-19 serum samples, indicating cross-reactivity of antibodies against coronavirus N proteins. Different conserved human coronaviruses (HCoVs) cross-reactive B epitopes against SARS-CoV-2 N protein are detected in a significant fraction of individuals not exposed to this pandemic virus. These results have potential clinical implications.


Subject(s)
Coronavirus Nucleocapsid Proteins/immunology , Coronavirus OC43, Human/immunology , Cross Reactions/immunology , Epitope Mapping/methods , Epitopes, B-Lymphocyte/immunology , SARS-CoV-2/immunology , Adult , Amino Acid Sequence , COVID-19/immunology , COVID-19/virology , Cohort Studies , Coronavirus Nucleocapsid Proteins/chemistry , Coronavirus Nucleocapsid Proteins/genetics , Coronavirus OC43, Human/genetics , Coronavirus OC43, Human/physiology , Cross Reactions/genetics , Enzyme-Linked Immunosorbent Assay/methods , Epitopes, B-Lymphocyte/metabolism , HEK293 Cells , Health Personnel/statistics & numerical data , Humans , Protein Domains , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Sequence Homology, Amino Acid , Spike Glycoprotein, Coronavirus/genetics , Spike Glycoprotein, Coronavirus/immunology
4.
J Med Virol ; 94(4): 1450-1456, 2022 04.
Article in English | MEDLINE | ID: covidwho-1718389

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic is an overwhelming crisis across the world. Human Coronavirus OC43 (HCoV-OC43) is a Betacoronavirus responsible mostly for mild respiratory symptoms. Since the presentations of HCoV-OC43 and severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) are believed to resemble a lot, the aim of this study was to evaluate the frequency and characteristics of HCoV-OC43 in the current pandemic and the rate of coinfection for the two viruses. One hundred and seventeen patients referred to Children's Medical Center, Tehran, Iran with respiratory symptoms were included. Real-time reverse transcription-polymerase chain reaction (RT-PCR) methods were performed for the detection of HCoV-OC43 and SARS-COV-2. Totally, 23 (20%) had a positive RT-PCR for HCoV-OC43 and 25 (21%) were positive for SARS-COV-2. Two patients (2%) had a positive PCR for both HCoV-OC43 and SARS-COV-2. The two groups showed significant differences in having contact with family members with suspected or confirmed COVID-19 (p = 0.017), fever (p = 0.02), edema (p = 0.036), vomiting (p < 0.001), abdominal complaints (p = 0.005), and myalgia (p = 0.02). The median level of lymphocyte count in patients with HCoV-OC43 was significantly lower than patients with SARS-COV-2 infection (p = 0.039). The same frequency of SARS-COV-2 and HCoV-OC43 was found in children with respiratory symptoms during the COVID-19 pandemic. The rate of coinfection of SARS-COV-2 with HCoV-OC43 in our study was 0.08. Further research into the cocirculation of endemic coronaviruses, such as HCoV-OC43 and SARS-CoV2, in different regions, is highly recommended. Attempts to determine the geographic distribution and recruit more flexible test panel designs are also highly recommended.


Subject(s)
COVID-19/diagnosis , Coronavirus OC43, Human/genetics , Respiratory Tract Infections/virology , SARS-CoV-2/genetics , Child , Child, Preschool , Female , Humans , Infant , Iran , Male , Reverse Transcriptase Polymerase Chain Reaction/methods
5.
Emerg Microbes Infect ; 11(1): 168-171, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-1623181

ABSTRACT

HCoV-OC43 is one of the mildly pathogenic coronaviruses with high infection rates in common population. Here, 43 HCoV-OC43 related cases with pneumonia were reported, corresponding genomes of HCoV-OC43 were obtained. Phylogenetic analyses based on complete genome, orf1ab and spike genes revealed that two novel genotypes of HCoV-OC43 have emerged in China. Obvious recombinant events also can be detected in the analysis of the evolutionary dynamics of novel HCoV-OC43 genotypes. Estimated divergence time analysis indicated that the two novel genotypes had apparently independent evolutionary routes. Efforts should be conducted for further investigation of genomic diversity and evolution analysis of mildly pathogenic coronaviruses.


Subject(s)
Common Cold/epidemiology , Coronavirus Infections/epidemiology , Coronavirus OC43, Human/genetics , Genome, Viral , Genotype , Pneumonia, Viral/epidemiology , Base Sequence , Bayes Theorem , Child , Child, Hospitalized , Child, Preschool , China/epidemiology , Common Cold/pathology , Common Cold/transmission , Common Cold/virology , Coronavirus Infections/pathology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Coronavirus OC43, Human/classification , Coronavirus OC43, Human/pathogenicity , Epidemiological Monitoring , Female , Humans , Infant , Male , Monte Carlo Method , Mutation , Phylogeny , Pneumonia, Viral/pathology , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Recombination, Genetic
6.
Intern Med ; 60(21): 3497-3501, 2021 Nov 01.
Article in English | MEDLINE | ID: covidwho-1572223

ABSTRACT

A 40-year-old woman developed a fever, sore throat, and cough. Coronavirus disease 2019 (COVID-19) was suspected; chest CT showed pan-lobular ground-glass opacity in the bilateral lower lobes suggesting viral pneumonia. Although a reverse transcription loop-mediated isothermal amplification (RT-LAMP) test for COVID-19 using a nasopharyngeal swab was negative, she was hospitalized and isolated because COVID-19 could not be ruled out. After admission, multiplex polymerase chain reaction (PCR) with the FilmArray Respiratory Panel 2.1 from a nasopharyngeal swab was positive for human coronavirus (HCoV) OC43. Therefore, the diagnosis was pneumonia due to HCoV-OC43. Multiplex PCR is useful for differentiating pneumonia due to COVID-19 from that due to other viral pneumonias.


Subject(s)
Coronavirus Infections/diagnosis , Coronavirus OC43, Human , Pneumonia, Viral/diagnosis , Adult , COVID-19 , Coronavirus OC43, Human/genetics , Diagnosis, Differential , Female , Humans , Molecular Diagnostic Techniques , Multiplex Polymerase Chain Reaction , Nucleic Acid Amplification Techniques , Pneumonia, Viral/virology
7.
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
8.
J Med Virol ; 94(4): 1450-1456, 2022 04.
Article in English | MEDLINE | ID: covidwho-1520243

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic is an overwhelming crisis across the world. Human Coronavirus OC43 (HCoV-OC43) is a Betacoronavirus responsible mostly for mild respiratory symptoms. Since the presentations of HCoV-OC43 and severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) are believed to resemble a lot, the aim of this study was to evaluate the frequency and characteristics of HCoV-OC43 in the current pandemic and the rate of coinfection for the two viruses. One hundred and seventeen patients referred to Children's Medical Center, Tehran, Iran with respiratory symptoms were included. Real-time reverse transcription-polymerase chain reaction (RT-PCR) methods were performed for the detection of HCoV-OC43 and SARS-COV-2. Totally, 23 (20%) had a positive RT-PCR for HCoV-OC43 and 25 (21%) were positive for SARS-COV-2. Two patients (2%) had a positive PCR for both HCoV-OC43 and SARS-COV-2. The two groups showed significant differences in having contact with family members with suspected or confirmed COVID-19 (p = 0.017), fever (p = 0.02), edema (p = 0.036), vomiting (p < 0.001), abdominal complaints (p = 0.005), and myalgia (p = 0.02). The median level of lymphocyte count in patients with HCoV-OC43 was significantly lower than patients with SARS-COV-2 infection (p = 0.039). The same frequency of SARS-COV-2 and HCoV-OC43 was found in children with respiratory symptoms during the COVID-19 pandemic. The rate of coinfection of SARS-COV-2 with HCoV-OC43 in our study was 0.08. Further research into the cocirculation of endemic coronaviruses, such as HCoV-OC43 and SARS-CoV2, in different regions, is highly recommended. Attempts to determine the geographic distribution and recruit more flexible test panel designs are also highly recommended.


Subject(s)
COVID-19/diagnosis , Coronavirus OC43, Human/genetics , Respiratory Tract Infections/virology , SARS-CoV-2/genetics , Child , Child, Preschool , Female , Humans , Infant , Iran , Male , Reverse Transcriptase Polymerase Chain Reaction/methods
9.
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
10.
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
11.
J Virol ; 95(12)2021 05 24.
Article in English | MEDLINE | ID: covidwho-1247318

ABSTRACT

The COVID-19 pandemic poses a serious global health threat. The rapid global spread of SARS-CoV-2 highlights an urgent need to develop effective therapeutics for blocking SARS-CoV-2 infection and spread. Stimulator of Interferon Genes (STING) is a chief element in host antiviral defense pathways. In this study, we examined the impact of the STING signaling pathway on coronavirus infection using the human coronavirus OC43 (HCoV-OC43) model. We found that HCoV-OC43 infection did not stimulate the STING signaling pathway, but the activation of STING signaling effectively inhibits HCoV-OC43 infection to a much greater extent than that of type I interferons (IFNs). We also discovered that IRF3, the key STING downstream innate immune effector, is essential for this anticoronavirus activity. In addition, we found that the amidobenzimidazole (ABZI)-based human STING agonist diABZI robustly blocks the infection of not only HCoV-OC43 but also SARS-CoV-2. Therefore, our study identifies the STING signaling pathway as a potential therapeutic target that could be exploited for developing broad-spectrum antiviral therapeutics against multiple coronavirus strains in order to face the challenge of future coronavirus outbreaks.IMPORTANCE The highly infectious and lethal SARS-CoV-2 is posing an unprecedented threat to public health. Other coronaviruses are likely to jump from a nonhuman animal to humans in the future. Novel broad-spectrum antiviral therapeutics are therefore needed to control known pathogenic coronaviruses such as SARS-CoV-2 and its newly mutated variants, as well as future coronavirus outbreaks. STING signaling is a well-established host defense pathway, but its role in coronavirus infection remains unclear. In the present study, we found that activation of the STING signaling pathway robustly inhibits infection of HCoV-OC43 and SARS-CoV-2. These results identified the STING pathway as a novel target for controlling the spread of known pathogenic coronaviruses, as well as emerging coronavirus outbreaks.


Subject(s)
COVID-19/metabolism , Coronavirus OC43, Human/metabolism , Membrane Proteins/metabolism , SARS-CoV-2/metabolism , Signal Transduction , A549 Cells , Animals , COVID-19/genetics , Chlorocebus aethiops , Coronavirus OC43, Human/genetics , HEK293 Cells , Humans , Interferon Regulatory Factor-3/genetics , Interferon Regulatory Factor-3/metabolism , Membrane Proteins/antagonists & inhibitors , Membrane Proteins/genetics , SARS-CoV-2/genetics , Vero Cells
12.
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
13.
Mol Cell ; 81(13): 2838-2850.e6, 2021 07 01.
Article in English | MEDLINE | ID: covidwho-1202181

ABSTRACT

SARS-CoV-2 is an RNA virus whose success as a pathogen relies on its abilities to repurpose host RNA-binding proteins (RBPs) and to evade antiviral RBPs. To uncover the SARS-CoV-2 RNA interactome, we here develop a robust ribonucleoprotein (RNP) capture protocol and identify 109 host factors that directly bind to SARS-CoV-2 RNAs. Applying RNP capture on another coronavirus, HCoV-OC43, revealed evolutionarily conserved interactions between coronaviral RNAs and host proteins. Transcriptome analyses and knockdown experiments delineated 17 antiviral RBPs, including ZC3HAV1, TRIM25, PARP12, and SHFL, and 8 proviral RBPs, such as EIF3D and CSDE1, which are responsible for co-opting multiple steps of the mRNA life cycle. This also led to the identification of LARP1, a downstream target of the mTOR signaling pathway, as an antiviral host factor that interacts with the SARS-CoV-2 RNAs. Overall, this study provides a comprehensive list of RBPs regulating coronaviral replication and opens new avenues for therapeutic interventions.


Subject(s)
Autoantigens/genetics , COVID-19/genetics , RNA, Viral/genetics , Ribonucleoproteins/genetics , SARS-CoV-2/genetics , COVID-19/virology , Coronavirus OC43, Human/genetics , Coronavirus OC43, Human/pathogenicity , HEK293 Cells , Host-Pathogen Interactions/genetics , Humans , Protein Binding/genetics , Protein Interaction Maps/genetics , RNA-Binding Proteins/genetics , SARS-CoV-2/pathogenicity , TOR Serine-Threonine Kinases/genetics , Transcription Factors/genetics , Transcriptome/genetics , Tripartite Motif Proteins/genetics , Ubiquitin-Protein Ligases/genetics , Virus Replication/genetics
14.
J Med Virol ; 93(2): 945-951, 2021 02.
Article in English | MEDLINE | ID: covidwho-1196429

ABSTRACT

Human coronavirus OC43 (HCoV-OC43) is divided into genotypes A to H based on genetic recombination including the spike (S) gene. To investigate the longitudinal transition of the phylogenetic feature of the HCoV-OC43 S gene in a community, phylogenetic analysis of the S1 region of the S gene was conducted using 208 strains detected in Yamagata during 2010 to 2017 with reference strains of the genotype. The S1 sequences were divisible into four groups: A to D. All Yamagata strains belonged to either group B or group D. In group B, 46 (90.2%) out of 51 Yamagata strains were clustered with those of genotype E reference strains (cluster E). In group D, 28 (17.8%) and 122 (77.7%) out of 157 Yamagata strains were clustered, respectively, with genotype F and genotype G reference strains. In cluster G, 28 strains formed a distinct cluster. Monthly distributions of HCoV-OC43 in Yamagata in 2010 to 2017 revealed that group B and group D appeared one after another. In group B, the cluster E strains were prevalent recurrently. In conclusion, epidemics of HCoV-OC43 in Yamagata, Japan might be attributable to two genetically different groups: group B showed a recurrent epidemic of strains belonging to a single phylogenetic cluster and group D showed epidemic strains belonging to multiple clusters.


Subject(s)
Coronavirus Infections/epidemiology , Coronavirus OC43, Human/genetics , Genotype , Phylogeny , Spike Glycoprotein, Coronavirus/genetics , Adolescent , Adult , Child , Child, Preschool , Coronavirus Infections/virology , Coronavirus OC43, Human/classification , Evolution, Molecular , Female , Humans , Infant , Infant, Newborn , Longitudinal Studies , Male , Middle Aged , RNA, Viral/genetics , Recombination, Genetic , Sequence Analysis, DNA , Young Adult
15.
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
16.
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
17.
Acta Chim Slov ; 67(3): 949-956, 2020 Sep.
Article in English | MEDLINE | ID: covidwho-1060696

ABSTRACT

Due to the current spreading of the new disease CoViD-19, the World Health Organization formally declared a world pandemic on March 11, 2020. The present trends indicate that the pandemic will have an enormous clinical and economic impact on population health. Infections are initiated by the transmembrane spike (S) glycoproteins of human coronavirus (hCoV) binding to host receptors. Ongoing research and therapeutic product development are of vital importance for the successful treatment of CoViD-19. To contribute somewhat to the overall effort, herein, single point mutations (SPMs) of the binding site residues in hCoV-OC43 S that recognizes cellular surface components containing 9-O-acetylated sialic acid (9-O-Ac-Sia) are explored using an in silico protein engineering approach, while their effects on the binding of 9-O-Ac-Sia and Hidroxychloroquine (Hcq) are evaluated using molecular docking simulations. Thr31Met and Val84Arg are predicted to be the critical - most likely SPMs in hCoV-OC43 S for the binding of 9-O-Ac-Sia and Hcq, respectively, even though Thr31Met is a very likely SPM in the case of Hcq too. The corresponding modes of interaction indicate a comparable strength of the Thr31Met/9-O-Ac-Sia and Val84Arg/Hcq (or Thr31Met/Hcq) complexes. Given that the binding site is conserved in all CoV S glycoproteins that associate with 9-O-acetyl-sialoglycans, the high hydrophobic affinity of Hcq to hCoV-OC43 S speaks in favor of its ability to competitively inhibit rapid S-mediated virion attachment in high-density receptor environments, but its considerably low specificity to hCoV-OC43 S may be one of the key obstacles in considering the potential of Hcq to become a drug candidate.


Subject(s)
Coronavirus Infections/virology , Coronavirus OC43, Human/genetics , Hydroxychloroquine/metabolism , Point Mutation , Sialic Acids/metabolism , Spike Glycoprotein, Coronavirus/genetics , Binding Sites , COVID-19/virology , Coronavirus Infections/metabolism , Coronavirus OC43, Human/chemistry , Coronavirus OC43, Human/metabolism , Humans , Molecular Docking Simulation/methods , Protein Engineering , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , Spike Glycoprotein, Coronavirus/chemistry , Spike Glycoprotein, Coronavirus/metabolism
18.
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
19.
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
20.
J Clin Microbiol ; 59(1)2020 12 17.
Article in English | MEDLINE | ID: covidwho-991749

ABSTRACT

Broad testing for respiratory viruses among persons under investigation (PUIs) for SARS-CoV-2 has been performed inconsistently, limiting our understanding of alternative viral infections and coinfections in these patients. RNA metagenomic next-generation sequencing (mNGS) offers an agnostic tool for the detection of both SARS-CoV-2 and other RNA respiratory viruses in PUIs. Here, we used RNA mNGS to assess the frequencies of alternative viral infections in SARS-CoV-2 RT-PCR-negative PUIs (n = 30) and viral coinfections in SARS-CoV-2 RT-PCR-positive PUIs (n = 45). mNGS identified all viruses detected by routine clinical testing (influenza A [n = 3], human metapneumovirus [n = 2], and human coronavirus OC43 [n = 2], and human coronavirus HKU1 [n = 1]). mNGS also identified both coinfections (1, 2.2%) and alternative viral infections (4, 13.3%) that were not detected by routine clinical workup (respiratory syncytial virus [n = 3], human metapneumovirus [n = 1], and human coronavirus NL63 [n = 1]). Among SARS-CoV-2 RT-PCR-positive PUIs, lower cycle threshold (CT ) values correlated with greater SARS-CoV-2 read recovery by mNGS (R 2, 0.65; P < 0.001). Our results suggest that current broad-spectrum molecular testing algorithms identify most respiratory viral infections among SARS-CoV-2 PUIs, when available and implemented consistently.


Subject(s)
Betacoronavirus/isolation & purification , COVID-19/diagnosis , Coronavirus OC43, Human/isolation & purification , Influenza A virus/isolation & purification , Metapneumovirus/isolation & purification , SARS-CoV-2/isolation & purification , Betacoronavirus/genetics , COVID-19 Nucleic Acid Testing/methods , Coinfection/virology , Coronavirus OC43, Human/genetics , Genome, Viral/genetics , High-Throughput Nucleotide Sequencing , Humans , Influenza A virus/genetics , Metagenome , Metagenomics , Metapneumovirus/genetics , SARS-CoV-2/genetics
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