Coronaviruses are a large family of viruses which include viruses that cause the common cold and severe acute respiratory syndrome (SARS) in humans and other diseases in animals. There are considerable genetic diversities within coronaviruses due to their wide rang hosts and their special gene replication and transcription mechanisms. During this process, gene recombinations often occur, resulting in novel subtype or coronavirus emerge constantly. Of note are SARS-like-CoVs and novel HCoV-EMC identified in 2012. This minireview summarized major advances of recently identified coronaviruses, focusing on the genome structures and interspecies jumping mechanism of coronavirus.
Animals ; Coronavirus ; classification ; genetics ; isolation & purification ; Coronavirus Infections ; transmission ; Humans ; Phylogeny

The deltacoronavirus is a new member of the subfamily Coronaviridae of the family Coronaviridae. Deltacoronaviruses can infect birds and mammals. Deltacoronaviruses were detected in early 2007 in Asian leopard cats and Chinese ferret badgers. In 2014, porcine deltacoronavirus (PDCoV) infection spread rapidly in the USA. Moreover, cell culture-adapted PDCoV has been obtained from infected piglets. Animal experiments have confirmed that the isolated PDCoV is highly pathogenic and causes severe diarrhea in piglets. Thus, the PDCoV can be considered to be a good model to study the deltacoronavirus. In this review, we discuss the etiology, epidemiology, pathogenicity, culture, and diagnostic methods of the PDCoV.
Animals ; Coronavirus ; classification ; genetics ; isolation & purification ; Coronavirus Infections ; veterinary ; virology ; Diarrhea ; veterinary ; virology ; Phylogeny ; Swine ; Swine Diseases ; virology

BACKGROUND: Direct antigen test (DAT) and culture are primary tests to diagnose infections by respiratory viruses, but are mainly available for the traditional viral pathogens such as respiratory syncytial virus (RSV), influenza virus, parainfluenza virus (PIV), and adenovirus in clinical laboratories. The objective of this study was to evaluate a multiplex reverse transcriptase-PCR method using Seeplex(TM) RV Detection kit (Seegene, Korea) for the detection of rhinovirus, coronavirus, and human metapneumovirus (hMPV). METHODS: From January to May 2007, nasopharyngeal aspirates (NPAs) from pediatric patients negative for culture and DAT of traditional viral pathogens were tested with Seeplex(TM). All the amplicons were directly sequenced and homology of the sequences was searched in the National Center for Biotechnology Information (NCBI) database. Patients' medical records were reviewed for clinical and demographic features. RESULTS: Forty-seven (26.4%) of 178 NPAs were positive: 18 rhinovirus, 15 hMPV, 4 RSV A, 3 coronavirus OC43, 3 influenza virus A, 2 adenovirus, 1 coronavirus NL63, and 1 RSV B. Based on maximum identity, each of the sequences indicating rhinovirus, hMPV, and coronavirus OC43 matched to the corresponding viruses with homology of 94-98%, 96-99%, and 98-100%, respectively. Seeplex(TM) positive patients were 0-11 yr old with a male:female ratio of 1.5:1. Clinical diagnoses included 9 pneumonia, 6 bronchiolitis, 2 cold, 1 asthma exacerbation for rhinovirus; 10 pneumonia, 4 bronchiolitis, and 1 clinical sepsis for hPMV; and 1 pneumonia, 2 croup, and 1 cold for coronavirus. CONCLUSIONS: Multiplex reverse transcriptase-PCR method using Seeplex(TM) RV Detection kit is a reliable test to detect rhinovirus, hMPV, and coronavirus. It may improve the diagnostic sensitivity for RSV, influenza virus, PIV, and adenovirus.
Adolescent ; Child ; Child, Preschool ; Coronavirus/classification/*isolation & purification ; Coronavirus 229E, Human/classification/genetics/isolation & purification ; Coronavirus OC43, Human/classification/genetics/isolation & purification ; Female ; Humans ; Infant ; Infant, Newborn ; Male ; Metapneumovirus/classification/genetics/*isolation & purification ; Phylogeny ; Reagent Kits, Diagnostic ; Respiratory Tract Infections/*diagnosis/virology ; Reverse Transcriptase Polymerase Chain Reaction/*methods ; Rhinovirus/classification/genetics/*isolation & purification ; Sequence Analysis, DNA

A simple, rapid and sensitive colorimetric reverse-transcription loop-mediated isothermal amplification (RT-LAMP) was developed for rapid detection of Middle East respiratory syndrome coronavirus (MERS-CoV). The method employed six primers that recognized sequences of a nucleocapsid gene for amplification of nucleic acids under isothermal conditions at 63 degrees C for 60 min. Products were detected through a LA-320c Loopamp Turbidimeter (real-time RT-LAMP) or visual inspection of color change by pre-addition of Hydroxynaphthol Blue dye (visual RT-LAMP). Specificity of RT-LAMP was validated by detection of several human coronaviruses and common respiratory viruses. MERS-CoV real-time RT-LAMP had a linear correlation (R2) of 0.995 at 10(3)-10(6) copies. The limit of detection of real-time RT-LAMP, visual RT-LAMP and quantitative real-time PCR was 500, 1000 and 100 copies/reaction, respectively. The established RT-LAMP assay was demonstrated to be a rapid screening tool for MERS-CoV infection, and could be suitable in resource-limited clinical sites and for field studies.
Coronavirus Infections ; virology ; DNA Primers ; genetics ; Humans ; Middle East Respiratory Syndrome Coronavirus ; classification ; genetics ; isolation & purification ; Nucleic Acid Amplification Techniques ; methods ; Reverse Transcription

OBJECTIVE: To investigate the CT findings of patients with different clinical types of coronavirus disease 2019 (COVID-19). METHODS: A total of 67 patients diagnosed as COVID-19 by nucleic acid testing were collected and divided into 4 groups according to the clinical stages based on . The CT imaging characteristics were analyzed among patients with different clinical types. RESULTS: Among 67 patients, 3(4.5%) were mild, 35 (52.2%) were moderate, 22 (32.8%) were severe, and 7(10.4%) were critical ill. No significant abnormality in chest CT imaging in mild patients. The 35 cases of moderate type included 3 (8.6%) single lesions, the 22 cases of severe cases included 1 (4.5%) single lesion and the rest cases were with multiple lesions. CT images of moderate patients were mainly manifested by solid plaque shadow and halo sign (18/35, 51.4%); while fibrous strip shadow with ground glass shadow was more frequent in severe cases (7/22, 31.8%). Consolidation shadow as the main lesion was observed in 7 cases, and all of them were severe or critical ill patients. CONCLUSIONS CT images of patients with different clinical types of COVID-19 have characteristic manifestations, and solid shadow may predict severe and critical illness.
Betacoronavirus ; isolation & purification ; Coronavirus Infections ; classification ; diagnostic imaging ; Humans ; Lung ; diagnostic imaging ; Pandemics ; classification ; Pneumonia, Viral ; classification ; diagnostic imaging ; Tomography, X-Ray Computed

Animals ; Chiroptera ; virology ; Coronavirus ; classification ; genetics ; isolation & purification ; Coronavirus Infections ; transmission ; virology ; Databases, Genetic ; Genome, Viral ; Humans ; Male ; Middle Aged ; Middle East ; Phylogeny ; SARS Virus ; classification ; genetics ; isolation & purification ; Severe Acute Respiratory Syndrome ; virology

We designed specific primers and fluorescence-labeled probes to develop real-time and conventional RT-PCR assays for detection of human coronavirus NL63 or HKU1. Subsequently, experiments were undertaken to assess diagnostic criteria such as specificity, sensitivity and reproducibility. The detection limit of the real-time RT-PCR assays was 10 RNA copies per reaction mixture. No cross-reactivity was observed between RNA samples derived from designed HCoV and other HCoV or human metapneumovirus. A total of 158 nasopharyngeal swab specimens collected from adult patients with acute respiratory tract infection in Beijing were screened for the presence of human coronavirus NL63 and HKU1 by using real-time RT-PCR and conventional RT-PCR method. The fluorescence quantitative RT-PCR method detected six specimens positive for human coronavirus NL63, five specimens positive for human coronavirus HKU1; and conventional RT-PCR method detected three HCoV-NL63 positive and three HCoV-HKU1 positive, respectively. The convention RT-PCR products of positive samples were obtained and sequence analysis confirmed the reliability of the above methods. In summary, the real-time RT-PCR assay for HCoV- NL63 or HKU1 was more sensitive than conventional RT-PCR and with less time (less than 4 hours) for completion. It may be suitable for molecular epidemiological surveillance and clinical diagnosis for human coronavirus NL63 and HKU1.
Coronavirus ; classification ; genetics ; isolation & purification ; Humans ; Nasopharynx ; virology ; Phylogeny ; Reverse Transcriptase Polymerase Chain Reaction ; methods ; Sensitivity and Specificity

The entire S1 protein gene of five infectious bronchitis (IB) vaccine strains (JAAS, IBN, Jilin, J9, H120) used in China were compared with that of the IB field isolate CK/CH/LDL/97 I present in China. The nucleotide and deduced amino acid similarities between the five IB vaccine strains and the field strain, CK/CH/LDL/97 I, were not more than 76.4% and 78.7%, respectively. Phylogenetic analysis based on the S1 gene showed that the vaccine strains and the field strain belonged to different clusters and had larger evolutionary distances, indicating that they were of different genotypes. The five vaccine strains were used for protection test against challenge of the field isolate CK/CH/LDL/97 I. The chickens inoculated with five vaccine strains showed morbidity as high as 30%-100% after challenged with the CK/CH/ LDL/97 I strain. The organ samples at 5 days post challenge showed that the viral detection rates were 50%-90% and 10%-30% for trachea and kidney, respectively. The live attenuated vaccines only provided partial protection to the vaccinated chickens against heterologous IBV infection, CK/CH/LDL/97 I.
Animals ; Antibodies, Viral ; blood ; Chickens ; virology ; Coronavirus Infections ; prevention & control ; veterinary ; Infectious bronchitis virus ; classification ; genetics ; immunology ; isolation & purification ; Membrane Glycoproteins ; genetics ; Phylogeny ; Poultry Diseases ; prevention & control ; Spike Glycoprotein, Coronavirus ; Vaccines, Attenuated ; immunology ; Viral Envelope Proteins ; genetics ; Viral Vaccines ; immunology

During the 2015 outbreak of Middle East respiratory syndrome coronavirus (MERS-CoV) in Korea, 186 persons were infected, resulting in 38 fatalities. We isolated MERS-CoV from the oropharyngeal sample obtained from a patient of the outbreak. Cytopathic effects showing detachment and rounding of cells were observed in Vero cell cultures 3 days after inoculation of the sample. Spherical virus particles were observed by transmission electron microscopy. Full-length genome sequence of the virus isolate was obtained and phylogenetic analyses showed that it clustered with clade B of MERS-CoV.
Animals ; Cercopithecus aethiops ; Coronavirus Infections/*diagnosis/epidemiology/*virology ; Disease Outbreaks ; Humans ; Microscopy, Electron ; Middle East Respiratory Syndrome Coronavirus/classification/genetics/*isolation & purification/ultrastructure ; Phylogeny ; Polymerase Chain Reaction ; RNA, Viral/analysis/chemistry/metabolism ; Republic of Korea/epidemiology ; Sequence Analysis, RNA ; Vero Cells

We wished to ascertain the prevalence as well as the genetic and antigenic variation of infectious bronchitis viruses (IBVs) circulating in the Guangxi Province of China in recent years. The S1 gene of 15 IBV field isolates during 2012-2013 underwent analyses in terms of the similarity of amino-acid sequences, creation of phylogenetic trees, recombination, and serologic identification. Similarities in amino-acid sequences among the 15 isolates of the S1 gene were 54.3%-99.6%, and 43.3%-99.3% among 15 isolates and reference strains. Compared with the vaccine strain H120, except for GX-YL130025, the other 14 isolates showed a lower similarity of amino-acid sequences of the S1 gene (65.1-81.4%). Phylogenetic analyses of the S1 gene suggested that 15 IBV isolates were classified into eight genotypes, with the predominant genotype being new-type II. Recombination analyses demonstrated that the S1 gene of the GX-NN130048 isolate originated from recombination events between vaccine strain 4/91 and a LX4-like isolate. Serotyping results suggested that seven serotypes prevailed during 2012-2013 in Guangxi Province, and that only one isolate was consistent with the vaccine strain H120 in serotype (which has been used widely in recent years). The serotype of recombinant isolate GX-NN130048 was different from those of its parent strains. These results suggested that not only the genotype, but also the serotype of IBV field isolates in Guangxi Province had distinct variations, and that increasing numbers of genotypes and serotypes are in circulation. We showed that recombination events can lead to the emergence of new serotypes. Our study provides new evidence for understanding of the molecular mechanisms of IBV variations, and the development of new vaccines against IBVs.
Animals ; Antibodies, Viral ; blood ; Chickens ; China ; Coronavirus Infections ; blood ; veterinary ; virology ; Genetic Variation ; Genotype ; Infectious bronchitis virus ; classification ; genetics ; immunology ; isolation & purification ; Molecular Sequence Data ; Phylogeny ; Poultry Diseases ; blood ; virology ; Sequence Homology, Amino Acid ; Spike Glycoprotein, Coronavirus ; chemistry ; genetics ; immunology