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1.
Hum Genomics ; 14(1): 17, 2020 05 12.
Artigo em Inglês | MEDLINE | ID: mdl-32398162

RESUMO

The recent coronavirus disease (COVID-19), caused by SARS-CoV-2, is inarguably the most challenging coronavirus outbreak relative to the previous outbreaks involving SARS-CoV and MERS-CoV. With the number of COVID-19 cases now exceeding 2 million worldwide, it is apparent that (i) transmission of SARS-CoV-2 is very high and (ii) there are large variations in disease severity, one component of which may be genetic variability in the response to the virus. Controlling current rates of infection and combating future waves require a better understanding of the routes of exposure to SARS-CoV-2 and the underlying genomic susceptibility to this disease. In this mini-review, we highlight possible genetic determinants of COVID-19 and the contribution of aerosol exposure as a potentially important transmission route of SARS-CoV-2.


Assuntos
Microbiologia do Ar , Betacoronavirus/fisiologia , Infecções por Coronavirus/genética , Infecções por Coronavirus/transmissão , Predisposição Genética para Doença , Pneumonia Viral/genética , Pneumonia Viral/transmissão , Infecções por Coronavirus/imunologia , Infecções por Coronavirus/prevenção & controle , Transmissão de Doença Infecciosa , Humanos , Pandemias/prevenção & controle , Equipamento de Proteção Individual , Pneumonia Viral/imunologia , Pneumonia Viral/prevenção & controle
2.
Nan Fang Yi Ke Da Xue Xue Bao ; 40(2): 152-158, 2020 Feb 29.
Artigo em Chinês | MEDLINE | ID: mdl-32376535

RESUMO

OBJECTIVE: To analyze the evolution and variation of SARS-CoV-2 during the epidemic starting at the end of 2019. METHODS: We downloaded the full-length genome sequence of SARS-CoV-2 from the databases of GISAID and NCBI. Using the software for bioinformatics including MEGA-X, BEAST, and TempEst, we constructed the genomic evolution tree, inferred the time evolution signal of the virus, calculated the tMRCA time of the virus and analyzed the selection pressure of the virus during evolution. RESULTS: The phylogenetic tree showed that SARS-CoV-2 belonged to the Sarbecovirus subgenus of ß Coronavirus genus together with bat coronavirus BetaCoV/bat/Yunnan/RaTG13/2013, bat-SL-CoVZC45, bat-SL-CoVZXC21 and SARS-CoV. The genomic sequences of SARS-CoV-2 isolated from the ongoing epidemic showed a weak time evolution signal with an average tMRCA time of 73 days (95% CI: 38.9-119.3 days). No positive time evolution signal was found between SARS-CoV-2 and BetaCoV/bat/Yunnan/RaTG13/2013, but the former virus had a strong positive temporal evolution relationship with bat-SL-CoVZC45 and SARS-CoV. The major cause for mutations of SARS-CoV-2 was the pressure of purification selection during the epidemic. CONCLUSIONS: SARS-CoV-2 may have emerged as early as November, 2019, originating most likely from bat-associated coronavirus. This finding may provide evidence for tracing the sources and evolution of the virus.


Assuntos
Betacoronavirus/genética , Quirópteros , Infecções por Coronavirus/virologia , Genoma Viral , Pneumonia Viral/virologia , Animais , Evolução Biológica , China , Quirópteros/virologia , Coronavirus/genética , Infecções por Coronavirus/genética , Pandemias , Filogenia , Pneumonia Viral/genética , Sequenciamento Completo do Genoma
3.
Rev Med Inst Mex Seguro Soc ; 58(1): 1-2, 2020 Jan 01.
Artigo em Espanhol | MEDLINE | ID: mdl-32412715

RESUMO

Every time a pandemic occurs, dozens of theories emerge to attribute the origin of the event to different facts. The COVID-19 pandemic that has hit virtually all the globe has been no exception. What is known so far about the origin of the virus that causes COVID 19? The first investigations on the origin of this disease have determined that it is a new type of virus, the origin of which is most likely zoonotic.


Assuntos
Infecções por Coronavirus/genética , Pneumonia Viral/genética , Zoonoses/virologia , Animais , Betacoronavirus , Infecções por Coronavirus/patologia , Humanos , Pandemias , Pneumonia Viral/patologia
4.
Int J Mol Sci ; 21(10)2020 May 14.
Artigo em Inglês | MEDLINE | ID: mdl-32423094

RESUMO

In December 2019, a novel severe acute respiratory syndrome (SARS) from a new coronavirus (SARS-CoV-2) was recognized in the city of Wuhan, China. Rapidly, it became an epidemic in China and has now spread throughout the world reaching pandemic proportions. High mortality rates characterize SARS-CoV-2 disease (COVID-19), which mainly affects the elderly, causing unrestrained cytokines-storm and subsequent pulmonary shutdown, also suspected micro thromboembolism events. At the present time, no specific and dedicated treatments, nor approved vaccines, are available, though very promising data come from the use of anti-inflammatory, anti-malaria, and anti-coagulant drugs. In addition, it seems that males are more susceptible to SARS-CoV-2 than females, with males 65% more likely to die from the infection than females. Data from the World Health Organization (WHO) and Chinese scientists show that of all cases about 1.7% of women who contract the virus will die compared with 2.8% of men, and data from Hong Kong hospitals state that 32% of male and 15% of female COVID-19 patients required intensive care or died. On the other hand, the long-term fallout of coronavirus may be worse for women than for men due to social and psychosocial reasons. Regardless of sex- or gender-biased data obtained from WHO and those gathered from sometimes controversial scientific journals, some central points should be considered. Firstly, SARS-CoV-2 has a strong interaction with the human ACE2 receptor, which plays an essential role in cell entry together with transmembrane serine protease 2 (TMPRSS2); it is interesting to note that the ACE2 gene lays on the X-chromosome, thus allowing females to be potentially heterozygous and differently assorted compared to men who are definitely hemizygous. Secondly, the higher ACE2 expression rate in females, though controversial, might ascribe them the worst prognosis, in contrast with worldwide epidemiological data. Finally, several genes involved in inflammation are located on the X-chromosome, which also contains high number of immune-related genes responsible for innate and adaptive immune responses to infection. Other genes, out from the RAS-pathway, might directly or indirectly impact on the ACE1/ACE2 balance by influencing its main actors (e.g., ABO locus, SRY, SOX3, ADAM17). Unexpectedly, the higher levels of ACE2 or ACE1/ACE2 rebalancing might improve the outcome of COVID-19 in both sexes by reducing inflammation, thrombosis, and death. Moreover, X-heterozygous females might also activate a mosaic advantage and show more pronounced sex-related differences resulting in a sex dimorphism, further favoring them in counteracting the progression of the SARS-CoV-2 infection.


Assuntos
Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/genética , Predisposição Genética para Doença , Pneumonia Viral/epidemiologia , Pneumonia Viral/genética , Betacoronavirus/fisiologia , Cromossomos Humanos X , Infecções por Coronavirus/imunologia , Feminino , Humanos , Masculino , Pandemias , Peptidil Dipeptidase A/genética , Pneumonia Viral/imunologia , Serina Endopeptidases/genética , Fatores Sexuais
5.
Viruses ; 12(5)2020 05 10.
Artigo em Inglês | MEDLINE | ID: mdl-32397688

RESUMO

The COVID-19 pandemic is due to infection caused by the novel SARS-CoV-2 virus that impacts the lower respiratory tract. The spectrum of symptoms ranges from asymptomatic infections to mild respiratory symptoms to the lethal form of COVID-19 which is associated with severe pneumonia, acute respiratory distress, and fatality. To address this global crisis, up-to-date information on viral genomics and transcriptomics is crucial for understanding the origins and global dispersion of the virus, providing insights into viral pathogenicity, transmission, and epidemiology, and enabling strategies for therapeutic interventions, drug discovery, and vaccine development. Therefore, this review provides a comprehensive overview of COVID-19 epidemiology, genomic etiology, findings from recent transcriptomic map analysis, viral-human protein interactions, molecular diagnostics, and the current status of vaccine and novel therapeutic intervention development. Moreover, we provide an extensive list of resources that will help the scientific community access numerous types of databases related to SARS-CoV-2 OMICs and approaches to therapeutics related to COVID-19 treatment.


Assuntos
Betacoronavirus/fisiologia , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/terapia , Pneumonia Viral/epidemiologia , Pneumonia Viral/terapia , Infecções por Coronavirus/tratamento farmacológico , Infecções por Coronavirus/genética , Infecções por Coronavirus/imunologia , Infecções por Coronavirus/prevenção & controle , Genômica , Humanos , Pandemias , Pneumonia Viral/genética , Pneumonia Viral/imunologia , Vacinas Virais/imunologia
6.
EMBO Mol Med ; 12(5): e12481, 2020 05 08.
Artigo em Inglês | MEDLINE | ID: mdl-32275804

RESUMO

The COVID-19 pandemic has spread to many countries around the world, but the infection and death rates vary widely. One country that appeared to have kept the infection under control despite limited societal restrictions is Japan. This commentary explores why Japan may have, up to now, been spared an escalation of the SARS-CoV-2 infections.


Assuntos
Betacoronavirus , Infecções por Coronavirus/epidemiologia , Pneumonia Viral/epidemiologia , Vacina BCG/imunologia , Infecções por Coronavirus/genética , Infecções por Coronavirus/imunologia , Cultura , Ácidos Graxos Monoinsaturados , Variação Genética , Antígenos de Histocompatibilidade Classe I/genética , Antígenos de Histocompatibilidade Classe I/imunologia , Humanos , Japão/epidemiologia , Pandemias , Peptidil Dipeptidase A/genética , Pneumonia Viral/genética , Pneumonia Viral/imunologia , Distância Social
7.
PLoS One ; 15(4): e0230295, 2020.
Artigo em Inglês | MEDLINE | ID: mdl-32298273

RESUMO

The new type of pneumonia caused by the SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) has been declared as a global public health concern by WHO. As of April 3, 2020, more than 1,000,000 human infections have been diagnosed around the world, which exhibited apparent person-to-person transmission characteristics of this virus. The capacity of vertical transmission in SARS-CoV-2 remains controversial recently. Angiotensin-converting enzyme 2 (ACE2) is now confirmed as the receptor of SARS-CoV-2 and plays essential roles in human infection and transmission. In present study, we collected the online available single-cell RNA sequencing (scRNA-seq) data to evaluate the cell specific expression of ACE2 in maternal-fetal interface as well as in multiple fetal organs. Our results revealed that ACE2 was highly expressed in maternal-fetal interface cells including stromal cells and perivascular cells of decidua, and cytotrophoblast and syncytiotrophoblast in placenta. Meanwhile, ACE2 was also expressed in specific cell types of human fetal heart, liver and lung, but not in kidney. And in a study containing series fetal and post-natal mouse lung, we observed ACE2 was dynamically changed over the time, and ACE2 was extremely high in neonatal mice at post-natal day 1~3. In summary, this study revealed that the SARS-CoV-2 receptor was widely spread in specific cell types of maternal-fetal interface and fetal organs. And thus, both the vertical transmission and the placenta dysfunction/abortion caused by SARS-CoV-2 need to be further carefully investigated in clinical practice.


Assuntos
Infecções por Coronavirus/metabolismo , Relações Materno-Fetais , Peptidil Dipeptidase A/metabolismo , Pneumonia Viral/metabolismo , Vírus da SARS/metabolismo , Animais , Infecções por Coronavirus/genética , Humanos , Camundongos , Pandemias , Peptidil Dipeptidase A/genética , Pneumonia Viral/genética , Análise de Célula Única , Transcriptoma
8.
Eur Rev Med Pharmacol Sci ; 24(6): 3360-3384, 2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32271454

RESUMO

Beginning in December 2019, coronavirus disease 2019 (COVID-19), due to 2019-nCoV infection, emerged in Wuhan and spread rapidly throughout China and even worldwide. Employing combined therapy of modern medicine and traditional Chinese medicine has been proposed, in which Ma Xing Shi Gan Decoction (MXSGD) was recommended as a basic prescription and applied widely in the clinical treatment of COVID-19. We investigated the underlying mechanism of MXSGD in treating COVID-19 utilizing the approaches of integrating network pharmacology. A total of 97 active ingredients of MXSGD were screened out, and 169 targets were predicted. The protein-protein interaction network exhibited hub targets of MXSGD, such as Heat shock protein 90, RAC-alpha serine/threonine-protein kinase, Transcription factor AP-1, Mitogen-activated protein kinase 1, Cellular tumor antigen p53, Vascular endothelial growth factor A, and Tumour necrosis factor. Gene Ontology functional enrichment analysis demonstrated that the biological processes altered within the body after taking MXSGD were closely related to the regulation of such processes as the acute inflammatory response, chemokine production, vascular permeability, response to oxygen radicals, oxidative stress-induced apoptosis, T cell differentiation involved in the immune response, immunoglobulin secretion, and extracellular matrix disassembly. KEGG enrichment analysis indicated that the targets of MXSGD were significantly enriched in inflammation-related pathways, immunomodulation-related pathways, and viral infection-related pathways. The therapeutic mechanisms of MXSGD on COVID-19 may primarily involve the following effects: reducing inflammation, suppressing cytokine storm, protecting the pulmonary alveolar-capillary barrier, alleviating pulmonary edema, regulating the immune response, and decreasing fever.


Assuntos
Betacoronavirus/efeitos dos fármacos , Infecções por Coronavirus/tratamento farmacológico , Medicina Tradicional Chinesa , Pneumonia Viral/tratamento farmacológico , Infecções por Coronavirus/genética , Infecções por Coronavirus/metabolismo , Redes Reguladoras de Genes/efeitos dos fármacos , Humanos , Pandemias , Pneumonia Viral/genética , Pneumonia Viral/metabolismo
10.
Emerg Microbes Infect ; 9(1): 761-770, 2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-32228226

RESUMO

Circulating in China and 158 other countries and areas, the ongoing COVID-19 outbreak has caused devastating mortality and posed a great threat to public health. However, efforts to identify effectively supportive therapeutic drugs and treatments has been hampered by our limited understanding of host immune response for this fatal disease. To characterize the transcriptional signatures of host inflammatory response to SARS-CoV-2 (HCoV-19) infection, we carried out transcriptome sequencing of the RNAs isolated from the bronchoalveolar lavage fluid (BALF) and peripheral blood mononuclear cells (PBMC) specimens of COVID-19 patients. Our results reveal distinct host inflammatory cytokine profiles to SARS-CoV-2 infection in patients, and highlight the association between COVID-19 pathogenesis and excessive cytokine release such as CCL2/MCP-1, CXCL10/IP-10, CCL3/MIP-1A, and CCL4/MIP1B. Furthermore, SARS-CoV-2 induced activation of apoptosis and P53 signalling pathway in lymphocytes may be the cause of patients' lymphopenia. The transcriptome dataset of COVID-19 patients would be a valuable resource for clinical guidance on anti-inflammatory medication and understanding the molecular mechansims of host response.


Assuntos
Líquido da Lavagem Broncoalveolar , Quimiocinas/análise , Infecções por Coronavirus/genética , Citocinas/análise , Leucócitos Mononucleares , Pneumonia Viral/genética , Transcriptoma , Apoptose , Betacoronavirus , Infecções por Coronavirus/sangue , Infecções por Coronavirus/imunologia , Humanos , Linfopenia , Pandemias , Pneumonia Viral/sangue , Pneumonia Viral/imunologia , RNA-Seq , Transdução de Sinais , Proteína Supressora de Tumor p53
11.
Mol Cancer ; 19(1): 80, 2020 04 28.
Artigo em Inglês | MEDLINE | ID: mdl-32345328

RESUMO

Recent studies have reported that COVID-19 patients with lung cancer have a higher risk of severe events than patients without cancer. In this study, we investigated the gene expression of angiotensin I-converting enzyme 2 (ACE2) and transmembrane serine protease 2 (TMPRSS2) with prognosis in lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). Lung cancer patients in each age stage, subtype, and pathological stage are susceptible to SARS-CoV-2 infection, except for the primitive subtype of LUSC. LUAD patients are more susceptible to SARS-CoV-2 infection than LUSC patients. The findings are unanimous on tissue expression in gene and protein levels.


Assuntos
Adenocarcinoma de Pulmão/complicações , Betacoronavirus , Carcinoma de Células Escamosas/complicações , Infecções por Coronavirus/etiologia , Neoplasias Pulmonares/complicações , Peptidil Dipeptidase A/genética , Pneumonia Viral/etiologia , Serina Endopeptidases/genética , Adenocarcinoma de Pulmão/genética , Animais , Carcinoma de Células Escamosas/genética , Linhagem Celular , Infecções por Coronavirus/genética , Suscetibilidade a Doenças , Perfilação da Expressão Gênica , Regulação Neoplásica da Expressão Gênica , Humanos , Neoplasias Pulmonares/genética , Camundongos , Camundongos Transgênicos , Pandemias , Peptidil Dipeptidase A/biossíntese , Pneumonia Viral/genética , Serina Endopeptidases/biossíntese
12.
EMBO J ; 39(10): e105114, 2020 05 18.
Artigo em Inglês | MEDLINE | ID: mdl-32246845

RESUMO

The SARS-CoV-2 pandemic affecting the human respiratory system severely challenges public health and urgently demands for increasing our understanding of COVID-19 pathogenesis, especially host factors facilitating virus infection and replication. SARS-CoV-2 was reported to enter cells via binding to ACE2, followed by its priming by TMPRSS2. Here, we investigate ACE2 and TMPRSS2 expression levels and their distribution across cell types in lung tissue (twelve donors, 39,778 cells) and in cells derived from subsegmental bronchial branches (four donors, 17,521 cells) by single nuclei and single cell RNA sequencing, respectively. While TMPRSS2 is strongly expressed in both tissues, in the subsegmental bronchial branches ACE2 is predominantly expressed in a transient secretory cell type. Interestingly, these transiently differentiating cells show an enrichment for pathways related to RHO GTPase function and viral processes suggesting increased vulnerability for SARS-CoV-2 infection. Our data provide a rich resource for future investigations of COVID-19 infection and pathogenesis.


Assuntos
Brônquios/citologia , Expressão Gênica , Pulmão/citologia , Peptidil Dipeptidase A/genética , Serina Endopeptidases/genética , Análise de Célula Única , Adulto , Envelhecimento , Brônquios/metabolismo , Células Cultivadas , Doença Crônica/epidemiologia , Infecções por Coronavirus/genética , Células Epiteliais/metabolismo , Feminino , Perfilação da Expressão Gênica , Alemanha , Células Caliciformes/metabolismo , Humanos , Pulmão/metabolismo , Masculino , Pessoa de Meia-Idade , Pandemias , Pneumonia Viral/genética , Padrões de Referência , Análise de Sequência de RNA , Caracteres Sexuais , Fumar , Bancos de Tecidos
13.
Washington; Organización Panamericana de la Salud; Mar. 30, 2020. 8 p.
Não convencional em Espanhol | Coleciona SUS | ID: biblio-1096617

RESUMO

Los coronavirus son un grupo de virus ARN altamente diversos de la familia Coronaviridae que se dividen en 4 géneros: alfa, beta, gamma y delta, y que causan enfermedades de leves a graves en humanos y animales (1-3). Existen coronavirus humanos endémicos como los alfacoronavirus 229E y NL63 y los betacoronavirus OC43 y HKU1 que pueden causar enfermedades de tipo influenza o neumonía en humanos (1, 3). Sin embargo, dos coronavirus zoonóticos que causan enfermedades graves en humanos han emergido: el coronavirus del Síndrome respiratorio agudo grave (SARS-CoV) en 2002-2003 y el coronavirus del Síndrome respiratorio de Oriente Medio (MERS-CoV) (1-5).


Assuntos
Humanos , Pneumonia Viral/genética , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/genética , Infecções por Coronavirus/virologia , Serviços Laboratoriais de Saúde Pública , Pandemias/prevenção & controle , Betacoronavirus/isolamento & purificação
14.
Ginebra; World Health Organization; Mar. 19, 2020. 7 p.
Monografia em Inglês | BIGG | ID: biblio-1053420

RESUMO

The purpose of this document is to provide interim guidance to laboratories and stakeholders involved in laboratory testing of patients who meet the definition of suspected case of pneumonia associated with a novel coronavirus identified in Wuhan, China.


Assuntos
Humanos , Pneumonia Viral/genética , Reação em Cadeia da Polimerase/instrumentação , Infecções por Coronavirus/genética , Betacoronavirus/genética , Ensaio de Imunoadsorção Enzimática/instrumentação , Vírus da SARS/genética , Serviços Laboratoriais de Saúde Pública
15.
Front Med ; 14(2): 185-192, 2020 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-32170560

RESUMO

It has been known that, the novel coronavirus, 2019-nCoV, which is considered similar to SARS-CoV, invades human cells via the receptor angiotensin converting enzyme II (ACE2). Moreover, lung cells that have ACE2 expression may be the main target cells during 2019-nCoV infection. However, some patients also exhibit non-respiratory symptoms, such as kidney failure, implying that 2019-nCoV could also invade other organs. To construct a risk map of different human organs, we analyzed the single-cell RNA sequencing (scRNA-seq) datasets derived from major human physiological systems, including the respiratory, cardiovascular, digestive, and urinary systems. Through scRNA-seq data analyses, we identified the organs at risk, such as lung, heart, esophagus, kidney, bladder, and ileum, and located specific cell types (i.e., type II alveolar cells (AT2), myocardial cells, proximal tubule cells of the kidney, ileum and esophagus epithelial cells, and bladder urothelial cells), which are vulnerable to 2019-nCoV infection. Based on the findings, we constructed a risk map indicating the vulnerability of different organs to 2019-nCoV infection. This study may provide potential clues for further investigation of the pathogenesis and route of 2019-nCoV infection.


Assuntos
Betacoronavirus/fisiologia , Infecções por Coronavirus/genética , Peptidil Dipeptidase A/genética , Pneumonia Viral/genética , Humanos , Especificidade de Órgãos , Pandemias , RNA-Seq , Fatores de Risco , Análise de Célula Única
17.
Euro Surveill ; 25(9)2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32156330

RESUMO

The need for timely establishment of diagnostic assays arose when Germany was confronted with the first travel-associated outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in Europe. We describe our laboratory experiences during a large contact tracing investigation, comparing previously published real-time RT-PCR assays in different PCR systems and a commercial kit. We found that assay performance using the same primers and probes with different PCR systems varied and the commercial kit performed well.


Assuntos
Betacoronavirus , Técnicas de Laboratório Clínico , Infecções por Coronavirus , Pneumonia Viral , Reação em Cadeia da Polimerase em Tempo Real/métodos , Betacoronavirus/genética , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Infecções por Coronavirus/genética , Alemanha , Humanos , Análise de Sequência com Séries de Oligonucleotídeos , Pneumonia Viral/diagnóstico , Pneumonia Viral/genética , Sensibilidade e Especificidade , Fatores de Tempo , Proteínas do Envelope Viral/análise , Proteínas do Envelope Viral/genética , Fluxo de Trabalho
18.
Euro Surveill ; 25(10)2020 03.
Artigo em Inglês | MEDLINE | ID: mdl-32183934

RESUMO

Since December 2019, 62 medical staff of Zhongnan Hospital in Wuhan, China have been hospitalised with coronavirus disease 2019. During the post-discharge surveillance after clinical recovery, swabs were positive in two asymptomatic cases (3.23%). Case 1 had presented typical clinical and radiological manifestations on admission, while manifestation in Case 2 was very mild. In conclusion, a small proportion of recovered patients may test positive after discharge, and post-discharge surveillance and isolation need to be strengthened.


Assuntos
Infecções Assintomáticas , Betacoronavirus/isolamento & purificação , Infecções por Coronavirus/diagnóstico , Transmissão de Doença Infecciosa do Paciente para o Profissional , Alta do Paciente , Faringe/virologia , Pneumonia Viral/genética , Adulto , Betacoronavirus/genética , Técnicas de Laboratório Clínico , Infecções por Coronavirus/genética , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/virologia , Feminino , Hospitalização , Humanos , Masculino , Pneumonia Viral/transmissão , Valor Preditivo dos Testes , Radiografia , Reação em Cadeia da Polimerase em Tempo Real , Tomografia Computadorizada por Raios X
19.
Infect Dis Poverty ; 9(1): 33, 2020 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-32209118

RESUMO

BACKGROUND: Coronavirus can cross the species barrier and infect humans with a severe respiratory syndrome. SARS-CoV-2 with potential origin of bat is still circulating in China. In this study, a prediction model is proposed to evaluate the infection risk of non-human-origin coronavirus for early warning. METHODS: The spike protein sequences of 2666 coronaviruses were collected from 2019 Novel Coronavirus Resource (2019nCoVR) Database of China National Genomics Data Center on Jan 29, 2020. A total of 507 human-origin viruses were regarded as positive samples, whereas 2159 non-human-origin viruses were regarded as negative. To capture the key information of the spike protein, three feature encoding algorithms (amino acid composition, AAC; parallel correlation-based pseudo-amino-acid composition, PC-PseAAC and G-gap dipeptide composition, GGAP) were used to train 41 random forest models. The optimal feature with the best performance was identified by the multidimensional scaling method, which was used to explore the pattern of human coronavirus. RESULTS: The 10-fold cross-validation results showed that well performance was achieved with the use of the GGAP (g = 3) feature. The predictive model achieved the maximum ACC of 98.18% coupled with the Matthews correlation coefficient (MCC) of 0.9638. Seven clusters for human coronaviruses (229E, NL63, OC43, HKU1, MERS-CoV, SARS-CoV, and SARS-CoV-2) were found. The cluster for SARS-CoV-2 was very close to that for SARS-CoV, which suggests that both of viruses have the same human receptor (angiotensin converting enzyme II). The big gap in the distance curve suggests that the origin of SARS-CoV-2 is not clear and further surveillance in the field should be made continuously. The smooth distance curve for SARS-CoV suggests that its close relatives still exist in nature and public health is challenged as usual. CONCLUSIONS: The optimal feature (GGAP, g = 3) performed well in terms of predicting infection risk and could be used to explore the evolutionary dynamic in a simple, fast and large-scale manner. The study may be beneficial for the surveillance of the genome mutation of coronavirus in the field.


Assuntos
Betacoronavirus/imunologia , Infecções por Coronavirus , Coronavirus/imunologia , Reservatórios de Doenças/virologia , Pandemias , Peptidil Dipeptidase A/metabolismo , Pneumonia Viral , Receptores Virais/genética , Glicoproteína da Espícula de Coronavírus/imunologia , Algoritmos , Aminoácidos/genética , Animais , Betacoronavirus/genética , China , Chlorocebus aethiops , Coronavirus/genética , Coronavirus/isolamento & purificação , Infecções por Coronavirus/genética , Infecções por Coronavirus/transmissão , Infecções por Coronavirus/virologia , Endopeptidases/genética , Endopeptidases/metabolismo , Genoma/genética , Genoma Viral/genética , Humanos , Pandemias/prevenção & controle , Peptidil Dipeptidase A/genética , Filogenia , Pneumonia Viral/genética , Pneumonia Viral/transmissão , Pneumonia Viral/virologia , Receptores Virais/metabolismo , Medição de Risco
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