RESUMO
PURPOSE: In this study, we present DeepVirusClassifier, a tool capable of accurately classifying Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) viral sequences among other subtypes of the coronaviridae family. This classification is achieved through a deep neural network model that relies on convolutional neural networks (CNNs). Since viruses within the same family share similar genetic and structural characteristics, the classification process becomes more challenging, necessitating more robust models. With the rapid evolution of viral genomes and the increasing need for timely classification, we aimed to provide a robust and efficient tool that could increase the accuracy of viral identification and classification processes. Contribute to advancing research in viral genomics and assist in surveilling emerging viral strains. METHODS: Based on a one-dimensional deep CNN, the proposed tool is capable of training and testing on the Coronaviridae family, including SARS-CoV-2. Our model's performance was assessed using various metrics, including F1-score and AUROC. Additionally, artificial mutation tests were conducted to evaluate the model's generalization ability across sequence variations. We also used the BLAST algorithm and conducted comprehensive processing time analyses for comparison. RESULTS: DeepVirusClassifier demonstrated exceptional performance across several evaluation metrics in the training and testing phases. Indicating its robust learning capacity. Notably, during testing on more than 10,000 viral sequences, the model exhibited a more than 99% sensitivity for sequences with fewer than 2000 mutations. The tool achieves superior accuracy and significantly reduced processing times compared to the Basic Local Alignment Search Tool algorithm. Furthermore, the results appear more reliable than the work discussed in the text, indicating that the tool has great potential to revolutionize viral genomic research. CONCLUSION: DeepVirusClassifier is a powerful tool for accurately classifying viral sequences, specifically focusing on SARS-CoV-2 and other subtypes within the Coronaviridae family. The superiority of our model becomes evident through rigorous evaluation and comparison with existing methods. Introducing artificial mutations into the sequences demonstrates the tool's ability to identify variations and significantly contributes to viral classification and genomic research. As viral surveillance becomes increasingly critical, our model holds promise in aiding rapid and accurate identification of emerging viral strains.
Assuntos
COVID-19 , Aprendizado Profundo , Genoma Viral , SARS-CoV-2 , SARS-CoV-2/genética , SARS-CoV-2/classificação , Genoma Viral/genética , COVID-19/virologia , Coronaviridae/genética , Coronaviridae/classificação , Humanos , Redes Neurais de ComputaçãoRESUMO
The novel SARS-CoV-2 coronavirus has attracted attention due to the high number of human cases around the world. It has been proposed that this virus originated in bats, possibly transmitted to humans by an intermediate host, making bats a group of great interest during this outbreak. Almost 10% of the world's bat species inhabit Mexico, and 14 previous novel CoVs have been recorded in Mexican bats. However, the phylogenetic relationships between these viruses and the novel coronavirus are unknown. The aim of this communication was therefore to describe the phylogenetic relationships between Mexican bat-CoVs and SARS-CoV-2. We showed that Mexican bat-CoVs sequences are grouped into two genera, Alphacoronavirus and Betacoronavirus, and the new coronavirus is an independent clade within Betacoronavirus. Due to the diversity of CoVs in Mexican bats, the propensity of CoVs to shift hosts, the invasion mechanisms described for this new virus, and previous reports of animals infected by SARS-CoV-2, the risk of possible infection from humans to Mexican bats should not be discarded and warrants further analyses. To avoid future zoonotic infectious diseases and to limit persecution of bats, we urge researchers and the general population to take extreme precautions and avoid manipulation of bats during the current and future similar outbreaks.
Assuntos
COVID-19/virologia , Quirópteros/virologia , SARS-CoV-2/genética , Alphacoronavirus/classificação , Alphacoronavirus/genética , Animais , COVID-19/epidemiologia , Doenças Transmissíveis Emergentes/virologia , Coronaviridae/classificação , Coronaviridae/genética , Evolução Molecular , Genoma Viral , Humanos , México/epidemiologia , Filogenia , SARS-CoV-2/classificação , Zoonoses/epidemiologiaRESUMO
OBJECTIVE: In December 2019 a novel coronavirus (SARS-CoV-2) that is causing the current COVID-19 pandemic was identified in Wuhan, China. Many questions have been raised about its origin and adaptation to humans. In the present work we performed a genetic analysis of the Spike glycoprotein (S) of SARS-CoV-2 and other related coronaviruses (CoVs) isolated from different hosts in order to trace the evolutionary history of this protein and the adaptation of SARS-CoV-2 to humans. RESULTS: Based on the sequence analysis of the S gene, we suggest that the origin of SARS-CoV-2 is the result of recombination events between bat and pangolin CoVs. The hybrid SARS-CoV-2 ancestor jumped to humans and has been maintained by natural selection. Although the S protein of RaTG13 bat CoV has a high nucleotide identity with the S protein of SARS-CoV-2, the phylogenetic tree and the haplotype network suggest a non-direct parental relationship between these CoVs. Moreover, it is likely that the basic function of the receptor-binding domain (RBD) of S protein was acquired by the SARS-CoV-2 from the MP789 pangolin CoV by recombination and it has been highly conserved.
Assuntos
Betacoronavirus/genética , Coronaviridae/genética , Recombinação Genética , Glicoproteína da Espícula de Coronavírus/genética , Adaptação Biológica/genética , Enzima de Conversão de Angiotensina 2 , Animais , Sítios de Ligação/genética , Quirópteros/virologia , Eutérios/virologia , Evolução Molecular , Furina/metabolismo , Especificidade de Hospedeiro , Humanos , Peptidil Dipeptidase A/metabolismo , Filogenia , SARS-CoV-2 , Seleção Genética , Glicoproteína da Espícula de Coronavírus/metabolismoRESUMO
BACKGROUND: In Brazil the implementation of the Sentinel Surveillance System of Influenza began in 2000. Central public health laboratories use reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis of respiratory viruses, but this protocol identifies only specific targets, resulted in inconclusive diagnosis for many samples. Thus, high-throughput sequencing (HTS) would be complementary method in the identification of pathogens in inconclusive samples for RT-qPCR or other specific detection protocols. OBJECTIVES: This study aimed to detect unidentified viruses using HTS approach in negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR collected in the Federal District, Brazil. METHODS: Nucleic acids were extracted from samples collected in winter period of 2016 and subjected to HTS. The results were confirmed by the multiplex PR21 RT-qPCR, which identifies 21 respiratory pathogens. FINDINGS: The main viruses identified by HTS were of families Herpesviridae, Coronaviridae, Parvoviridae and Picornaviridae, with the emphasis on rhinoviruses. The presence of respiratory viruses in the samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus, enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as well as by HTS analyses. MAIN CONCLUSIONS: Wide virus diversity was found by different methodologies and high frequency of rhinovirus occurrence was confirmed in population in winter, showing its relevance for public health.
Assuntos
Coronaviridae/isolamento & purificação , Herpesviridae/isolamento & purificação , Nasofaringe/virologia , Parvoviridae/isolamento & purificação , Picornaviridae/isolamento & purificação , Traqueia/virologia , Coronaviridae/classificação , Coronaviridae/genética , DNA Viral/genética , Herpesviridae/classificação , Herpesviridae/genética , Humanos , Parvoviridae/classificação , Parvoviridae/genética , Picornaviridae/classificação , Picornaviridae/genética , RNA Viral/genética , Reação em Cadeia da Polimerase em Tempo Real , Reação em Cadeia da Polimerase Via Transcriptase ReversaRESUMO
We identified two RNA (paramyxovirus and coronavirus) and two DNA (adenovirus and herpesvirus) viruses in a common aquatic bird, the Neotropic Cormorant ( Phalacrocorax brasilianus), and determined their phylogenetic relationships to other global circulating variants. We analyzed 104 cloacal swabs from individuals collected at locations in Central Chile. Sequences were obtained from amplicons using consensus primers targeting conserved genes of the virus families Paramyxoviridae, Coronaviridae, Adenoviridae, and Herpesviridae. A total of 20.2% of the samples was positive for coronavirus, 8.7% for adenovirus, and 3.8% for herpesvirus. No paramyxoviruses were detected. All coronaviruses were identified as viruses of the Gammacoronavirus genus, closely related to the infectious bronchitis virus clade (bootstrap clade support=75%). All adenovirus samples were identified as Aviadenovirus, related to a gull and falcon adenovirus (Bayesian posterior probability=0.86). The herpesviruses identified were related to the infectious laryngotracheitis virus ( Gallid herpesvirus 1) of the genus Iltovirus (bootstrap clade support=99%). We provide information about the diversity of viruses circulating among apparently healthy Neotropic Cormorants.
Assuntos
Adenoviridae/genética , Doenças das Aves/virologia , Aves/virologia , Coronaviridae/genética , Herpesviridae/genética , Adenoviridae/isolamento & purificação , Infecções por Adenoviridae/epidemiologia , Infecções por Adenoviridae/veterinária , Infecções por Adenoviridae/virologia , Animais , Doenças das Aves/epidemiologia , Chile/epidemiologia , Coronaviridae/isolamento & purificação , Infecções por Coronavirus/epidemiologia , Infecções por Coronavirus/veterinária , Infecções por Coronavirus/virologia , Herpesviridae/isolamento & purificação , Infecções por Herpesviridae/epidemiologia , Infecções por Herpesviridae/veterinária , Infecções por Herpesviridae/virologia , FilogeniaRESUMO
BACKGROUND In Brazil the implementation of the Sentinel Surveillance System of Influenza began in 2000. Central public health laboratories use reverse transcription-quantitative polymerase chain reaction (RT-qPCR) for diagnosis of respiratory viruses, but this protocol identifies only specific targets, resulted in inconclusive diagnosis for many samples. Thus, high-throughput sequencing (HTS) would be complementary method in the identification of pathogens in inconclusive samples for RT-qPCR or other specific detection protocols. OBJECTIVES This study aimed to detect unidentified viruses using HTS approach in negative samples of nasopharynx/tracheal secretions by the standard RT-qPCR collected in the Federal District, Brazil. METHODS Nucleic acids were extracted from samples collected in winter period of 2016 and subjected to HTS. The results were confirmed by the multiplex PR21 RT-qPCR, which identifies 21 respiratory pathogens. FINDINGS The main viruses identified by HTS were of families Herpesviridae, Coronaviridae, Parvoviridae and Picornaviridae, with the emphasis on rhinoviruses. The presence of respiratory viruses in the samples was confirmed by the PR21 multiplex RT-qPCR. Coronavirus, enterovirus, bocavirus and rhinovirus were found by multiplex RT-qPCR as well as by HTS analyses. MAIN CONCLUSIONS Wide virus diversity was found by different methodologies and high frequency of rhinovirus occurrence was confirmed in population in winter, showing its relevance for public health.
Assuntos
Humanos , Parvoviridae/isolamento & purificação , Picornaviridae/isolamento & purificação , Traqueia/virologia , Nasofaringe/virologia , Coronaviridae/isolamento & purificação , Herpesviridae/isolamento & purificação , Parvoviridae/classificação , Parvoviridae/genética , Picornaviridae/classificação , Picornaviridae/genética , DNA Viral/genética , RNA Viral/genética , Coronaviridae/classificação , Coronaviridae/genética , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Reação em Cadeia da Polimerase em Tempo Real , Herpesviridae/classificação , Herpesviridae/genéticaRESUMO
A survey was carried out in search for bat coronaviruses in an urban maternity roost of about 500 specimens of two species of insectivorous bats, Molossus molossus and Tadarida brasiliensis, in Southern Brazil. Twenty-nine out of 150 pooled fecal samples tested positive by reverse transcription-PCR contained fragments of the RNA-dependent RNA polymerase gene of coronavirus-related viruses. The sequences clustered along with bat alphacoronaviruses, forming a subcluster within this group. Our findings point to the need for risk assessment and continued surveillance of coronavirus infections of bats in Brazil.
Assuntos
Quirópteros/virologia , Infecções por Coronaviridae/veterinária , Coronaviridae/isolamento & purificação , Animais , Brasil , Quirópteros/classificação , Coronaviridae/classificação , Coronaviridae/genética , Infecções por Coronaviridae/virologia , Dados de Sequência Molecular , FilogeniaRESUMO
Recently discovered respiratory viruses were detected in 19 (9.2%) of 205 nasal swab specimens from children in Brazil with respiratory illnesses. Five each were positive for human metapneumovirus (HMPV) alone and human bocavirus (HBoV) alone, 3 for human coronaviruses (HCoV-HKU1 or -NL63) alone, and 6 for more than 1 recently discovered virus.