RESUMO
Background and objectives: The human respiratory syncytial virus (hRSV) is among the important respiratory pathogens affecting children. Genotype-specific attachment (G) gene sequencing is usually used to determine the virus genotype. The reliability of the fusion (F) gene vs. G gene genotype-specific sequencing was screened. Materials and Methods: Archival RNA from Saudi children who tested positive for hRSV-A were used. Samples were subjected to a conventional one-step RT-PCR for both F and G genes and direct gene sequencing of the amplicons using the same primer sets. Phylogeny and mutational analysis of the obtained sequences were conducted. Results: The generic primer set succeeded to amplify target gene sequences. The phylogenetic tree based on partial F gene sequencing resulted in an efficient genotyping of hRSV-A strains equivalent to the partial G gene genotyping method. NA1, ON1, and GA5 genotypes were detected in the clinical samples. The latter was detected for the first time in Saudi Arabia. Different mutations in both conserved and escape-mutant domains were detected in both F and G. Conclusion: It was concluded that a partial F gene sequence can be used efficiently for hRSV-A genotyping.
Assuntos
Vírus Sinciciais Respiratórios/genética , Análise de Sequência de DNA/métodos , Variação Genética/genética , Técnicas de Genotipagem/métodos , Humanos , Arábia SauditaRESUMO
The human respiratory syncytial virus is a common respiratory pathogen in children. Improved diagnosis of the virus is dependent on the development of tools for the rapid detection and estimation of the viral loads. In the current study, RT-qPCR using TaqMan hydrolysis probe based on the F gene detection was developed to identify and quantify hRSV in clinical samples. The assay was validated by comparing the results with a commercially available RT-qPCR kit. The newly developed assay was sensitive in detecting hRSV positive samples (59/126) which were equivalent to those detected by the commercial kit (57/126) with a detection limit of 1 × 102 copies/mL. A high correlation was found between the results of the newly developed assay and the commercial one. It was concluded that the newly developed RT-qPCR assay can be used as a sensitive detection tool for hRSV-A.
Assuntos
Reação em Cadeia da Polimerase em Tempo Real , Infecções por Vírus Respiratório Sincicial/diagnóstico , Vírus Sincicial Respiratório Humano/isolamento & purificação , Proteínas Virais/isolamento & purificação , Criança , Pré-Escolar , Feminino , Humanos , Lactente , Masculino , RNA Viral/genética , Infecções por Vírus Respiratório Sincicial/genética , Infecções por Vírus Respiratório Sincicial/virologia , Vírus Sincicial Respiratório Humano/genética , Vírus Sincicial Respiratório Humano/patogenicidade , Arábia Saudita , Carga Viral/genética , Proteínas Virais/genéticaRESUMO
Group A rotavirus is responsible for inducing severe diarrhea in young children worldwide. Rotavirus vaccines are used to control the disease in many countries. In the current study, the sequences of human rotavirus G and P types in Saudi Arabia are reported and compared to different relevant published sequences. In addition, the VP4 and VP7 genes of the G1P[8] strains are compared to different antigenic epitopes of the rotavirus vaccines. Stool samples were collected from children under 2 years suffering from severe diarrhea. Screening of the rotavirus-positive samples was performed with rapid antigen detection kit. RNA was amplified from rotavirus-positive samples by reverse transcriptase polymerase chain reaction assay for both VP4 and VP7 genes. Direct sequencing of the VP4 and VP7 genes was conducted and the obtained sequences were compared to each other and to the rotavirus vaccines. Both G1P[8] G1P[4] genotypes were detected. Phylogenetic analysis revealed that the detected strains belong to G1 lineage 1 and 2, P[8] lineage 3, and to P[4] lineage 5. Multiple amino acid substitutions were detected between the Saudi RVA strains and the commonly used vaccines. The current findings emphasize the importance of the continuous surveillance of the circulating rotavirus strains, which is crucial for monitoring virus evolution and helping in predicting the protection level afforded by rotavirus vaccines.
Assuntos
Antígenos Virais/genética , Proteínas do Capsídeo/genética , RNA Viral/química , Rotavirus/genética , Sequência de Bases , Diarreia/virologia , Fezes/virologia , Variação Genética/genética , Humanos , Lactente , Dados de Sequência Molecular , Filogenia , RNA Viral/isolamento & purificação , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Rotavirus/classificação , Infecções por Rotavirus/epidemiologia , Infecções por Rotavirus/prevenção & controle , Infecções por Rotavirus/virologia , Vacinas contra Rotavirus , Arábia Saudita/epidemiologia , Especificidade da EspécieRESUMO
Human bocavirus (HBoV) was recently discovered in children with respiratory distress and/or diarrhea. To our knowledge, no previous study has reported the existence of bocavirus in Saudi Arabia. Swabs samples from 80 children with respiratory tract infections were examined for the presence of HBoV. Real-time polymerase chain reaction was used as a sensitive method to detect the HBoV. Direct gene sequencing was used to determine the genotype of the detected virus isolates. HBoV was detected in 22.5% of the examined patients. The NP1 partial gene sequence from all patients showed that the circulated strains were related to HBoV-1 genotype. Most of HBoV infected patients showed evidence of mixed coinfection with other viral pathogens. The current study clearly demonstrated that genetically conserved HBoV1 circulates in Saudi Arabia. Interestingly, most of the HBoV1 infected cases were associated with high rates of co-infections with other viruses.