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Phylogenetic analysis revealed that the NM strain was closely related to the reference strains isolated from America, which belong to the A2 type. Homology comparison of nucleotides between the NM strain and reference strains showed that the sequence homology of gag and env were 77.1%-86.8% and 67.7%-75.5%, respectively. Sequence analysis indicated that its whole-genome length is 9193 bp. Therefore, in this study, we conducted next-generation sequencing on an MVV strain obtained from northwest China to reveal its genetic evolution via phylogenetic analysis.Ī MVV strain obtained from Inner Mongolia (NM) of China was identified.
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In China, MVV has been detected in several regions, but its molecular characteristics and genetic variations were not thoroughly investigated. Maedi/Visna virus (MVV) is a contagious viral pathogen that causes considerable economic losses to the sheep industry worldwide. Understanding how these different viruses present clinically and influence oral health will advance our understanding of multifactorial oral diseases and their association with viruses. The emergence of a recent pathogen SARS-CoV-2 and its tropism for salivary and periodontal tissues further highlights the relevance of the oral cavity in host-pathogen interaction. This review presents a summary of major mammalian viruses and associated diseases in the human oral cavity. However, challenges in viral detection and the lack of reproducible in vitro and in vivo infection models have limited our progress in understanding viruses and their contribution to oral diseases. Human herpesviruses are the most extensively studied viruses in different oral inflammatory diseases. Recent investigations have demonstrated the abundance of certain viruses in oral inflammatory diseases, suggesting an association between viruses and disease. Therefore, understanding viral prevalence, pathogenicity, and preference regarding oral tissues is critical to understanding the holistic effects of viruses on oral infections. In the past, the discussion of microbiological aspects of oral disease has traditionally focused on bacteria and fungi, but viruses are attracting increasing attention as pathogens in oral inflammatory diseases. Given the exposed nature of the mouth, oral tissues constantly encounter infectious agents, forming a complex ecological community. The human oral cavity contains a plethora of habitats and tissue environments, such as teeth, tongue, and gingiva, which are home to a rich microbial flora including bacteria, fungi, and viruses. Next-generation sequencing with viral enrichment could be used to detect and characterise challenging samples when conventional workflows are insufficient. This is further supported by the persistence of EV-C104 in the patient, despite the clearance of other viral infections. We observed an increase in single-nucleotide variations between sample dates from a rapidly declining patient, suggesting mutations are weakly deleterious and have not been purged during selection. A chronic infection resulting in respiratory failure from a relatively rare enterovirus was observed in a transplant recipient. Although positive selection pressure was identified in the EV-C104 reference sequences, the genomes recovered from the patient samples alone showed an overall negative selection pressure in multiple codon sites along the genome. Phylodynamic analysis including ten available EV-C104 genomes, along with the patient sequences, estimated the most recent common ancestor to occur in the middle of 2005 with an overall estimated evolution rate of 2.97 × 10-3 substitutions per year. The recovered genomes clustered with a recently reported EV-C104 from Belgium in August 2018. Near-complete genomes of enterovirus C104 (EV-C104) were recovered in all respiratory samples but not in the faecal sample. Intra-host variant detection, using a Fixed Ploidy algorithm, and selection pressure, using a Fixed Effect Likelihood and a Mixed Effects Model of Evolution, were also used to explore the patient samples. Phylogenetic analysis was performed using a maximum likelihood method, along with a root-to-tip regression and time-scaled phylogenetic analysis to estimate evolutionary changes between sample dates. Long-read sequencing was performed using viral targeted sequence capture on four respiratory and one faecal sample. We aimed to identify the enterovirus genotype responsible for the infection and to determine potential evolutionary changes. This study describes a fatal case associated with a chronic untypeable enterovirus infection in an immunocompromised patient admitted to a Dutch university hospital over nine months. Chronic enterovirus infections can cause significant morbidity, particularly in immunocompromised patients.