The human body is inhabited by a diverse microbial community that is collectively coined as commensal microbiota. Recent research has greatly advanced our understanding of how the commensal microbiota affects host health. Among the various kinds of pathogenic infections of the host, viral infections constitute one of the most serious public health problems worldwide. During the infection process, viruses may have substantial and intimate interactions with the commensal microbiota. A plethora of evidence suggests that the commensal microbiota regulates and is in turn regulated by invading viruses through diverse mechanisms, thereby having stimulatory or suppressive roles in viral infections. Furthermore, the integrity of the commensal microbiota can be disturbed by invading viruses, causing dysbiosis in the host and further influencing virus infectivity. In the present article, we discuss current insights into the regulation of viral infection by the commensal microbiota. We also draw attention to the disruption of microbiota homeostasis by several viruses.

Parapoxvirus (PPV) has been identified in some mammals and poses a great threat to both the livestock production and public health. However, the prevalence and evolution of this virus are still not fully understood. Here, we performed an in silico analysis to investigate the genomic features and evolution of PPVs. We noticed that although there were significant differences of GC contents between orf virus (ORFV) and other three species of PPVs, all PPVs showed almost identical nucleotide bias, that is GC richness. The structural analysis of PPV genomes showed the divergence of different PPV species, which may be due to the specific adaptation to their natural hosts. Additionally, we estimated the phylogenetic diversity of seven different genes of PPV. According to all available sequences, our results suggested that during 2010–2018, ORFV was the dominant virus species under the selective pressure of the optimal gene patterns. Furthermore, we found the substitution rates ranged from 3.56 × 10−5 to 4.21 × 10−4 in different PPV segments, and the PPV VIR gene evolved at the highest substitution rate. In these seven protein-coding regions, purifying selection was the major evolutionary pressure, while the GIF and VIR genes suffered the greatest positive selection pressure. These results may provide useful knowledge on the virus genetic evolution from a new perspective which could help to create prevention and control strategies.

Orf is a zoonotic and highly contagious disease caused by Orf virus (ORFV) infection. Orf outbreaks in sheep and goats usually lead to high culling rate and mortality in newborn kids and lambs, posing a great threat to the development of goat and sheep industry. Human Orf occurs via direct contact with infected animals or fomites. While this disease is traditionally thought to spread through direct contact, whether other transmission routes exist remains unclear. Herein, we report the detection of ORFV in the saliva and milk of dairy goats without clinical Orf symptoms. Further analyses showed that these ORFV are infectious, as they can induce characteristic cytopathic changes in primary mammary and lip cells. Importantly, these ORFV can induce typical Orf lesions after inoculation in ORFV-free dairy goats. This is the first study showing that live, infectious ORFV can be isolated from the saliva and milk of asymptomatic goats, highlighting novel potential transmission routes of ORFV. These findings provide a novel idea for the prevention and control of Orf spread.