Evolution of enhanced innate immune suppression by SARS-CoV-2 Omicron subvariants.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) human adaptation resulted in distinct lineages with enhanced transmissibility called variants of concern (VOCs). Omicron is the first VOC to evolve distinct globally dominant subvariants. Here we compared their replication in human cell lines and primary airway cultures and measured host responses to infection. We discovered that subvariants BA.4 and BA.5 have improved their suppression of innate immunity when compared with earlier subvariants BA.1 and BA.2. Similarly, more recent subvariants (BA.2.75 and XBB lineages) also triggered reduced innate immune activation. This correlated with increased expression of viral innate antagonists Orf6 and nucleocapsid, reminiscent of VOCs Alpha to Delta. Increased Orf6 levels suppressed host innate responses to infection by decreasing IRF3 and STAT1 signalling measured by transcription factor phosphorylation and nuclear translocation. Our data suggest that convergent evolution of enhanced innate immune antagonist expression is a common pathway of human adaptation and link Omicron subvariant dominance to improved innate immune evasion.

Use of an internal standard in a TaqMan nested reverse transcription-polymerase chain reaction for the detection of bovine viral diarrhoea virus.

The aim of this study was to improve molecular methods for the detection of bovine viral diarrhoea virus (BVDV). A single-tube nested reverse-transcriptase polymerase chain reaction (nRT-PCR) employing the 5'-3'-exonuclease assay (TaqMan) system was optimised for use with bulk milk, semen and whole blood samples. An artificial template (mimic) was engineered to provide in-tube validation of negative samples by demonstrating the absence of substances inhibitory to RT or PCR. This mimic was constructed by disrupting the BVDV amplicon at the TaqMan probe site by inserting a 295bp fragment of human genomic DNA. The mimic amplicon was discriminated from the BVDV RT-PCR products using a second TaqMan probe, with a different fluorochrome specific for the inserted DNA. This new method was more sensitive than BVDV antigen ELISA methods and the existing RT-PCR method used in the laboratory for detection of BVDV in bulk milk. Furthermore, RNA extracted by robotic methods has proved suitable for use in this assay. This TaqMan nRT-PCR will be a valuable method for the detection of BVDV in a variety of biological matrices including milk and semen.

Classical swine fever virus induces proinflammatory cytokines and tissue factor expression and inhibits apoptosis and interferon synthesis during the establishment of long-term infection of porcine vascular endothelial cells.

Infection with virulent strains of classical swine fever virus (CSFV) results in an acute haemorrhagic disease of pigs, characterized by disseminated intravascular coagulation, thrombocytopenia and immunosuppression, whereas for less virulent isolates infection can become chronic. In view of the haemorrhagic pathology of the disease, the effects of the virus on vascular endothelial cells was studied by using relative quantitative PCR and ELISA. Following infection, there was an initial and short-lived increase in the transcript levels of the proinflammatory cytokines interleukins 1, 6 and 8 at 3 h followed by a second more sustained increase 24 h post-infection. Transcription levels for the coagulation factor, tissue factor and vascular endothelial cell growth factor involved in endothelial cell permeability were also increased. Increases in these factors correlated with activation of the transcription factor NF-kappaB. Interestingly, the virus produced a chronic infection of endothelial cells and infected cells were unable to produce type I interferon. Infected cells were also protected from apoptosis induced by synthetic ouble-stranded RNA. These results demonstrate that, in common with the related pestivirus bovine viral diarrhoea virus, CSFV can actively block anti-viral and apoptotic responses and this may contribute to virus persistence. They also point to a central role for infection of vascular endothelial cells during the pathogenesis of the disease, where a proinflammatory and procoagulant endothelium induced by the virus may disrupt the haemostatic balance and lead to the coagulation and thrombosis seen in acute disease.