Influenza A virus infections are known to predispose infected individuals to bacterial infections of the respiratory tract that result in co-infection with severe disease outcomes. Co-infections involving influenza A viruses and streptococcus bacteria result in protein–protein interactions that can alter disease outcomes, promoting bacterial colonisation, immune evasion, and tissue damage. Focusing on the synergistic effects of proteins from different pathogens during co-infection, this scoping review evaluated evidence for protein–protein interactions between influenza A virus proteins and streptococcus bacterial proteins. Of the 2366 studies initially identified, only 32 satisfied all the inclusion criteria. Analysis of the 32 studies showed that viral and bacterial neuraminidases (including NanA, NanB and NanC) are key players in desialylating host cell receptors, promoting bacterial adherence and colonisation of the respiratory tract. Virus hemagglutinin modulates bacterial virulence factors, hence aiding bacterial internalisation. Pneumococcal surface proteins (PspA and PspK), bacterial M protein, and pneumolysin (PLY) enhance immune evasion during influenza co-infections thus altering disease severity. This review highlights the importance of understanding the interaction of viral and bacterial proteins during influenza virus infection, which could provide opportunities to mitigate the severity of secondary bacterial infections through synergistic mechanisms.

Respiratory viral-bacterial co-infections cause severe disease across species, yet the molecular mechanisms underlying enhanced pathogenesis remain poorly understood. This study characterised H3N8 equine influenza A virus (IAV) and Streptococcus equi subspecies zooepidemicus (SEZ) co-infections using complementary ultrastructural and transcriptomic approaches. Transmission electron microscopy demonstrated direct physical binding between spherical (A/equine/Miami/63) and filamentous (A/equine/Sussex/89 and A/equine/Newmarket/5/2003) IAV isolates and SEZ, including when SEZ was heat-inactivated (θSEZ). Lectin staining revealed that SEZ expresses predominantly α2,3-linked sialic acids, the receptor for equine IAV. However, virus-bacteria binding persisted despite neuraminidase treatment. Scanning electron microscopy quantification demonstrated that viral pre-infection significantly enhanced bacterial adherence to cells of the DH82α canine macrophage-like cell line (2-fold increase, p<0.01) but not ExtEqFL (equine lung-derived) cells, revealing cell-type-specific enhancement. RNA-sequencing analysis showed that bacterial infection drove most transcriptional changes during co-infection with little difference in the number of differentially expressed genes (DEGs) between infection with SEZ alone (146 DEGS) or after pre-infection with either A/equine/Sussex/89 (166 DEGS) or A/equine/Newmarket/5/2003 (149 DEGS). Validation of upregulation of selected cytokines by RT-qPCR and ELISA demonstrated that SEZ infection drives dramatic cytokine upregulation compared to mock or θSEZ controls. Viral pre-infection did not alter the SEZ-induced pro-inflammatory cytokine responses (IL-6, IL-8, TNF-α) but significantly reduced IFN-β expression compared to SEZ infection alone. These findings suggest that direct virus-bacteria physical interactions may drive cell-type-specific enhancement of bacterial colonisation, fundamentally advancing our understanding of respiratory co-infection pathogenesis.