Reduced accumulation of defective viral genomes contributes to severe outcome in influenza virus infected patients

Abstract

Influenza A virus (IAV) infection can be severe or even lethal in toddlers, the elderly and patients with certain medical conditions. Infection of apparently healthy individuals nonetheless accounts for many severe disease cases and deaths, suggesting that viruses with increased pathogenicity co-circulate with pandemic or epidemic viruses. Looking for potential virulence factors, we have identified a polymerase PA D529N mutation detected in a fatal IAV case, whose introduction into two different recombinant virus backbones, led to reduced defective viral genomes (DVGs) production. This mutation conferred low induction of antiviral response in infected cells and increased pathogenesis in mice. To analyze the association between low DVGs production and pathogenesis in humans, we performed a genomic analysis of viruses isolated from a cohort of previously healthy individuals who suffered highly severe IAV infection requiring admission to Intensive Care Unit and patients with fatal outcome who additionally showed underlying medical conditions. These viruses were compared with those isolated from a cohort of mild IAV patients. Viruses with fewer DVGs accumulation were observed in patients with highly severe/fatal outcome than in those with mild disease, suggesting that low DVGs abundance constitutes a new virulence pathogenic marker in humans.

Defective viral genomes are key drivers of the virus–host interaction

“…In addition, during influenza virus infection, variations in the elongation capacity of the polymerase associate with differential generation of DVGs 64 . A role for the polymerase multimerization activity was also recently proposed as a driver of DVG generation during influenza virus infection 62 . Viral proteins implicated in the regulation of viral transcription and replication are also associated with the generation of DVGs.…”

“…In mice infected with the respiratory viruses SeV, influenza or RSV, IFNs and pro-inflammatory cytokines are strongly induced only after DVGs have accumulated to detectable levels 54,55 . Detection of DVGs in respiratory secretions of children infected with RSV correlates with expression of antiviral genes 55 , and highly pathogenic influenza virus isolates that fail to induce potent antiviral responses in humans have an impaired ability to generate DVGs 62 .…”

Single-cell analysis of upper airway cells reveals host-viral dynamics in influenza infected adults

“…IAV and IBV genomes each contain eight segments, with some segments encoding more than one protein through alternative splicing, some of which disrupt interferon production of the host cell (Garfinkel and Katze, 1993;Kochs et al, 2007a). Success in expressing all eight influenza genome segments in a cell is critical for reproductive infection for both IAV and IBV (Sheng et al, 2018;Vasilijevic et al, 2017). An expression hierarchy of M>NS>>NP>NA>HA>>PB2~PB1~PA was reported by previous in vitro single cell transcriptome 05 studies in IAV-infected A549 cells and by bulk measurements of IAV-infected MDCK cells (Hatada et al, 1989;Russell et al, 2018).…”

“…It is unclear whether this expression pattern holds true in vivo. Viruses lacking one or more segments have a higher chance of being recognized by the host (Vasilijevic et al, 2017). IAV deficient in the segment NS has been associated with higher antiviral response in vitro (Russell et al, 2019a).…”

A specific sequence in the genome of respiratory syncytial virus regulates the generation of copy-back defective viral genomes

“…However, the development of DVG specific PCR and next-generation deep sequencing has allowed for DVG identification in samples from patients infected with various viruses including dengue, influenza A, and respiratory syncytial virus (RSV) [11][12][13] . DVGs potentiate the host innate immune response and attenuate infection in animal models 6,[13][14][15][16] . Importantly, naturally generated DVGs correlate with stronger antiviral responses in RSV-infected patients 13 , as well as with reduced disease severity in influenza-infected patients 15 .…”