Detection of H3N8 influenza A virus with multiple mammalian-adaptive mutations in a rescued Grey seal (Halichoerus grypus) pup

Abstract

Avian influenza A viruses (IAVs) in different species of seals display a spectrum of pathogenicity, from sub-clinical infection to mass mortality events. Here we present an investigation of avian IAV infection in a 3- to 4-month-old Grey seal (Halichoerus grypus) pup, rescued from St Michael’s Mount, Cornwall in 2017. The pup underwent medical treatment but died after two weeks; post-mortem examination and histology indicated sepsis as the cause of death. IAV NP antigen was detected by immunohistochemistry in the nasal mucosa, and sensitive real-time reverse transcription polymerase chain reaction assays detected trace amounts of viral RNA within the lower respiratory tract, suggesting that the infection may have been cleared naturally. IAV prevalence among Grey seals may therefore be underestimated. Moreover, contact with humans during the rescue raised concerns about potential zoonotic risk. Nucleotide sequencing revealed the virus to be of subtype H3N8. Combining a GISAID database BLAST search and time-scaled phylogenetic analyses, we inferred that the seal virus originated from an unsampled, locally circulating (in Northern Europe) viruses, likely from wild Anseriformes. From examining the protein alignments, we found several residue changes in the seal virus that did not occur in the bird viruses, including D701N in the PB2 segment, a rare mutation, and a hallmark of mammalian adaptation of bird viruses. IAVs of H3N8 subtype have been noted for their particular ability to cross the species barrier and cause productive infections, including historical records suggesting that they may have caused the 1889 pandemic. Therefore, infections such as the one we report here may be of interest to pandemic surveillance and risk and help us better understand the determinants and drivers of mammalian adaptation in influenza.

A universal RT-qPCR assay for “One Health” detection of influenza A viruses

“…This small concern warrants the ongoing assessment of primers and probe sequences in silico in order to monitor for any sustained mutational trends in this region. Nevertheless, the assay’s high inclusivity for various species combined with high sensitivity predestines the SVIP-MPv2 as a universal IAV screening tool, not only for the One Health species, but also for minor or occasional mammalian hosts which merit investigation as a risk for zoonotic infection [ 65 , 66 ]. The careful design of the SVIP-MPv2 assay has taken into account the long term evolutionary trends which continue within conserved genes such as MP1, so reducing the need for future modifications or adjustments which were required for the assay of Spackman et al, [ 16 ] to provide detection of pandemic H1N1 viruses in swine [ 36 ] or H5 HPAI viruses in wild and domestic birds [ 23 , 67 , 68 ].…”

Comparison of Clinical Features and Outcomes of Medically Attended COVID-19 and Influenza Patients in a Defined Population in the 2020 Respiratory Virus Season

“…Several adaptation mutations have been identified in different segments of influenza A virus, and thoroughly researched mutations, including E627K and D701N on PB2 of avian flu virus and other subtypes, promote polymerase activity and adaption to act cooperatively with humans ( 52 , 53 ). Adaptive mutations in SARS-COV-2 have also been reported, and the most important mutation in spike is D614G, which has attracted global attention ( 54 , 55 ).…”

A universal RT-qPCR assay for “One Health” detection of influenza A viruses

“…This small concern warrants the ongoing assessment of primers and probe sequences in silico in order to monitor for any sustained mutational trends in this region. Nevertheless, the assay's high inclusivity for various species combined with high sensitivity predestines the SVIP-MPv2 as a universal IAV screening tool, not only for the One Health species, but also for minor or occasional mammalian hosts which merit investigation as a risk for zoonotic infection [65,66]. The careful design of the SVIP-MPv2 assay has taken into account the long term evolutionary trends which continue within conserved genes such as MP1, so reducing the need for future modifications or adjustments which were required for the assay of Spackman et al, [16] to provide detection of pandemic H1N1 viruses in swine [36] or H5 HPAI viruses in wild and domestic birds [23,67,68].…”