Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites

Examples of MBCS insertions in HPAI viruses. (A) Substitutions and duplications of Arg codons in the HA RNA from HPAI strain A/chicken/Netherlands/1/03 (H7N7) as compared to closely related HA RNA from LPAI virus A/mallard/Netherlands/12/2000(H7N3) (Fouchier et al. 2004). (B) Substitution creating the MBCS site of A/chicken/TX/298313/2004(H5N2) as compared to LPAI strain A/chicken/Texas/167280-4/2002(H5N3) (Lee et al. 2005). (C) Recombination of HA RNA with 28S rRNA leading to the insertion of nine codons in the HPAI virus A/chicken/Tennessee/17-007147-2/2017(H7N9) as compared to related LPAI strain A/chicken/Tennessee/17-007431-3/2017(H7N9) (Lee et al. 2017). Inserted or mutated nucleotides are in red, locations of HA0 cleavage sites are shown by arrows.