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

Figures

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  FIGURE 1.. 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.

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  FIGURE 2.. Recombination of the influenza virus H7 HA RNA with host RNAs. (A–E) The insertions in the HA segments created by recombination with 28S rRNA and the binding sites of snoRNAs near the recombination sites. The HA RNA sequences from HPAI strains (Khatchikian et al. 1989; Banks et al. 2001; Berhane et al. 2009; Iglesias et al. 2010; Maurer-Stroh et al. 2013; Lee et al. 2017; Beerens et al. 2020) are aligned to HA sequences of most closely related LPAI viruses. The apical stem between two parts of the SNORA22 antisense element is shown schematically. (F) The 12-nt sequence inserted in the Italian H7N1 (1999) and Dutch H7N3 (2003) HPAI strains is complementary to the region encompassing anticodon of chicken tRNA-Val. Base pairs of the tRNA-Val anticodon stem are shown with bracket view. Anticodon nucleotides are underlined. Chicken tRNA-Val is aligned to human tRNA-Met in order to illustrate the location of the C/D box snoRNA binding site in the tRNA-Met (Vitali and Kiss 2019). Inserted sequences and their complements in 28S rRNA and tRNA are shown in red. Locations between the codons for conserved amino acids Arg and Gly, corresponding to the HA0 polyprotein cleavage sites, are…

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  FIGURE 3.. MBCS amino acid sequences in H7 HA RNAs yielded by recombination (Khatchikian et al. 1989; Orlich et al. 1994; Banks et al. 2001; Hirst et al. 2004; Suarez et al. 2004; Berhane et al. 2009; Iglesias et al. 2010; Maurer-Stroh et al. 2013; Lee et al. 2017; Beerens et al. 2020). Amino acids at eight positions upstream of the cleavage site (P1–P8) which could affect cleavage by furin-like proteases (Duckert et al. 2004) are shown, inserted amino acids are underlined. Important basic residues at positions P1, P2, P4, and P6 are highlighted, cleavage site is shown by arrow. For strain abbreviations, see Materials and Methods.

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  FIGURE 4.. Putative snoRNA binding at the recombination sites of HA RNAs with other influenza A virus segments. The sequences of NP and M segments involved in the recombination are from the LPAI progenitors: (A) Orlich et al. (1994); (B) Suarez et al. (2004); (C) Hirst et al. (2004). Chicken orphan H/ACA snoRNA GGoACA5 has been identified by Shao et al. (2009). Notations are similar to those in Figure 2.