Gultyaev Alexander P, Richard Mathilde, Spronken Monique I, Olsthoorn René C L, Fouchier Ron A M
Department of Viroscience, Erasmus Medical Center, Dr. Molewaterplein 40, 3015 GD Rotterdam, The Netherlands.
Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, PO Box 9512, 2300 RA Leiden, The Netherlands.
Virus Evol. 2019 Aug 21;5(2):vez034. doi: 10.1093/ve/vez034. eCollection 2019 Jul.
The acquisition of a multibasic cleavage site (MBCS) in the hemagglutinin (HA) glycoprotein is the main determinant of the conversion of low pathogenic avian influenza viruses into highly pathogenic strains, facilitating HA cleavage and virus replication in a broader range of host cells. In nature, substitutions or insertions in HA RNA genomic segments that code for multiple basic amino acids have been observed only in the HA genes of two out of sixteen subtypes circulating in birds, H5 and H7. Given the compatibility of MBCS motifs with HA proteins of numerous subtypes, this selectivity was hypothesized to be determined by the existence of specific motifs in HA RNA, in particular structured domains. In H5 and H7 HA RNAs, predictions of such domains have yielded alternative conserved stem-loop structures with the cleavage site codons in the hairpin loops. Here, potential RNA secondary structures were analyzed in the cleavage site regions of HA segments of influenza viruses of different types and subtypes. H5- and H7-like stem-loop structures were found in all known influenza A virus subtypes and in influenza B and C viruses with homology modeling. Nucleotide covariations supported this conservation to be determined by RNA structural constraints that are stronger in the domain-closing bottom stems as compared to apical parts. The structured character of this region in (sub-)types other than H5 and H7 indicates its functional importance beyond the ability to evolve toward an MBCS responsible for a highly pathogenic phenotype.
血凝素（HA）糖蛋白中多碱性裂解位点（MBCS）的获得是低致病性禽流感病毒转变为高致病性毒株的主要决定因素，它促进了HA的裂解以及病毒在更广泛宿主细胞中的复制。在自然界中，编码多个碱性氨基酸的HA RNA基因组片段中的替换或插入仅在鸟类中传播的16种亚型中的两种，即H5和H7的HA基因中被观察到。鉴于MBCS基序与众多亚型的HA蛋白具有兼容性，这种选择性被推测是由HA RNA中特定基序的存在所决定的，尤其是结构域。在H5和H7 HA RNA中，对这些结构域的预测产生了替代的保守茎环结构，其裂解位点密码子位于发夹环中。在此，对不同类型和亚型流感病毒HA片段裂解位点区域的潜在RNA二级结构进行了分析。通过同源建模，在所有已知的甲型流感病毒亚型以及乙型和丙型流感病毒中发现了类似H5和H7的茎环结构。核苷酸共变支持这种保守性是由RNA结构限制所决定的，与顶端部分相比，在结构域封闭的底部茎中这种限制更强。除H5和H7之外的（亚）型中该区域的结构化特征表明，其功能重要性不仅仅在于向负责高致病性表型的MBCS进化的能力。
