Mechanisms of G-gene heterogeneities and a new method of genotyping of human metapneumovirus

Human metapneumovirus (HMPV) is similar to AMPV and HRSV single-stranded RNA viruses. Controversy of HMPV G-gene heterogeneities due to duplication, deletion, recombination and termination codon mutation (TCM) complicated genotyping of a HMPV virus since 2015. Analysis of G-proteins from complete genomes suggested [~]88% sequence homology between A and B genotypes and still sub-genotyping possible. From extensive multi-alignment studies, we concluded that the G-gene (219aa) of HMPV A-genotype (MZ504961, LC671558) was duplicated 180nt first producing G-gene with 279aa protein of A1-genotype (OL794403, OP904094,) and then 69nt deletion occurred generating G-protein with 256aa protein of A2-genotype (OP904007, MZ851793). The few amino acids lower or higher A-genotype G-proteins like 265aa (LC769214), 261aa (PV052163), 254aa (MN745086), 236aa (KC403976), 228 (KJ627377), 222aa (AY327804), 217aa (OP904044) and 194aa (OL794386) are known due to generation of TCM. The destruction of termination codon (TC) used downstream alternate termination codon (ATC) extending few AAs but generation of new TC upstream produced short length G-proteins. The 228aa G protein was produced from 219aa lineage due to TCM and used ATC. The 254aa G-protein was generated from 256aaG lineage due to early TCM (CAA=TAA; C6870T). While 261aa G-protein was generated due to TCM (TAG=CAG) and used second ATC (TAA). The generation of B-genotype of HMPV occurred due to deletion as well as extensive editing to produce 236-242aa or smaller G-proteins [224aa (OL794406), 231aa (MZ504963), 233aa (MK989732), 236aa (KC562228), 237aa (MZ504966), 238aa (KC403971), 241aa (LC769218) and 242aa (KC562242)] but B-genotypes with 219aa, 256aa or 279aa lengths G-protein were not detected. The 236aa length G-protein found in both A-genotype and B-genotype as early as 1982. The 236aa A-genotype G-protein had different C-terminal sequence than 219aaG A-genotype, 256aaG A2-genotype and 279aaG A1-genotype. Thus, we concluded 236aaG clone might be primitive HMPV lineage. We observed G-protein of A -genotype likely ended with STMQK while B-genotype 236aa G-protein ended with YNQTS. The G-protein of B1-genotype preferred HTGISPK at the carboxy-end while B2-genotype ended with SSLSS. However, mutational difference was quite high between two 219aaG or 256aaG genotypes isolated 5-10 years gap. We suggested that a new genotype method like A.236.1.US.1, A.219.1.IN.1, A2.256.1.CN.1 or A1.279.1.JP.1. This is first bioinformatics worldwide analysis of HMPV WGS sequences suggesting a new method of genotyping and compared with very neglected Indian scenario.