Genetic diversity, seasonality and transmission network of human metapneumovirus: identification of a unique sub-lineage of the fusion and attachment genes

Abstract

Human metapneumovirus (HMPV) is an important viral respiratory pathogen worldwide. Current knowledge regarding the genetic diversity, seasonality and transmission dynamics of HMPV among adults and children living in tropical climate remains limited. HMPV prevailed at 2.2% (n = 86/3,935) among individuals presented with acute respiratory tract infections in Kuala Lumpur, Malaysia between 2012 and 2014. Seasonal peaks were observed during the northeast monsoon season (November–April) and correlated with higher relative humidity and number of rainy days (P < 0.05). Phylogenetic analysis of the fusion and attachment genes identified the co-circulation of three known HMPV sub-lineages, A2b and B1 (30.2% each, 26/86) and B2 (20.9%, 18/86), with genotype shift from sub-lineage B1 to A2b observed in 2013. Interestingly, a previously unrecognized sub-lineage of A2 was identified in 18.6% (16/86) of the population. Using a custom script for network construction based on the TN93 pairwise genetic distance, we identified up to nine HMPV transmission clusters circulating as multiple sub-epidemics. Although no apparent major outbreak was observed, the increased frequency of transmission clusters (dyads) during seasonal peaks suggests the potential roles of transmission clusters in driving the spread of HMPV. Our findings provide essential information for therapeutic research, prevention strategies, and disease outbreak monitoring of HMPV.

Genetic characterization of human metapneumovirus identified through community and facility‐based surveillance of infants in Dhaka, Bangladesh

“…There were no A1, A2a, or B2 sublineages identified in the study population. A similar genetic diversity of hMPV was found in other countries in Asia . A study in France showed that hMPV genotype distribution shifted over time .…”

“…To investigate the genetic diversity of hMPV strains, the nucleotide sequences of the N and F gene fragments were analyzed. A number of previous studies also identified the genetic diversity of hMPV through considering the nucleotide fragment of F and N genes . F gene corresponds to the fusion protein (F protein), which is a surface glycoprotein.…”

“…A2b, initially considered as a novel sublineage that was first reported in 2006, in Germany, using the samples that were collected during 2002 and 2004 . Another unique clade of hMPV, which was also considered as novel clade, was reported from the sample collected in between 2006‐14 in different countries including Vietnam, Cambodia, China, Malaysia, Japan, Germany, Turkey, and Croatia . This unique clade of hMPV has seemingly become a seasonal strain and thus it is most appropriate to no longer consider it as a novel strain.…”

“…This unique clade of hMPV has seemingly become a seasonal strain and thus it is most appropriate to no longer consider it as a novel strain. Different epidemiological studies named the clade as sublineage A2c . Multiple different strains of hMPV typically cocirculate and their relative distribution varies both within and between communities .…”

Genetic Variability and Sequence Relatedness of Matrix Protein in Viruses of the Families Paramyxoviridae and Pneumoviridae

“…Despite a conservative nature of M protein, there were still substitutions that could separate major genotypes in both viruses, and there was even 1 substitution in HMPV M proteins that could distinguish a recently discovered A2c subgroup [26, 49] from the other 2 subgroups. This was unexpected, as such substitutions were previously only present in G proteins, for which extensive variations are probably the result of immunogenic pressure in a similar manner as was postulated for HRSV [50].…”