Molecular Comparisons of Full Length Metapneumovirus (MPV) Genomes, Including Newly Determined French AMPV-C and –D Isolates, Further Supports Possible Subclassification within the MPV Genus

Abstract

Four avian metapneumovirus (AMPV) subgroups (A–D) have been reported previously based on genetic and antigenic differences. However, until now full length sequences of the only known isolates of European subgroup C and subgroup D viruses (duck and turkey origin, respectively) have been unavailable. These full length sequences were determined and compared with other full length AMPV and human metapneumoviruses (HMPV) sequences reported previously, using phylogenetics, comparisons of nucleic and amino acid sequences and study of codon usage bias. Results confirmed that subgroup C viruses were more closely related to HMPV than they were to the other AMPV subgroups in the study. This was consistent with previous findings using partial genome sequences. Closer relationships between AMPV-A, B and D were also evident throughout the majority of results. Three metapneumovirus “clusters” HMPV, AMPV-C and AMPV-A, B and D were further supported by codon bias and phylogenetics. The data presented here together with those of previous studies describing antigenic relationships also between AMPV-A, B and D and between AMPV-C and HMPV may call for a subclassification of metapneumoviruses similar to that used for avian paramyxoviruses, grouping AMPV-A, B and D as type I metapneumoviruses and AMPV-C and HMPV as type II.

Single reaction, real time RT-PCR detection of all known avian and human metapneumoviruses

“…Metapneumoviruses are subdivided into avian and human strains although phylogenetic analysis have shown that the avian subgroup C viruses are more closely related to the human viruses than they are to the other avian viruses (A, B and D). For this reason it may be clearer to consider AMPV A, B and D as type I metapneumoviruses and AMPV C and HMPV as type II as has been previously suggested (Brown et al, 2014). The molecular relationships between HMPV and AMPV-C have led to the hypothesis that these viruses could be have been generated by a crossing of the species barrier (de Graaf et al, 2008).…”

A comparison of AMPV subtypes A and B full genomes, gene transcripts and proteins led to reverse-genetics systems rescuing both subtypes

“…The L gene transcription start sequences proved an exception and minigenome studies showed a reduced transcription efficiency (Edworthy & Easton, 2005), as might be expected for a gene coding a protein needed in smaller amounts. Surprisingly gene starts of the otherwise more distantly related subtype C viruses (Brown et al, 2014) like the subtype A viruses all used CCCUGUUCA, but again with the exception of the L gene. Clearly lack of gene start differences would mean that gene start differences would not preclude a subtype independent RG system for AMPV.…”

“…Comparison of complete genome sequences has shown that subtypes A, B and D are more related to each other than subtype C (Brown et al, 2014), and another comparison of subtypes A, B and C showed subtypes A and B to have the most similar genomes (Jacobs et al, 2003). Subtypes A and B also appear to be most similar in their species specificity and behaviours in the field, hence live subtype A and B vaccines have been employed largely interchangeably to control disease in commercial turkeys and chickens, albeit with an increasing bias toward subtype B. Cross-protection and antigenic studies have suggested that some protective and antigenic differences do exist (Collins et al, 1993;Cook et al, 1993;Van de Zande et al, 2000) and this highlighted the need for an RG system to enable the generation of improved live subtype B vaccines, as well as to understand other properties of this subtype.…”

Proteome Analysis in a Mammalian Cell Line Reveals that PLK2 Is Involved in Avian Metapneumovirus Type C (aMPV/C)-Induced Apoptosis

“…There are four subtypes of aMPV, termed A, B, C and D, which are based on genetic and antigenic differences [4]. There is a high similarity between subtype C aMPV and hMPV [5][6][7]. The infection of subtype C aMPV (aMPV/C) in Muscovy ducks has been reported in France and China [8,9] as well as in turkeys and wild birds in the USA [10], forming two distinct genetic lineages, one North American and the other Eurasian.…”