Genetic heterogeneity in the leader and P1-coding regions of foot-and-mouth disease virus serotypes A and O in Africa

Abstract

Genetic information regarding the leader (L) and complete capsid-coding (P1) region of FMD serotype A and O viruses prevalent on the African continent is lacking. Here, we present the complete L-P1 sequences for eight serotype A and nine serotype O viruses recovered from FMDV outbreaks in East and West Africa over the last 33 years. Phylogenetic analysis of the P1 and capsid-coding regions revealed that the African isolates grouped according to serotype, and certain clusters were indicative of transboundary as well as intra-regional spread of the virus. However, similar analysis of the L region revealed random groupings of isolates from serotypes O and A. Comparisons between the phylogenetic trees derived from the structural coding regions and the L region pointed to a possibility of genetic recombination. The intertypic nucleotide and amino acid variation of all the isolates in this study supported results from previous studies where the externally located 1D was the most variable whilst the internally located 1A was the most conserved, which likely reflects the selective pressures on these proteins. Amino acids identified previously as important for FMDV structure and functioning were found to be highly conserved. The information gained from this study will contribute to the construction of structurally designed FMDV vaccines in Africa.Electronic supplementary materialThe online version of this article (doi:10.1007/s00705-013-1838-9) contains supplementary material, which is available to authorized users.

Genomics and outbreaks: foot and mouth disease

“…Recombination events are rarely observed in the capsid proteins (46), and are more frequently observed in the nonstructural coding regions (105). Studies with field isolates have also reported these observations through the analysis of WGS, confirming these observations with several serotypes, including A and Asia 1 (18,40,60), and reconfirming that the non-structural regions are more likely to be involved in recombination events, particularly in regions where cocirculation of the multiple serotypes and/or topotypes is present.…”

“…One of the most important applications for FMDV nucleotide sequence data has been in the field of molecular epidemiology (7), where phylogenetic comparisons of VP1 sequence data are widely and routinely used to monitor outbreaks (13,14,15,16). Although VP1 has become the most commonly used and robust genetic marker for outbreak tracing, other studies have also focused on the phylogenetic analysis of other FMDV genomic regions (17,18,19). Phylogenetic analysis of VP1 can be applied to categorise field strains into discrete topotypes and lineages which, despite the tendency for the virus to spread, frequently show geographical clustering based on the historical distribution of the virus (20).…”

Genetic and immunologic relationships between vaccine and field strains for vaccine selection of type A foot-and-mouth disease virus circulating in East Asia

“…2) except for VP2 134. [14]. The coloration represents topotype-specific sites in the axes of viral surfaces.…”

“…The VP1 with antigenic site 1 (twofold axis, 135-163 amino acids [aa]), site 2 (threefold axis, 193-213 aa), and site 4 (fivefold axis, 167-178 aa); VP2 with antigenic site 3 (twofold axis, 79-88 aa; threefold axis, 188-198 aa); and VP3 with antigenic site 5 (threefold axis, 58-72 aa) and site 3 (threefold axis, 132-142 aa) were analyzed for similarity rates with the full amino acid sequence of each structural viral protein [14].…”

“…Type A FMD virus consists of five antigenic sites [14], and we analyzed the key antigenic sites 1, 2, and 4 (the most important among VP1, VP2, and VP3) of VP1 (Fig. 2) Fig.…”