Intra-herd genetic variability of the A/Argentina/2001 foot-and-mouth disease virus.

MARCELO GÖTTE; ANDRÉS PEREZ; GUSTAVO SEBASTIÁN CABANNE; ENRIQUE LAGO; GUIDO KÖNIG

Arusha

Workshop; 2013 GFRA Scientific Workshop; 2013

Foot-and-mouth disease virus (FMDV) genetic variability has been extensively assessed. However, most of the studies have been aimed at quantifying the genetic variation between FMD outbreaks or, alternative, assess the variability in vitro. Here, we quantified the variability of the FMDV within naturally infected herds and assessed the effect of such variability in the outcomes of a phylogenetic analysis. We selected eight herd-outbreaks naturally infected in Argentina during 2001, for which two to four tissue samples from different animals were available. Sampled herd-outbreaks were located in different locations, namely, Balcarce, General Guido, and Mercedes in Buenos Aires province; Goya and Monte Caseros in Corrientes province; Paraná in Entre Ríos province; Vera in Santa Fe province; and San Miguel de Tucumán, in Tucumán province. The FMDV, was inactivated and RT-PCR were performed in order to amplify the complete genome in seven 0.4-2.0 Kb-long PCR fragments. An automated Sanger method was used for sequencing, obtaining a mean coverage of 3.75X. Finally, 22 complete genome sequences were obtained from the 8 herd-outbreaks and used for the analysis of the Intra-herd variability (IH). Additionally, two others datasets obtained previously from the 2001 Argentinean epidemic, containing 21 genome sequences from different outbreaks on one single location (Mar Chiquita), and 24 genome sequences from different locations in Argentina were used to assess the intra-location (IL) and intra-epidemic (IE) variability of the virus. Pair-wise differences in the IH and IE genetic variation were assessed using AMOVA tests. Significant differences (FST > 0,67) were found between these groups. We also analyzed the tree topology created with three different methodologies (Neighbor Joining, Maximum Likelihood, and Maximum Parsimony) combining the three datasets. All samples in each group clustered together without mixing with any other group. Moreover, random selection of only one sequence from each outbreak to build the tree did not affect the tree topology. In conclusion, analysis of multiple samples collected from single outbreaks did not modify the prediction obtained when one single sample was collected and sequenced. For that reason, one single sample may be sufficient to quantify the variation of the strain assessed here; note, however, that such statement may not be true for virus strains or epidemiological conditions different to those assessed here, which limits the generalizability of our findings.