1A). For the A-Iran-05 strain, viruses isolated in early years reacted well with check details A22/Iraq anti-sera, whereas isolates after 2006 exhibited lower reactivity (Fig. 1C). Most of these viruses exhibited higher cross-reactivity with the newer A/TUR/2006

vaccine antisera. However, viruses from Iran, Pakistan and Turkey belonging to sub-lineages BAR-08 and ARD-07 exhibited lower cross-reactivity with the A/TUR/2006 antisera (Fig. 1C). The complete capsid sequence of 57 serotype A viruses generated in this study were 2205 nt long except A/IRQ/108/2002 (A-Iran-96 strain) that had a 3-nt deletion at position 1984–1986 of P1, resulting in deletion of an aa at position VP1-138 in the G–H loop which has been reported to be a dominant antigenic site [4]. When compared to the sequence of the A22/Iraq v/s there was 17.0–20.6% nt variation between these viruses: A/IRN/03/96 sharing the closest

nt identity and A/IRN/45/2011 being the most variable. Analysis of the capsid aa sequences revealed 6.1–18.1% variation, A/IRN/30/2005 and A/IRN/05/2006 having the closest, and A/IRN/45/2011 having the lowest aa identity, respectively. Similarly, when compared to the capsid sequence of the A/TUR/2006 v/s, the nt variability was found to vary from 0.8 (A/TUR/02/2006) to 19.3% (A/TUR/04/2003) with a 0.5 (A/IRN/07/2006) to 9.1% (A/TUR/04/2003) variation at the aa level. Phylogenetic analysis CHIR 99021 of the capsid sequences revealed all the viruses Idoxuridine belong to the ASIA topotype

within serotype A FMDV. The viruses isolated from 2004 onwards formed a new genetic strain, A-Iran-05, distinct from previous virus strains reported to be present in the region, similar to an earlier report [10]. Various sub-lineages within the A-Iran-05 strain have been defined based on the analysis of VP1 sequences. The samples used in this study included 9 samples from BAR-08, 11 from AFG-07, 4 from ARD-07 and one each from ESF-10, FAR-09, QAZ-11 and EZM-07 (Supplementary table). The sub-lineages, BAR-08 and AFG-07 shared a common ancestor which evolved into two distinct sub-lineages over time, whereas most of the contemporary viruses gradually died out. A/IRN/78/2009 belongs to sub-lineage FAR-09 that has evolved from the AFG-07 sub-lineage, and is currently circulating in the region. A/AFG/12/2011 has not been assigned a sub-lineage yet, however, shares a common ancestor (AFG-07 sub-lineage) with A/IRN/78/2009. This pattern is also consistent with that observed when phylogenetic trees are drawn using only VP1 sequences (data not shown). Additional phylogenetic analysis of seven A-Iran-05 isolates from Pakistan and Afghanistan [13] revealed that the isolates belonging to AFG-07 or BAR-08 sub-lineages cluster with sequences of viruses from the same sub-lineage used in this study (data not shown).