Kinetics of Interferon gamma and Interleukin-21 response following foot and mouth disease virus infection.

Foot and mouth disease (FMD) is one of the most contagious diseases of cloven footed animals causing significant economic impediment in livestock production system. The immune response to FMD virus (FMDV) infection is regulated by a complex interplay between various cells, cytokines and other immune components. Based on the well established role of Interferon-gamma (IFN-γ) and Interleukin-21 (IL-21) in viral infections, this study aimed to determine expression level of these cytokines in clinically infected adults and calves; and the results were compared with those in the subclinically infected animals up to 120 days post outbreak (DPO) in a vaccinated cattle herd. The expression level of IFN-γ and IL-21 was assayed on 0, 7, 14, 28, 60, 90, and 120 DPO by enzyme linked immunosorbent assay (ELISA) with simultaneous assessment of FMDV structural protein-antibody titer against serotype 'O' by liquid phase blocking ELISA (LPBE) and nonstructural protein-antibody, a differential marker of infection, using r3AB3 indirect ELISA (r3AB3 I-ELISA). Although, the peak expression of IFN-γ was observed on 14 DPO across all categories of animals, the clinically infected animals registered a significant increase in IFN-γ level as compared to the subclinically infected population possibly due to the difference in the extent of virus replication and inflammation. The IL-21 level increased significantly during 14-28 DPO and highest expression was noticed on 28 DPO. The increase in the expression level of IFN-γ and IL-21 at 28 DPO correlated with the increase in antibody titer as determined by LPBE suggesting the role of these cytokines in augmenting immune response to FMDV infection.

Evidence of subclinical foot-and-mouth disease virus infection in young calves born from clinically recovered cow under natural condition.

Foot-and-mouth disease (FMD) is a highly contagious and economically important, transboundary viral disease of cloven-hoofed animals. It is known that an asymptomatic, persistent FMD virus (FMDV) infection may occur subsequent to acute or subclinical FMDV infection in adult ruminants. However, virus persistence in young calves has not been studied. In the current investigation, FMDV infection parameters were examined for calves born to FMD-clinically recovered cows (CRC), asymptomatic cows from infected herds (ASC) and cows from with no history of FMD (NHF). The study was conducted in natural condition after FMD outbreaks in two dairy herds in India. No calves described herein had any clinical signs of FMD. Six out of 12 calves born to CRC had detectable FMDV RNA in oesophageal-pharyngeal fluid consistent with asymptomatic FMDV infection. Three of the 12 calves of CRC group had seroreactivity against FMDV non-structural proteins. One calf had detectable FMDV RNA at two consecutive samplings at 2 months apart. However, infectious FMDV was not isolated from any calf in the study. None of the calves in the ASC or NHF groups had any evidence of FMDV infection. Overall, these data are consistent with earlier report on calves having been infected in utero. Further investigation of FMDV persistence in calves under controlled conditions may lead to greater understanding of the viral pathogenesis.

Capsid coding region diversity of re-emerging lineage C foot-and-mouth disease virus serotype Asia1 from India.

Foot-and-mouth disease virus (FMDV) serotype Asia1 was first reported in India in 1951, where three major genetic lineages (B, C and D) of this serotype have been described until now. In this study, the capsid protein coding region of serotype Asia1 viruses (n = 99) from India were analyzed, giving importance to the viruses circulating since 2007. All of the isolates (n = 50) recovered during 2007-2013 were found to group within the re-emerging cluster of lineage C (designated as sublineage C(R)). The evolutionary rate of sublineage C(R) was estimated to be slightly higher than that of the serotype as a whole, and the time of the most recent common ancestor for this cluster was estimated to be approximately 2001. In comparison to the older isolates of lineage C (1993-2001), the re-emerging viruses showed variation at eight amino acid positions, including substitutions at the antigenically critical residues VP279 and VP2131. However, no direct correlation was found between sequence variations and antigenic relationships. The number of codons under positive selection and the nature of the selection pressure varied widely among the structural proteins, implying a heterogeneous pattern of evolution in serotype Asia1. While episodic diversifying selection appears to play a major role in shaping the evolution of VP1 and VP3, selection pressure acting on codons of VP2 is largely pervasive. Further, episodic positive selection appears to be responsible for the early diversification of lineage C. Recombination events identified in the structural protein coding region indicates its probable role in adaptive evolution of serotype Asia1 viruses.

Evolutionary dynamics of foot-and-mouth disease virus O/ME-SA/Ind2001 lineage.

Foot-and-mouth disease (FMD) virus serotype O Ind2001 lineage within the Middle East-South Asia topotype is the major cause of recent FMD incidences in India. A sub-lineage of Ind2001 caused severe outbreaks in the southern region of the country during 2013 and also reported for the first time from Libya. In this study, we conducted a detailed evolutionary analysis of Ind2001 lineage. Phylogenetic analysis of Ind2001 lineage based on maximum likelihood method revealed two major splits and three sub-lineages. The mean nucleotide substitution rate for this lineage was calculated to be 6.338×10(-3)substitutions/site/year (s/s/y), which is similar to those of PanAsian sub-lineages. Evolutionary time scale analysis indicated that the Ind2001 lineage might have originated in 1989. The sub-lineage Ind2001d that caused 2013 outbreaks seems to be relatively more divergent genetically from other Ind2001 sub-lineages. Seven codons in the VP1 region of Ind2001 were found to be under positive selection. Four out of 24 recent Ind2001 strains tested in 2D-MNT had antigenic relationship value of <0.3 with the serotype O vaccine strain indicating intra-epidemic antigenic diversity. Amino acid substitutions found in these minor variants with reference to antigenic diversity have been discussed. The dominance of antigenically homologous strains indicates absence of vaccine immunity in the majority of the affected hosts. Taken together, the evolution of Ind2001 lineage deviates from the strict molecular clock and a typical lineage evolutionary dynamics characterized by periodic emergence and re-emergence of Ind2001 and PanAsia lineage have been observed in respect of serotype O.

Serosurveillance of foot-and-mouth disease in sheep and goat population of India.

Serological investigation to detect foot-and-mouth disease (FMD) virus circulation in the domestic small ruminant population of India was conducted. A total of 4407 and 4035 serum samples from sheep and goats, respectively were collected at random covering majority of the states across the country during 2010-2012. These samples were analyzed for antibodies against the non-structural proteins (NSP) of FMD virus in an indirect 3AB NSP ELISA and against the structural proteins (SP) in a liquid phase blocking (LPB) ELISA. A total of 20.35% sheep and 13.60% goats were found to be positive for 3AB NSP antibodies providing a serological evidence of extensive viral activity. In LPB ELISA, only 4.54% sheep and 6.27% goats were found to have protective antibody (log10 titre of ≥1.8) against all three serotype strains in the vaccine, which correlates with "no or sparse vaccination" scenario in these species in the country. Hence, to check silent amplification and dissemination of virus in a mixed farming set up, small ruminants may be brought under the ambit of routine vaccination and surveillance programmes.

Efficient rescue of foot-and-mouth disease virus in cultured cells transfected with RNA extracted from clinical samples.

In this study, an RNA transfection was used to rescue infectious foot-and-mouth disease (FMD) virus from clinical samples in BHK-21 cell line for diagnosis of FMD. Tissue samples (n=190) were subjected to FMD virus isolation by conventional cell culture and also by RNA transfection. FMD virus was isolated from 62% of the clinical samples by RNA transfection, whereas virus was isolated only from 16% of the clinical samples in conventional cell culture method, suggesting better performance of the RNA transfection. Virus was rescued from 67% and 10% of ELISA negative but multiplex PCR positive samples by RNA transfection and conventional cell culture, respectively. The efficiency of transfection was studied on clinical samples subjected to temperature as high as 37°C and varying pH (pH 4-9). Except up to 1 week of storage at 4°C at pH 7.5, virus isolation was not possible by cell culture. Virus was rescued by transfection from samples stored at 4°C for any of the applied pH up to 4 weeks, and when stored at 37°C virus could be rescued up to 4 weeks at pH 7.5 suggesting the fitness of transfection to isolate virus from clinical samples stored under inappropriate conditions. The sequence data and antigenic relationships with the vaccine strains, between virus rescued by transfection and conventional cell culture, were comparable. The RNA transfection will help to increase the efficiency of virus isolation, diagnosis and molecular epidemiological studies.

Phylogeny and genetic diversity of foot and mouth disease virus serotype Asia1 in India during 1964-2012.

Foot and mouth disease virus (FMDV) serotype Asia1 was first identified in India in 1951 and since then causing significant proportion of FMD outbreaks in the country. In this paper genetic analysis of 219 isolates from India collected over a period of 48 years is described. Bayesian approach was used to estimate the date of divergence and evolutionary rate. Phylogenetic analysis indicated the circulation of three lineages (B, C and D) of which lineage B formed one genotype (I) which was prevalent during 1964-2000. Genotype II constituted by lineage C and D has been in circulation since 1979 till date. We observed dramatic form of clade turnover in serotype Asia1 in India. The time scale analysis indicated that the most recent common ancestors for Indian Asia1 strains existed around 77 years ago. The evolutionary rate of serotype Asia1 viruses (genotype II) from India was estimated at 5.871×10(-3) substitutions per site, per year. We observed several connections in our phylogeographic analysis indicating intense flow of virus among states. The antigenically critical sites were frequently substituted and positive selection was evident at many sites. Maximum likelihood analysis suggested that the strains circulating in the country since 2005 were different from the genetic groups (I-VII) identified earlier and designated here as Group VIII.

Emergence of a novel lineage genetically divergent from the predominant Ind2001 lineage of serotype O foot-and-mouth disease virus in India.

In India, emergence of Ind2001 lineage of foot-and-mouth disease virus (FMDV) serotype O was recorded in the year 2001. After causing sporadic incidences, the Ind2001 lineage that re-surged in 2008 out-competed PanAsia from the field during 2009 and continued its dominance during 2010 and 2011 as well. The lineage has diversified in due course of time, leading to two sub-lineages (Ind2001a and Ind2001b). The sub-lineage Ind2001a include isolates collected during 2001-2002 and sub-lineage Ind2001b is constituted largely by isolates collected during 2008-2012. The nucleotide substitution rate of sub-lineage Ind2001b was estimated at 6.58×10⁻³ substitutions/site/year. The most stable PanAsia lineage is restricted only to few outbreaks. During 2011, emergence of a new genetic group with >9% nucleotide divergence from rest of the lineages circulating in the country was detected and named as lineage Ind2011. Two specific amino acid substitutions at positions VP1-36 (F) and VP2-133 (T) were observed in the Ind2011 lineage. The new lineage at present is restricted only to southern states of the country. It is uncertain whether the emergence was triggered by immune pressure or due to a bottleneck in transmission or selected for higher fitness value. Six sites (4, 68, 83, 135, 138 and 209) in VP1 protein were identified to undergo episodic diversifying selection in serotype O field isolates. Both emerging and re-emerging lineages had appropriate antigenic match with currently used vaccine strain, INDR2/1975. Irrespective of genetic variability, the field isolates showed remarkable conservation at antigenically critical residues that might contribute to the observed antigenic stability. With the emergence of a new genetic group after a span of 10 years, the overall epidemiological scenario in the region is expected to change in the coming years.