A sudden upsurge of
fever cases with
joint pain was observed in the outpatient department, Community Health Centre, Rangat during July-August 2010 in Rangat Middle Andaman, India. The aetiological agent responsible for the outbreak was identified as chikungunya virus (CHIKV), by using RT-PCR and
IgM ELISA. The study investigated the association of polymorphisms in the human leucocyte
antigen class II genes with susceptibility or protection against CHIKV. One hundred and one patients with clinical features suggestive of CHIKV
infection and 104 healthy subjects were included in the study.
DNA was extracted and typed for
HLA-DRB1 and DQB1 alleles. Based on the amino acid sequences of
HLA-DQB1 retrieved from the IMGT/HLA database, critical
amino acid differences in the specific
peptide-binding pockets of
HLA-DQB1 molecules were investigated. The frequencies of
HLA-DRB1 alleles were not significantly different, whereas lower frequency of
HLA-DQB1*03:03 was observed in CHIKV patients compared with the control population [P = 0·001, corrected P = 0·024; odds ratio (OR) = 0, 95% confidence interval (95% CI) 0·0-0·331; Peto's OR = 0·1317, 95% CI 0·0428-0·405). Significantly lower frequency of
glutamic acid at position 86 of
peptide-binding pocket 1 coding
HLA-DQB1 genotypes was observed in CHIKV patients compared with healthy controls (P = 0·004, OR = 0·307, 95% CI 0·125-0·707). Computational binding predictions of CD4
epitopes of CHIKV by NetMHCII revealed that
HLA-DQ molecules are known to bind more CHIKV
peptides than
HLA-DRB1 molecules. The results suggest that
HLA-DQB1 alleles and critical
amino acid differences in the
peptide-binding pockets of
HLA-DQB1 alleles might have role in influencing
infection and pathogenesis of CHIKV.