Copy number variation of Chikungunya ECSA virus with disease symptoms among Indian patients

After a gap of three decades, from 2005 onwards, a series of Chikungunya virus (CHIKV) outbreaks occurred worldwide. This study was performed to detect CHIKV infection, its genotype among symptomatic Eastern Indian patients and to analyze any association between the presence of CHIKV genome in patient body with appearance of disease symptoms (n = 199). Plasma-extracted viral RNA was reverse transcribed to cDNA and PCR-amplified followed by agarose gel electrophoresis. Viral load among CHIKV-positive patients was determined by real time RT-PCR. CHIKV-IgM in sera was detected by ELISA. Sequencing and phylogenetic analysis of plasma-extracted PCR products was done. CHIKV genome and IgM were detected among 65.3% (n = 130) and 41.2% (n = 82) patients respectively. Joint swelling was significantly associated with CHIKV infection (P-value: 0.0003). CHIKV PCR positive patients were grouped in two categories: Group-I: viral load <10(4)  copies/ml and Group-II: viral load ≥10(4)  copies/ml. Higher number of acute stage patients clustered in Group-II. Fever and joint swelling were significantly more prevalent among Group-II patients, whereas rash and diarrhoea among Group-I patients (P-value <0.05). Patient-isolated CHIKV sequences clustered with CHIKV ECSA genotypes in the phylogenetic tree, with two types of CHIKV strains found to circulate among them-as indicated by their different nucleotide sequences. This is the first study detecting the presence of CHIKV ECSA genotype among Eastern Indian patients. Fever and joint swelling might have appeared first followed by rash, diarrhea during disease progression-as indicated by CHIK viral load in patients. Thus, viral load can be used as unique diagnostic and prognostic marker of Chikungunya disease pathogenesis.