Co-circulation of Chikungunya and Dengue viruses in Dengue endemic region of New Delhi, India during 2016

Abstract

Co-circulation of Chikungunya and Dengue viral infections (CHIKV and DENV) have been reported mainly due to transmission by common Aedes vector. The purpose of the study was to identify and characterise the circulating strains of CHIKV and DENV in DENV endemic region of New Delhi during 2016. CHIKV and DENV were identified in the blood samples (n = 130) collected from suspected patients by RT-PCR. CHIKV was identified in 26 of 65 samples (40%). Similarly, DENV was detected in 48 of 120 samples (40%). Co-infection with both the viruses was identified in five (9%) of the samples. Interestingly, concurrent infection with DENV, CHIKV and Plasmodium vivax was detected in two samples. CHIKV strains (n = 11) belonged to the ECSA genotype whereas DENV-3 sequences (n = eight) clustered in Genotype III by phylogenetic analysis. Selection pressure of E1 protein of CHIKV and CprM protein of DENV-3 revealed purifying selection with four and two positive sites, respectively. Four amino acids of the CHIKV were positively selected and had high entropy suggesting probable variations. Co-circulation of both viruses in DENV endemic regions warrants effective monitoring of these emerging pathogens via comprehensive surveillance for implementation of effective control measures.

Keywords: Chikungunya virus; Dengue virus; co-circulation; co-infection; phylogenetic analysis.

Fig. 1.

Schematic representation of samples analysed for Chikungunya and Dengue viruses.

Fig. 2.

Demographic details of the (a) CHIKV and (b) DENV patients. (i) The column graph showing correlation between number of clinical samples and CHIKV/DENV positive cases with the age group. (ii) The graph showing correlation between total percentage of males and females with affected cases. (iii) The graph showing total cases with days of fever.

Fig. 3.

(a) Neighbour-Joining Phylogenetic tree of CHIKV based on E1 gene and (b) Maximum Likelihood Phylogenetic Tree of DENV-3 based on CprM region. The study sequences are marked by the solid diamond (♦). The tree was constructed based on the Tamura-Nei model. Bootstrap values are represented by the numbers on nodes generated by 1000 replications. The study sequences clustered with the ECSA and genotype III respectively.

Fig. 4.

Shannon Entropy plot of (a) E1 gene of CHIKV and (b) CprM region of DENV. Shannon entropy was analysed at different amino acids residues using Bioedit 7.0 software. Threshold value of entropy was set at 0.2. Highest entropy value shows the maximum number of chance of variability/mutation at that position given in the protein sequence.

Fig. 5.

(a) The co-circulation and co-infection of CHIKV and DENV in different parts of India. The freely available map of India was downloaded from the website presentationmagzine.com (https://www.presentationmagazine.com/powerpoint-map-of-india-647.htm) and edited in power point. (b) World map showing the co-circulation and co-infection of CHIKV and DENV in different geographical regions. The freely available map of India was downloaded from the website presentationmagzine.com (https://www.presentationmagazine.com/world-maps-vector-editable-507.htm) and edited in power point.