Identification and phylogenetic analysis of herpes simplex virus-1 from clinical isolates in India

Abstract

Human herpes simplex virus (HSV)-1 infection is acquired in childhood and persists throughout a person's lifetime. Here, we present two cases from India; one showing symptoms of postpartum haemorrhage with disseminated intravascular coagulation, and the second one showing signs of acute encephalitis syndrome. The aetiological agent in both cases was identified as HSV-1 using the PCR method. The next-generation sequencing method retrieved ~97 % of the viral genome from the isolates of the clinical samples. The phylogenetic analysis of the retrieved genomes revealed that they belong to clade II of HSV-1. This study identifies a few sequence variations in the glycoprotein region of HSV-1 during two different clinical manifestations. There are a couple of papers that analyse variations in the glycoprotein region of clinical samples. Further, this study also highlights the importance of considering HSV-1 during differential diagnosis when analysing the nosocomial infection.

Keywords: Herpes Simplex Virus-1; Next-generation sequencing; clade II; glycoproteins.

Fig. 1.

Comparative HSV-1 genome structure obtained by aligning the retrieved HSV-1 genome from India (MG646679) and reference sequence (NC_0.001806.1). Sequences were aligned using the alignment program embedded in the CLC genomic workbench version 10.1. The protein coding region is depicted using the light green arrows along with the conservation in the bottom row. Red, blue and black indicate higher, lower and medium conservation amongst the two sequences.

Fig. 2.

Comparative HSV-1 genome structure obtained by aligning the retrieved HSV-1 genome from India (MH319852) and reference sequence (NC_0.001806.1). Sequences were aligned using the alignment program embedded in the CLC genomic workbench version 10.1. The protein coding region is depicted using the light green arrows along with the conservation in the bottom row. Red, blue and black indicate higher, lower and medium conservation amongst the two sequences.

Fig. 3.

Phylogenetic tree of two isolates of the HSV-1 complete genome isolated from India: a phylogenetic tree was created for 37 complete genome sequences using a general time reversible model. Gamma distribution (0.1045) was used to model the evolutionary rate along with the variation (I=61.33 %) for some sites.

Fig. 4.

Phylogenetic tree of the HSV-1 glycoprotein region. A phylogenetic tree was created for 37 complete genome sequences using a general time reversible model.

Fig. 5.

Recombination analysis of the MG646679 strain of HSV-1: recombination analysis was performed using Simplot and Bootscan using a window size of 3000 bps and a step size of 200 bp. In total, 1000 pseudo-replicates were used for running Bootscan analysis.

Fig. 6.

Recombination analysis of the MH319852 strain of HSV-1: recombination analysis was performed using Simplot and Bootscan using a window size of 3000 bps and a step size of 200 bp. In total, 1000 pseudo-replicates were used for running Bootscan analysis.