Phylogenetic analysis of haemagglutinin gene deciphering a new genetically distinct lineage of canine distemper virus circulating among domestic dogs in India

Abstract

Summary Canine distemper (CD) is one of the highly contagious and invariably fatal viral diseases of dogs and other carnivores. Despite the widespread use of modified live vaccines to control CD, the prevalence of disease has increased at an alarming rate in recent years. Although a number of factors may be ascribed for vaccine failure, antigenic differences among the vaccine and wild‐type strains have gained the interest of researchers. Considering the high genetic variability of haemagglutinin gene (H gene) and its role in eliciting the immune response to canine distemper virus (CDV), we have generated nine full‐length CDV H gene sequences from infected dogs including three vaccinated cases. Bayesian analysis was performed using 102 full‐length H gene nucleotide sequences over a time frame of 76 years (1940–2016) from 18 countries. The time to the most recent common ancestor (tMRCA) of CDV was estimated to be 1696 AD. Phylogenetic reconstruction clustered Indian wild‐type viruses into a distinct monophyletic group clearly separated from the previously established CDV lineages. This signifies the presence of a novel genetic variant (proposed as “Lineage India‐1/Asia‐5”) circulating among dog population in India. To investigate the importance of substitutions at amino acid residues 530 and 549 of CDV H protein in determining the host switches from canid to non‐canid hosts, we analysed 125 H gene sequences including nine sequences generated in this study. Selection pressure analysis and analysis of amino acid sequences revealed a trend towards adaptation of 549H variants in non‐canid hosts although no role of G/E530R/D/N substitution could be identified. This is the first comprehensive study about the nature and ecology of CDV circulating among dog population in India. Outbreaks in vaccinated animals as observed in this study have raised a concern towards the effectiveness of current vaccine strains warranting detailed investigation.

H Gene-based Molecular Characterization of Field Isolates of Canine Distemper Virus from Cases of Canine Gastroenteritis

“…As previously reported the H gene region is highly variable with more number of amino acid variations (Martella et al, 2006;Sarute et al, 2013). Of all the reported amino acid variations in this study, we noticed that D530G was previously reported and was consistently reported in four isolates here (Bhatt et al, 2019).…”

“…All the eight isolates show distant relationship with vaccine strains (America-1) and other isolates from the NCBI database (Fig 4). However, the previous reports suggested that the Indian isolates were grouped either under European lineage (Swati et al, 2015;Ashmi et al, 2017) or Asia-5/ India-1 (Bhatt et al, 2019). Our findings suggest some CDV strains circulating in India were evolving from South America-2 or Asia-4.…”

“…CDV is one among the viral etiology that can cause gastroenteritis in canines. CDV was grouped into Asia-1, Asia-2, Asia-3, Asia-4, Asia-5/ India-1, South America-1/Europe-1, South America-2, South America-3, European wild life, America-1, America-2, Africa-1, Africa-2, Arctic and Rockborn like lineages (Bhatt et al, 2019). The virus is mainly shed from occulo-nasal Lanes 1,4,7,9,11,12,15,17,18 shows the amplification of 449 bp for Nobivac DHPPi vaccine, F102/PVNRTVU/2019, F107/PVNRTVU/ 2019, F108/PVNRTVU/2019, F115/ PVNRTVU/2019, F128/PVNRTVU/2019, F129/PVNRTVU/2019, F158/PVNRTVU/2019 and F200/ PVNRTVU/ 2019 respectively.…”

“…Based on the molecular evolutionary patterns, CDV is grouped into Asia-1, Asia-2, Asia-3, Asia-4, Asia-5/India-1, South America-1/Europe-1, South America-2, South America-3, European wild life, America-1, America-2, Africa-1, H Gene-based Molecular Characterization of Field Isolates of Canine Distemper Virus from Cases of Canine Gastroenteritis Africa-2, Arctic, Rockborn like lineages (Bhatt et al, 2019). In India, there were reports of isolation of CDV from ocular, nasal (Swati et al, 2015;Ashmi et al, 2017), brain tissue (Pawar et al, 2011) and blood (Aarthi et al, 2015); however, we couldn't find any report of isolation of virus from enteric samples collected from clinical cases of gastroenteritis in India.…”

Genetic Adaptations, Biases, and Evolutionary Analysis of Canine Distemper Virus Asia-4 Lineage in a Fatal Outbreak of Wild-Caught Civets in Thailand

“…This scenario may result in the adaptation of CDV to be able to infect different hosts. Due to the global distribution of the CDV, phylogenetic genotyping of this virus has been based on the H gene sequence and segregated it into several major clades: America-1, America-2, Asia-1, Asia-2, Africa-1, Africa-2, European wildlife, Arctic, and Europe-1/SouthAmerica-1 [6], while the latest clades have recently been described as America-3 to -5, Asia-3 to -5, South America-2, and South America-3 [23,24]. In addition, the Caspian clade was recently isolated as the cause of a mass die-off of Caspian seals since 1988 [25].…”