Continued circulation, recombination and evolution of the ancient subcontinent lineage despite predominance of the recent arctic-like lineage rabies viruses (RABV) in India

Portable Rabies Virus Sequencing in Canine Rabies Endemic Countries Using the Oxford Nanopore MinION

“…Portable sequencing with the MinION allowed for in-country sequencing of these high-priority samples in a veterinary diagnostic laboratory that lacked molecular biology laboratory equipment. All sequences generated from Goa belonged to the Arctic-like 1a canine rabies virus lineage (Figure 2), in agreement with sequences from canine isolates from Goa in 2014 and an isolate from a UK traveler to Goa in 2005 [84,85]. None of the almost 100 samples sequenced in the current study were of the Indian Subcontinent lineage, and the genetic diversity of isolates collected was much lower than for samples collected in 2014.…”

“…A total of 80 complete N gene and 97 complete G gene sequences were generated (Table 5). All sequences clustered in the Arctic-like 1a rabies virus lineage (Figure 2), in agreement with previous sequences from Goa, India [84,85]. No sequences fell into the Indian Subcontinent lineage, although a previous non-peer reviewed study identified one isolate from this lineage in Goa in 2014 (Figure 2) [85].…”

“…All sequences clustered in the Arctic-like 1a rabies virus lineage (Figure 2), in agreement with previous sequences from Goa, India [84,85]. No sequences fell into the Indian Subcontinent lineage, although a previous non-peer reviewed study identified one isolate from this lineage in Goa in 2014 (Figure 2) [85]. All newly generated sequences from Goa were >99% identical to each other, except for one sequence that was only 96% identical to the other Goa sequences.…”

“…Further investigation revealed this sample was collected from a dog that was transported from Rajasthan in Northern India into Goa. The remaining sequences were most similar to sequences from canine samples collected in Goa during 2014 [85] and a human case from Goa in 2005 [84] (Figure 2). Clustering in the phylogenetic analysis did not correlate with host animal species (canine, feline, or bovine); rather, sequences from all host species clustered together, suggesting one predominant enzootic transmission cycle in dogs.…”

Elimination of human rabies in Goa, India through an integrated One Health approach

“…Reference sequences included in the time-scaled phylogenetic analyses were chosen based on sequence length (full-length nucleoprotein gene and at least 1317 nt of glycoprotein gene), isolation in India or neighboring countries, inclusion in Arctic-like 1a lineage, year of isolation available, and sequence quality. Sequences published by Deventhiran et al (2018) 66 were not included in these analyses as several sequencing errors were observed and phylogenetic clustering of nucleoprotein and glycoprotein gene sequences from that study was inconsistent. Arctic rabies virus variant sequences KX148105 and JQ148105, Arctic-like 3 sequence KX148228, and Arctic-like 1b sequences KX148225, KX148226, HE802676, KX148227, KF150745, KF150744, and MK760761 were used as outgroups 67 .…”