Nipah Virus Sequences from Humans and Bats during Nipah Outbreak, Kerala, India, 2018

Abstract

We retrieved Nipah virus (NiV) sequences from 4 human and 3 fruit bat (Pteropus medius) samples from a 2018 outbreak in Kerala, India. Phylogenetic analysis demonstrated that NiV from humans was 96.15% similar to a Bangladesh strain but 99.7%-100% similar to virus from Pteropus spp. bats, indicating bats were the source of the outbreak.

Keywords: Human; India; Kerala; Nipah virus; Pteropus medius; next-generation sequencing; qRT-PCR; viruses.

Figure 1

Cytopathic effect (CPE) of Nipah virus from throat swab samples of a patient in Kerala, India, 2018. Virus was inoculated into Vero CCL81 cells. A) CPE at postinfection days 1 (top) and 2 (bottom). Left panels depict the control cell; right panels depict the NiV-infected cell. B) NiV-infected cells. Original magnification ×10.

Figure 2

Maximum-likelihood phylogenetic tree of the nucleocapsid gene (region 1293–1608) of Nipah virus from Kerala, India, 2018, and reference sequences. A) Complete coding region. The evolution distance for 17 complete sequences was generated using the Tamura-Nei model plus gamma distance using different isolates. Bootstrap replication of 500 replications cycle was used for the statistical assessment of the generated tree. B) Partial nucleocapsid gene. The evolution distance for 25 nucleocapsid gene sequences of length 316 nt was generated using the Tamura-Nei model plus gamma distance using different isolates. Bootstrap replication of 500-replication cycle was used for the statistical assessment of the generated tree. GenBank accession numbers are provided for all sequences. Scale bars indicate nucleotide substitutions per site.