Detection of Nipah virus in Pteropus medius in 2019 outbreak from Ernakulam district, Kerala, India

• Published in: BMC infectious diseases Vol. 21; no. 1; pp. 162 - 7
• Main Authors: Sudeep, A. B., Yadav, Pragya D., Gokhale, Mangesh D., Balasubramanian, R., Gupta, Nivedita, Shete, Anita, Jain, Rajlaxmi, Patil, Savita, Sahay, Rima R., Nyayanit, Dimpal A., Gopale, Sanjay, Pardeshi, Prachi G., Majumdar, Triparna D., Patil, Dilip R., Sugunan, A. P., Mourya, Devendra T.
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 09.02.2021; BioMed Central; BMC
• Subjects: Animals; Antibodies; Antibodies, Viral - blood; Antigens; Chiroptera; Chiroptera - virology; Disease hot spots; Disease Outbreaks; Distribution; Divergence; Enzyme-linked immunosorbent assay; Ernakulum; Genomes; Genotypes; Health aspects; Henipavirus Infections - diagnosis; Henipavirus Infections - epidemiology; Henipavirus Infections - veterinary; Henipavirus Infections - virology; High-Throughput Nucleotide Sequencing; Host-virus relationships; IgG ELISA; Immunoglobulin G; Immunoglobulin G - blood; India - epidemiology; Infectious diseases; Liver; Methods; Next-generation sequencing; NGS; Nipah virus; Nipah Virus - classification; Nipah Virus - genetics; Nipah Virus - immunology; Nucleotides; Phylogenetics; Phylogeny; Polymerase chain reaction; Pteropus; Pteropus spp; Random sampling; Real-Time Polymerase Chain Reaction; Rectum; Rectum - virology; RNA, Viral - chemistry; RNA, Viral - metabolism; RNA-directed DNA polymerase; Sentinel health events; Spleen; Statistical sampling; India; Bangladesh; Kerala India; Malaysia; Singapore; United States > US; Nipah virus; IgG ELISA; NGS; Ernakulum; Pteropus spp
• ISSN: 1471-2334; 1471-2334
• DOI: 10.1186/s12879-021-05865-7

In June 2019, Nipah virus (NiV) infection was detected in a 21-year-old male (index case) of Ernakulum, Kerala, India. This study was undertaken to determine if NiV was in circulation in Pteropus species (spp) in those areas where the index case had visit history in 1 month. Specialized techniques were used to trap the Pteropus medius bats (random sampling) in the vicinity of the index case area. Throat and rectal swabs samples of 141 bats along with visceral organs of 92 bats were collected to detect the presence of NiV by real-time reverse transcriptase-polymerase chain reaction (qRTPCR). Serum samples of 52 bats were tested for anti-NiV Immunoglobulin (Ig) G antibodies by Enzyme-Linked Immunosorbent Assay (ELISA). The complete genome of NiV was sequenced by next-generation sequencing (NGS) from the tissues and swab samples of bats. One rectal swab sample and three bats visceral organs were found positive for the NiV. Interestingly, 20.68% (12/58) of Pteropus were positive for anti-NiV IgG antibodies. NiV sequences of 18,172; 17,200 and 15,100 nucleotide bps could be retrieved from three Pteropus bats. A distinct cluster of NiV sequences, with significant net-evolutionary nucleotide divergence, was obtained, suggesting the circulation of new genotype (I-India) in South India. NiV Positivity in Pteropus spp. of bats revealed that NiV is circulating in many districts of Kerala state, and active surveillance of NiV should be immediately set up to know the hotspot area for NiV infection.