Absence of Nipah virus antibodies and detection of Porcine kobuvirus, Porcine enterovirus-9 and Bocavirus in pigs during a Nipah virus outbreak investigation in West Bengal, India

The Nipah virus (NiV) is a highly lethal zoonotic virus that causes respiratory disease and encephalitis in humans. Historically, the NiV outbreaks in Malaysia and Singapore (1998–1999) involved domestic pigs as amplifying intermediate hosts, whereas subsequent outbreaks in India and Bangladesh have primarily been attributed to direct bat-to-human transmission or nosocomial spread, with no documented involvement of livestock. The role of intermediate hosts in NiV transmission is less studied. We report findings from a study conducted in West Bengal during the NiV outbreak in January 2026, investigating the role of local pig populations in NiV transmission and screening diseased pigs for other etiologies using metagenomic sequencing. Blood, nasal, rectal, throat and ocular swab samples were collected from 119 domestic pigs in Nadia, Kolkata, North 24 Paraganas, and Purba Bardhaman districts of West Bengal. Virological and serological tests for NiV infection were performed using real-time qRT-PCR and swine IgG ELISA. A subset of nasal and rectal swab samples from diseased pigs also underwent metagenomic sequencing. All swab samples tested negative for NiV RNA, and no antibodies were found in the serum samples. Metagenomic sequencing detected genomes of Porcine Kobuvirus (PKV) and Porcine enterovirus 9 (PEV9), prevalent in the Indian pig population as well as Porcine Bocavirus (PBoV), adding to the limited molecular reports of PBoV from India. The serological and virological investigation conducted in 119 pigs from West Bengal revealed no evidence of NiV infection. The detection of other prevalent porcine viruses and PBoV, a relatively infrequently reported virus from India, emphasizes the need for genomic surveillance and incorporation of the One Health concept into disease surveillance.