Genetic diversity of Nipah virus in Bangladesh

Abstract

Background: Nipah virus (NiV) infection, often fatal in humans, is primarily transmitted in Bangladesh through the consumption of date palm sap contaminated by Pteropus bats. Person-to-person transmission is also common and increases the concern of large outbreaks. This study aimed to characterize the molecular epidemiology, phylogenetic relationship, and the evolution of the nucleocapsid gene (N gene) of NiV. Methods: We conducted molecular detection, genetic characterization, and Bayesian time-scale evolution analyses of NiV using pooled Pteropid bat roost urine samples from an outbreak area in 2012 and archived RNA samples from NiV case patients identified during 2012-2018 in Bangladesh. Results: NiV-RNA was detected in 19% (38/456) of bat roost urine samples and among them; nine N gene sequences were recovered. We also retrieved sequences from 53% (21 out of 39) of archived RNA samples from patients. Phylogenetic analysis revealed that all Bangladeshi strains belonged to NiV-BD genotype and had an evolutionary rate of 4.64 Â 10 À4 substitutions/site/year. The analyses suggested that the strains of NiV-BD genotype diverged during 1995 and formed two sublineages. Conclusion: This analysis provides further evidence that the NiV strains of the Malaysian and Bangladesh genotypes diverged recently and continue to evolve. More extensive surveillance of NiV in bats and human will be helpful to explore strain diversity and virulence potential to infect humans through direct or person-to-person virus transmission.

Nipah virus detection at bat roosts following spillover events in Bangladesh, 2012–2019

“…Genetic and phenotypic diversity among Nipah viruses exists, but the human health implications of this variation are unclear. Nipah virus genotypes from Bangladesh and India are genetically distinct from Malaysian genotypes (21)(22)(23). While the Malaysian genotypes are less diverse than those from Bangladesh and India (23), genotypes from Malaysia derive solely from pigs, humans, and bats during the 1998-1999 outbreak whereas genotypes from Bangladesh derive from multiple human outbreaks and surveys of bats since 2004.…”

“…Nipah virus genotypes from Bangladesh and India are genetically distinct from Malaysian genotypes (21)(22)(23). While the Malaysian genotypes are less diverse than those from Bangladesh and India (23), genotypes from Malaysia derive solely from pigs, humans, and bats during the 1998-1999 outbreak whereas genotypes from Bangladesh derive from multiple human outbreaks and surveys of bats since 2004. Another widely cited difference is that person-to-person transmission of Nipah virus was observed rarely in Malaysia (28)(29)(30) whereas in Bangladesh it accounted for a third of reported cases (8) and in India, over 75% of cases (1,9,31).…”

“…Although documented genetic diversity within Nipah viruses is limited (19)(20)(21)(22)(23), the high mutation rates observed in RNA viruses are an important predictor of zoonotic potential (24) and could theoretically produce variants with sufficient transmissibility in humans to cause a sustained epidemic (25,26). Given the wide geographic range and unsampled diversity of Nipah viruses, it is possible that variants exist and circulate in bats that are more transmissible among humans, and each spillover event is an opportunity for a more transmissible virus to emerge (27).…”

“…However, our knowledge of Nipah virus diversity is limited to the few virus sequences obtained to date. According to GenBank and recent studies (19,23), only 76 Nipah virus genomes and 153 nucleocapsid protein genes have been sequenced, 51 and 37 of which derive from human patients, respectively. Current research efforts are not optimized to characterize Nipah virus genotypes circulating in bats.…”

A small-scale survey to evaluating the perception of the Nipah virus in Bangladeshi rural community

“…Bangladesh has reported 225 deaths out of 319 positive cases in 20 years (2001)(2002)(2003)(2004)(2005)(2006)(2007)(2008)(2009)(2010)(2011)(2012)(2013)(2014)(2015)(2016)(2017)(2018)(2019)(2020), according to The Institute of Epidemiology, Disease Control and Research (IEDCR) (The Institute of Epidemiology 2020, January 30) and nearly one-third of cases occurred from person-to-person transmission (Rahman et al 2021). Previously, the NiV disease were found to be linked with consuming date palms juice but now infection has been found in various places with no link to such food habit (McKee et al 2021).…”