Nipah virus outbreak in Kerala state, India amidst of COVID-19 pandemic (preprint)

Background: We report here a Nipah virus (NiV) outbreak in Kozhikode district of Kerala state, India which had caused fatal encephalitis in an adolescent male and the outbreak response which led to the successful containment of the disease and the related investigations. Methods: Quantitative real-time RT-PCR, ELISA based antibody detection and whole genome sequencing were performed to confirm the Nipah virus infection. Contacts of the index case were traced and isolated based on risk categorization. Bats from the areas near the epicentre of the outbreak were sampled for throat swabs, rectal swabs and blood samples for Nipah virus screening by real time RT-PCR and anti-Nipah virus bat IgG ELISA. Plaque reduction neutralization test was performed for the detection of neutralizing antibodies. Results: Nipah viral RNA and anti-NiV IgG antibodies were detected in the serum of the index case. Rapid establishment of an onsite NiV diagnostic facility and contact tracing helped in quick containment of the outbreak. NiV sequences retrieved from the clinical specimen of the index case formed a sub-cluster with the earlier reported Nipah I genotype sequences from India with more than 95% similarity. Anti-NiV IgG positivity could be detected in 21% of Pteropus medius and 37.73% of Rousettus leschenaultia. Neutralizing antibodies against NiV could be detected in P.medius. Conclusions: Stringent surveillance and awareness campaigns needs to be implemented in the area to reduce human-bat interactions and minimize spill over events which can lead to sporadic outbreaks of NiV.

Psychosocial Effects of Isolation on Nipah Virus Infection Suspects During an Outbreak (preprint)

Background and Methodology: Nipah Virus (NiV) belonging to the genus Henipavirus is a biosafety level 4 pathogen with high human to human transmission. Nipah Virus outbreak of 2018 in Kozhikode, Kerala has evoked immense panic and fear in the system. Other viral infections with similar transmission pattern (Ebola, SARS, MERS or COVID 19) also identified with the negative impacts of isolation. This retrospective observational study was planned during November –December 2018 to understand the psychosocial effects among the subjects in Nipah isolation facility. The symptoms of Post-traumatic stress disorder (PTSD) were assessed using the Impact of Events Scale-Revised version (IES-R). Results and Conclusions: Of the 81 subjects, 73 could be contacted with a response rate of 90.12%. The mean age was 38 years (SD = 15.43) and 13.7% were health care workers. 63% of the subjects experienced fear of death during isolation stay and 12.3% of the subjects had lost their relatives or friends to Nipah infection. The mean IES score obtained was 10.78 (SD: 9.679, range 0-49) and 5 subjects had above the cut off 22. Nipah outbreak had evoked significant psychological disturbances in subjects who remained in isolation with its negative impacts.Funding Statement: No financial support received for this study.Declaration of Interests: Authors state that they do not have any commercial or other association that might pose a conflict of interest.Ethics Approval Statement: Approved by the Institutional Ethics Committee.

Initial insights into the genetic epidemiology of SARS-CoV-2 isolates from Kerala suggest local spread from limited introductions (preprint)

Coronavirus disease 2019 (COVID-19) rapidly spread from a city in China to almost every country in the world, affecting millions of individuals. Genomic approaches have been extensively used to understand the evolution and epidemiology of SARS-CoV-2 across the world. Kerala is a unique state in India well connected with the rest of the world through a large number of expatriates, trade, and tourism. The first case of COVID-19 in India was reported in Kerala in January 2020, during the initial days of the pandemic. The rapid increase in the COVID-19 cases in the state of Kerala has necessitated the understanding of the genetic epidemiology of circulating virus, evolution, and mutations in SARS-CoV-2. We sequenced a total of 200 samples from patients at a tertiary hospital in Kerala using COVIDSeq protocol at a mean coverage of 7,755X. The analysis identified 166 unique high-quality variants encompassing 4 novel variants and 89 new variants identified for the first time in SARS-CoV-2 samples isolated from India. Phylogenetic and haplotype analysis revealed that the circulating population of the virus was dominated (94.6% of genomes) by three distinct introductions followed by local spread, apart from identifying polytomies suggesting recent outbreaks. The genomes formed a monophyletic distribution exclusively mapping to the A2a clade. Further analysis of the functional variants revealed two variants in the S gene of the virus reportedly associated with increased infectivity and 5 variants that mapped to five primer/probe binding sites that could potentially compromise the efficacy of RT-PCR detection. To the best of our knowledge, this is the first and most comprehensive report of genetic epidemiology and evolution of SARS-CoV-2 isolates from Kerala.