Background 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. Methods 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. Results 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. Conclusion 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.

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We report here a Nipah virus (NiV) outbreak in Kozhikode district of Kerala state, India, which had caused fatal encephalitis in a 12-year-old boy and the outbreak response, which led to the successful containment of the disease and the related investigations. Quantitative real-time reverse transcription (RT)-PCR, ELISA-based antibody detection, and whole genome sequencing (WGS) were performed to confirm the NiV infection. Contacts of the index case were traced and isolated based on risk categorization. Bats from the areas near the epicenter of the outbreak were sampled for throat swabs, rectal swabs, and blood samples for NiV screening by real-time RT-PCR and anti-NiV bat immunoglobulin G (IgG) ELISA. A plaque reduction neutralization test was performed for the detection of neutralizing antibodies. Nipah viral RNA could be detected from blood, bronchial wash, endotracheal (ET) secretion, and cerebrospinal fluid (CSF) and anti-NiV immunoglobulin M (IgM) antibodies from the serum sample 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 (P. medius) and 37.73% of Rousettus leschenaultia (R. leschenaultia). Neutralizing antibodies against NiV could be detected in P. medius. Stringent surveillance and awareness campaigns need to be implemented in the area to reduce human-bat interactions and minimize spillover events, which can lead to sporadic outbreaks of NiV.

Tick borne zoonotic diseases are one of the major emerging threats to live stock and public health in India, especially in Western Ghats of south India. Since livestock and wild animals share habitats and grasslands, it is important to know the species composition of major tick parasitism on live stock as well as their geographical distribution for effective control of tick and tick borne diseases. This study provides basic knowledge that is necessary to initiate Kyasanur Forest Disease (KFD) prevention programs in these areas. Ticks were sampled from Wayanad districts of Kerala from domestic animals and identified morphologically. A total of 195 cattle searched, in which 168 (86.15%) cattle were infested with ticks and a total of 3633 ticks comprising three genera and seven species were collected, Rhipicephalus microplus (52.71%) was prevalent species followed by Haemaphysalis bispinosa (16.9%), Rhipicephalus decoloratus (15.77%), Haemaphysalis turturis (11.42%), Rhipicephalus sanguineus (1.32%), Amblyomma integrum (1.15%) and Haemaphysalis spinigera (0.71%) were identified based on their morphological characters. As R. microplus was the prevalent species, the risk of transmission of babesiosis and anaplasmosis to cattle increases and the presence of Haemaphysalis sp. point out the risk of KFD in among the tribal colony people and it can be reduced by applying with acaricides on domestic animals.

This paper has studied the impact of crop diversification on dietary diversity of households in different regions of Tamil Nadu. Two different types of data set were used: (1) National Sample Survey Organization's (NSSO) consumer expenditure survey data for the years TE 2004-05 and TE 2012-13, and (2) Cropping pattern data from Season and Crop report for the years TE 2004 and TE 2012-13. Multiple linear regression model was used to study the linkages between crop and dietary diversification. The study has revealed that dietary diversification of Cauvery delta zone, Northern zone and Northeastern zone was parallel with crop diversification. The crop diversification influenced positively the dietary diversification, whereas vegetable diversification was negatively related with diet diversification, irrespective of income groups in the state. Also, larger household size, presence of own land, older age and higher education level of household-head have been found positively related with dietary diversity of households in Tamil Nadu. The current nutrients intake pattern has been found about 50 per cent of the RDA, particularly of crude fibre and iron and about two-thirds in case of energy and vitamin A. The nutrient intake gap is further widened in low-income non-farm groups. Appropriate nutritional security programmes maybe initiated particularly covering children, pregnant women and aged people.

The CERES (Crop Estimation through Resource and Environment Synthesis)-rice model incorporated in DSSAT version 4.5 was calibrated for genetic coefficients of rice cultivars by conducting field experiments during the kharif season at Jorhat, Kalyani, Ranchi and Bhagalpur, the results of which were used to estimate the gap in rice yield. The trend of potential yield was found to be positive and with a rate of change of 26, 36.9, 57.6 and 3.7 kg ha -1 year -1 at Jorhat, Kalyani, Ranchi and Bhagalpur districts respectively. Delayed sowing in these districts resulted in a decrease in rice yield to the tune of 35.3, 1.9, 48.6 and 17.1 kg ha -1 day -1 respectively. Finding reveals that DSSAT crop simulation model is an effective tool for decision support system. Estimation of yield gap based on the past crop data and subsequent adjustment of appropriate sowing window may help to obtain the potential yields.

Background & objectives: Bats are considered to be the natural reservoir for many viruses, of which some are potential human pathogens. In India, an association of Pteropus medius bats with the Nipah virus was reported in the past. It is suspected that the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) also has its association with bats. To assess the presence of CoVs in bats, we performed identification and characterization of bat CoV (BtCoV) in P. medius and Rousettus species from representative States in India, collected during 2018 and 2019. Methods: Representative rectal swab (RS) and throat swab specimens of Pteropus and Rousettus spp. bats were screened for CoVs using a pan-CoV reverse transcription-polymerase chain reaction (RT-PCR) targeting the RNA-dependent RNA polymerase ( RdRp ) gene. A single-step RT-PCR was performed on the RNA extracted from the bat specimens. Next-generation sequencing (NGS) was performed on a few representative bat specimens that were tested positive. Phylogenetic analysis was carried out on the partial sequences of RdRp gene sequences retrieved from both the bat species and complete viral genomes recovered from Rousettus spp. Results: Bat samples from the seven States were screened, and the RS specimens of eight Rousettus spp. and 21 Pteropus spp. were found positive for CoV RdRp gene. Among these, by Sanger sequencing, partial RdRp sequences could be retrieved from three Rousettus and eight Pteropus bat specimens. Phylogenetic analysis of the partial RdRp region demonstrated distinct subclustering of the BtCoV sequences retrieved from these Rousettus and Pteropus spp. bats. NGS led to the recovery of four sequences covering approximately 94.3 per cent of the whole genome of the BtCoVs from Rousettus bats. Three BtCoV sequences had 93.69 per cent identity to CoV BtRt-BetaCoV/GX2018. The fourth BtCoV sequence was 96.8 per cent identical to BtCoV HKU9-1. Interpretation & conclusions: This study was a step towards understanding the CoV circulation in Indian bats. Detection of potentially pathogenic CoVs in Indian bats stresses the need for enhanced screening for novel viruses in them. One Health approach with collaborative activities by the animal health and human health sectors in these surveillance activities shall be of use to public health. This would help in the development of diagnostic assays for novel viruses with outbreak potential and be useful in disease inter...

Summaryobjective To identify the aetiological agent ⁄ s of an outbreak of chikungunya-like illness with high morbidity and several fatalities in Tamil Nadu, India, 2009-2010.methods Two hundred and seventeen serum samples were collected from the affected areas and screened for chikungunya virus (CHIKV), dengue virus (DENV) and Japanese encephalitis virus (JEV) IgM antibodies using MAC-ELISA kits. A few selected samples were also tested for Ross River, Sindbis, and Murrey Valley viruses by RT-PCR and Hantan virus by serology. Twelve acute serum and mosquito samples were processed for virus isolation in C6 ⁄ 36 cells. CHIKV isolate was characterised by RT-PCR and sequencing.results Diagnostic levels of IgM antibodies were detected in 107 (49.3%) CHIKV samples and 22 (10.1%) DENV samples. IgM antibodies against JEV were not detected (n = 46). Characterisation of the CHIKV isolate at genetic level demonstrated it as ECSA (E1: 226A). Thirty-six selected samples were also negative for Ross River, Sindbis, Murrey Valley and Hantan viruses.conclusion High prevalence of CHIKV IgM antibody positivity, clinical symptoms, virus isolation and the presence of vector mosquitoes clearly suggest CHIKV as the aetiological agent responsible for the outbreak.