Currently available SARS-CoV-2 neutralisation tests continue to face trade-offs between rapid turnaround and large-scale applicability. They either fail to capture the complete spectrum of functional neutralizing antibodies, or difficult to scale up for large-cohort studies. Therefore, we present a live-virus immunocolorimetric neutralization test (LVINT) that overcomes these limitations. A total of 403 human sera collected during the year 2021 to 2025 were employed for evaluation of diagnostic performance of LVINT against surrogate virus neutralization test (sVNT) and Plaque reduction neutralization test (PRNT50) for screening of neutralizing antibodies (nABs). We also evaluated independent clinical utility of LVINT to assess nABs against Wuhan-like, Delta and predominantly circulating, XFG variants. Precision and analytical sensitivity were also measured. The LVINT exhibited a strong correlation with both the sVNT (rS = 1.000, p < 0.0001), and PRNT50 (rS = 0.910, p < 0.0001). Moreover, it showed a perfect diagnostic concordance with PRNT50 (weighted kappa = 0.90650, SE = 0.06, 95 %CI = 0.779 to 1.000), validating the use of intracellular nucleocapsid protein quantification for determining the neutralizing capacity of antibodies. The clinical utility of LVINT was further evaluated against Delta and XFG variants, revealing a declining trend of nABs titers against Delta (56.14 %) and XFG (47.36 %) variants compared with Wuhan-like variant (80.59 %). These findings prove the clinical utility of LVINT for measuring nABs against both existing and newly emerging SARS-CoV-2 variants. Collectively, the LVINT offers a rapid and scalable alternative to currently available neutralization tests.

Bird species are very sensitive to environmental changes and are good indicators of ecosystem health. Avian species distribution depends on habitat configuration and environmental factors. To understand the winter visitor bird distribution and consequences of environmental variables on waterbird species, a study was conducted during summer and winter seasons (January 2023 to December 2024) in the selective wetlands of the western Himalayas foothills in Uttarakhand. The point count method and canonical correspondence analysis (CCA) were used for the waterbird survey and association with dissolved oxygen, water pH, and temperature respectively. Total forty eight waterbird species including twenty two winter visitors were reported among the study sites and the significantly (df = 2, p < 0.04) high abundance of waterbird species were analysed at protective wetland site. The waterbird diversity significant negative relationship with atmospheric temperature (r = − 0.65, p = 0.004; r = − 0.81, p = 0.006; and r = − 0.82, p = 0.004) in all the wetlands. Among the environmental variables, temperature was one of the major influencing factors recorded in the study sites. The present study provides a baseline assessment of waterbird species distribution and relationship with the habitat variables among the wetlands and suggests a regular interval monitoring of temperature fluctuations around the wetlands in the foothills of the Western Himalayas must be prioritise.

Unbiased and accurate estimation of bird density are prerequisites to monitor the impact of urbanization on avian communities. Synanthropic birds are reliable indicators of landscape modification in small tropical cities with rural-urban ecological settings. We conducted 183 fixed-width point counts to record avian communities along the rural-urban gradient in Mirzapur and Bhadohi. We applied hierarchical distance-sampling to estimate the summer density of 35 bird species across eight foraging guilds in response to vegetation, land cover, human activity and housing type, accounting for detection probability as a function of weather. Twenty-seven species (77%) showed differences in density across the landscape gradient. The density of frugivores was highest in urban gradient, a carnivore was highest in rural, and a scavenger was highest in the semi-urban gradient thereby supporting the resource concentration hypothesis. Insectivores, granivores and omnivores showed variable density patterns along the gradient. The relatively lower density of synanthropic birds in semi-urban and urban fringes indicates the need for enhanced green space and vegetation structure along intermediate landscape gradient. The habitat associations and population sizes of synanthropic birds are useful for landscape managers and local stakeholders to maximize avifaunal diversity in the intermediate landscapes of the rural-urban continuum in Uttar Pradesh.

Wetland ecosystems play a crucial role to conservation flora and fauna and provide an exclusive habitat for the waterbird species. Anthropogenic activities and water quality also influence the waterbird species population. A study was conducted at Asan wetland of Dehradun to recognize the waterbird distribution, composition and association with wetland quality. Total twenty five waterbird species, high abundance of dabbling ducks including three winter visitor and two threaten species recorded. The waterbird species composition was significant positive correlated with the wetland water Dissolved oxygen (r = 0.72, p = 0.007) and significantly negative relationship (r = –0.78, p = 0.003) with the wetland water temperature. This study indicates the variety of food availability is major influencing factors as compare the wetland water quality parameters in the study area. We would suggest a regular interval monitoring is required to understand the habitat quality and atmospheric changes effect on waterbird species distribution.

Newcastle disease (ND) is a highly pathogenic infectious disease of poultry, causing significant economic losses globally. Wild birds act as natural reservoir of Newcastle disease virus (NDV) and spread the virus to domestic poultry. Frequent exposure of backyard poultry to wild birds andor their excretions increases the risk of acquiring infection from wild birds. In the present study, tracheal andor cloacal swabs were collected from a total of 242 apparently healthy chicken and ducks from the backyards. The samples were tested for the presence of NDV using matrix (M) gene based quantitative real time polymerase chain reaction (RT-qPCR), where all the samples were found negative. Virus isolation was attempted using specific pathogen free- embryonated chicken eggs (SPF-ECEs). Out of 242 samples, 22 samples (9.09) showed haemagglutination (HA) across different passages. Genome of NDV could not be amplified in any of these HA-positive samples by using M gene-based RT-qPCR, and L- and F- genes based conventional reverse transcription polymerase chain reaction (RT-PCR). This indicates the presence of haemagglutinating agent other than NDV in the samples. Further studies are needed to identify the haemagglutinating agent detected in this study. All the samples in the present study were negative for NDV which might be due to absence of active infection during sample collection and vaccination status of the birds.

Haploblocks are regions of the genome that coalesce to an ancestor as a single unit. Differentiated haplotypes in these regions can result from the accumulation of mutational differences in low-recombination chromosomal regions, especially when selective sweeps occur within geographically structured populations. We introduce a method to identify large well-differentiated haploblock regions (LHBRs), based on the variance in standardised heterozygosity (ViSHet) of single nucleotide polymorphism (SNP) genotypes among individuals, calculated across a genomic region (500 SNPs in our case). We apply this method to the greenish warbler (Phylloscopus trochiloides) ring species, using a newly assembled reference genome and genotypes at more than 1 million SNPs among 257 individuals. Most chromosomes carry a single distinctive LHBR, containing 4-6 distinct haplotypes that are associated with geography, enabling detection of hybridisation events and transition zones between differentiated populations. LHBRs have exceptionally low within-haplotype nucleotide variation and moderately low between-haplotype nucleotide distance, suggesting their establishment through recurrent selective sweeps at varying geographic scales. Meiotic drive is potentially a powerful mechanism of producing such selective sweeps, and the LHBRs are likely to often represent centromeric regions where recombination is restricted. Links between populations enable introgression of favoured haplotypes and we identify one haploblock showing a highly discordant distribution compared to most of the genome, being present in two distantly separated geographic regions that are at similar latitudes in both east and central Asia. Our results set the stage for detailed studies of haploblocks, including their genomic location, gene content and contribution to reproductive isolation.

Remote sensing technology enables broad-scale ecological studies, with birds indicating global changes and validating its data. Despite its global relevance, the integration of remote sensing in ornithological research in India remains limited and fragmented. We conducted extensive literature review on the remote sensing applications in ornithological studies in India from 1992 to 2022 to reorient ornithological research primarily focusing on the existing satellite data, telemetry and GIS tools. The objectives of the review are: (1) to provide an overview of remote-sensing data applications in avian ecological studies, (2) to report the spatiotemporal trends and patterns in the characteristics of remote sensing data (scale, resolution, data source) applied in the studies, and identify the region-specific approaches and (3) to identify the research gaps, improve the methods and propose priority research themes by outlining the future scope of its applications in avian ecology and the conservation efforts as an opportunity to strengthen avian research using remote sensing technology in rapidly changing landscapes. We systematically reviewed literature (N = 108) that related remotely sensed data to bird distribution, abundance assessment, and migration. Our review covered 132 bird species across 19 orders and 5 feeding guilds. Forest birds were more frequently studied than wetland birds, with nearly 50

Despite the recognized significance of intrinsically disordered proteins (IDPs) in cellular processes and diseases, the landscape of intrinsic disorder within bat proteomes remains unexplored. Here, we systematically analyzed the prevalence and functional implications of IDPs across the complete proteomes of fourteen bat species and compared these to the human proteome. We first assessed ten widely used IDP predictors using a dataset of experimentally resolved disordered regions, identifying fIDPnn as the most suitable among the predictors benchmarked here for large-scale analyses of mammalian proteins. The results showed that the bat proteomes exhibit significantly lower IDP content (ranging from 12.6 % to 18.6 %) compared to humans (32.8 %). Correlation analyses revealed an inverse relationship between protein size and disorder content across both bats and humans. By integrating functional annotations with disorder contents, we found that intrinsic disorder enrichment or depletion in bat proteins aids in the species-specific immune gene regulation to coexist with a diverse array of pathogens. Our findings provide the first comprehensive map of intrinsic disorder in bat proteomes, highlighting distinct evolutionary and functional patterns relative to humans, and offer valuable insights into the molecular underpinnings of bat biology and their role as viral reservoirs.

Diagnostics employing multiple modalities have been essential for controlling and managing COVID-19, caused by SARS-CoV-2. However, scaling up Reverse Transcription-Quantitative Polymerase Chain Reaction (RT-qPCR), the gold standard for SARS-CoV-2 detection, remains challenging in low and middle-income countries. Cost-effective and high-throughput alternatives like enzyme-linked immunosorbent assay (ELISA) could address this issue. We developed an in-house SARS-CoV-2 nucleocapsid capture ELISA, and validated on 271 nasopharyngeal swab samples from humans (n = 252), bovines (n = 10), and dogs (n = 9). This ELISA has a detection limit of 195 pg/100 µL of nucleocapsid protein and does not cross-react with related coronaviruses, ensuring high specificity to SARS-CoV-2. Diagnostic performance was evaluated using receiver operating characteristic curve analysis, showing a diagnostic sensitivity of 67.78 % and specificity of 100 %. Sensitivity improved to 74.32 % when excluding positive clinical samples with RT-qPCR Ct values > 25. Furthermore, inter-rater reliability analysis demonstrated substantial agreement (κ values = 0.73-0.80) with the VIRALDTECT II Multiplex RT-qPCR kit and perfect agreement with the CoVeasy™ COVID-19 rapid antigen self-test (κ values = 0.89-0.93). Our findings demonstrated that the in-house nucleocapsid capture ELISA is suitable for SARS-CoV-2 testing in humans and animals, meeting the necessary sensitivity and specificity thresholds for cost-effective, large-scale screening.

A highly divergent bovine calicivirus was identified in an Indian calf with enteritis. The whole genome of this virus was sequenced, revealing distinct amino acid motifs in the polyprotein encoded by open reading frame 1 (ORF1) that are unique to caliciviruses. Phylogenetic analysis showed that it was related to members of the genus Nebovirus of the family Caliciviridae. Although it showed only 33.7-34.2% sequence identity in the VP1 protein to the nebovirus prototype strains, it showed 90.6% identity in VP1 to Kirklareli virus, a nebovirus detected in calves with enteritis in Turkey in 2012. An in-house-designed and optimized reverse transcription polymerase chain reaction (RT-PCR) assay was used to screen 120 archived bovine diarrhoeic fecal samples, 40 each from the Indian states of Uttar Pradesh, Haryana, and Himachal Pradesh, revealing frequent circulation of these divergent caliciviruses in the bovine population, with an overall positivity rate of 64.17% (77/120). This underscores the importance of conducting a comprehensive investigation of the prevalence of these divergent caliciviruses and assessing their associations with other pathogens responsible for enteritis in India.

Resource availability, predator-prey interaction, anthropogenic disturbances, climatic and topographic factors often determine the ecological association of a species with its environment. We measured the ecological association of Indian peafowl (Pavo cristatus), and grey junglefowl (Gallus sonneratii), with predator, habitat, and human disturbance using camera traps, following an occupancy modelling framework at the Male Mahadeshwara Hills Wildlife Sanctuary, Karnataka. We collected single-season data from 172 camera trap stations during 30 days. Site occupancy for junglefowl was found to be 0.40 ± 0.08, whereas for peafowl it was 0.31 ± 0.06. The detection probability for junglefowl was 0.06 ± 0.006, and for peafowl, it was 0.08 ± 0.007. Junglefowl occupancy was negatively associated with tiger (Panthera tigris) abundance because of the difference in the habitat preferences. Contrastingly, relative abundance of leopard (Panthera pardus) and jungle cat (Felis chaus) positively influenced the occupancy of pheasants due to similar habitat preferences and predator-prey interactions. Elevation and tree density were positively associated to Junglefowl occupancy due to the availability of good foliage and climatic conditions. However, occupancy probability of peafowl and detection probability showed negative relationship with tree density and goat-sheep abundance respectively. This indicates that peafowls rely on the undergrowth in open forests, scrub jungles, and cultivation areas, and require understory vegetation for nesting, roosting, and feeding. Our study helps to fill the knowledge gap to understand the ecological interaction of less studied ground-dwelling birds.

In 2015, a novel highly divergent bovine calicivirus was detected in an Indian calf with enteritis. Phylogenetic analysis linked it to the Nebovirus with only 38.5% sequence identities, emphasizing the need for separate taxonomic classification. Furthermore, PCR screening detected these unique caliciviruses widely in India’s northern states.

Indian hare Lepus nigricollis have a vast distribution in southern Asia with several subspecies.Even though it is distributed in a large area, the species lacks regional assessment and has been understudied for taxonomy, ecology, and demography.The species is stated to be absent from the high reaches of the Himalayas; however, several records reveal the presence of the species in the higher reaches of the Himalayas.In this article, we present records of Indian hare from the higher reaches of the Himalayas based on questionnaire survey, literature review, and directed sightings, which could be used to reassign its distribution range.

Abstract Gorals are distributed in varied ranges of habitats in South and South–East Asia, and the existence of the number of species in the genus Naemorhedus has been greatly debated from time to time. A school of thought supports the presence of three species, while a recent genetic study recognizes five species of goral throughout their distribution range. However, the unavailability of DNA sequences of gorals from India left a gap in understanding the species occurrence in Indian Himalayan Region (IHR). We revisited goral taxonomy by sequencing mitochondrial Cytochrome b gene (∼404 bp) and control region (∼225 bp) of 75 Himalayan gorals from Western and Central Himalayas in India. Based on various species delineating methods, we suggest that Himalayan goral (N. goral) is a highly diverged species and possibly exists into two subspecies, i.e. N. g. bedfordi in Western Himalayas and N. g. goral in the Central Himalayas. We validate the presence of plausibly six species of gorals across the distribution and recognize N. griseus and N. goral are two distinct species considering the observed discrepancy in the available sequences. We also propose that goral populations distributed in Western and Central Himalayas may be considered as two evolutionary significant units (ESUs). This recognition will bring concentrated efforts in further exploring the natural populations and ecological information required for prioritizing conservation and management of Himalayan goral.

The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence of a highly divergent variant of concern (VOC) defined as Omicron or B.1.1.529. This VOC is of particular concern because it has the potential to evade most therapeutic antibodies and has undergone a sustained genetic evolution, resulting in the emergence of five distinct sub-lineages. However, the evolutionary dynamics of the initially identified Omicron BA.1 and BA.2 sub-lineages remain poorly understood. Herein, we combined Bayesian phylogenetic analysis, mutational profiling, and selection pressure analysis to track the virus’s genetic changes that drive the early evolutionary dynamics of the Omicron. Based on the Omicron dataset chosen for the improved temporal signals and sampled globally between November 2021 and January 2022, the most recent common ancestor (tMRCA) and substitution rates for BA.1 were estimated to be that of 18 September 2021 (95% highest posterior density (HPD), 4 August–22 October 2021) and 1.435 × 10−3 (95% HPD = 1.021 × 10−3 − 1.869 × 10−3) substitution/site/year, respectively, whereas 3 November 2021 (95% highest posterior density (HPD) 26 September–28 November 2021) and 1.074 × 10−3 (95% HPD = 6.444 × 10−4 − 1.586 × 10−3) substitution/site/year were estimated for the BA.2 sub-lineage. The findings of this study suggest that the Omicron BA.1 and BA.2 sub-lineages originated independently and evolved over time. Furthermore, we identified multiple sites in the spike protein undergoing continued diversifying selection that may alter the neutralization profile of BA.1. This study sheds light on the ongoing global genomic surveillance and Bayesian molecular dating analyses to better understand the evolutionary dynamics of the virus and, as a result, mitigate the impact of emerging variants on public health.

The avian haemosporidians (Plasmodium and Haemoproteus) are widely distributed and may affect the host populations from body damage at individual level to the extinction of a population. The knowledge about their status may help in future avifauna conservation plans. Hence, we examined the avian haemosporidians status, in selected bird groups (Old world Flycatchers, Warblers, Babblers, and Thrushes) of India, and their phylogenetic relationships with other known lineages of the world. We used the common genetic marker (Cytochrome b gene fragment of 479 bp) with information on the geographic distribution of parasite and host species available at MalAvi database. The prevalence of avian haemosporidians, from northern, eastern, and southern parts of India and phylogenetic genetic analysis of lineages was carried out to know the genetic relatedness among them at local and world level. The MCC tree revealed six Haemosporidian lineages in which one was common (H_MSP01) and five were unique (H_CYOPOL01, H_CHD01, H_CYORUB01, H_EUMTHA01, and P_GEOCIT01). The avian host richness Index was 2.0852. 9.9%, prevalence of Haemosporidian infection was found in 111 DNA samples belonging to 6 host species. The Haemoproteus prevalence was found to be 9.0 % across five host species (Phylloscopus trochiloides, Cyornis poliogenys, C. hainanus dialilaemus, C. rubeculoides, Eumiyas thalassinus) and Plasmodium prevalence was 0.9% in Geokichla citrina. Spatial phylogeny at global level showed H_MSP01 lineage, found in different host species in India, was genetically related to H. pallidus lineages (COLL2 and PFC1) in parts of Africa, Europe, North America, Malaysia, and Philippines. The Plasmodium lineage (P_GEOCIT01) was related to PADOM16 in Egypt with poor sequence similarity (93.89%). The statistical analysis suggested that the haemosporidian’s host species distribution range was directly and significantly associated with the altitude, minimum temperature, and relative humidity. H_MSP01 distribution was in accordance with H. pallidus having a wide geographic and host range.

most s s We ed Birds are the most prominent wildlife species in forest and ecosystem attempt to enlist the existing avifaunal species in .trans-Himalayan Lahaul and Spiti, Himachal Pradesh based on our observations, previously published checklists/observations and eBird data.22 A s have been reliably recorded in this region that s total of 278 species belonging to 20 order and 59 families of birds .Species belong to the Muscicapidae family were the most sighted during We also report six new Short-eared owl ( the study period.species for the region: Asio flammeu , ) Lesser Cuckoo( ), Large-spotted Nutcracker ( ) Scarlet Minivet ( Blyth's Cuculus poliocephalus Nucifraga multipunctate , Pericrocotus flammeus , ) Leaf-warbler( ) and Red-tailed Wheatear ( ).Large-spotted Nutcracker Scarlet Phylloscopus reguloides Oenanthe chrysopygia , Among these, Minivet andBlyth's Leaf-warbler were sighted frequently during the study period but reported .never been previously for the region