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Zoonotic Implications of the Co-Circulation of Clade 2.3.4.4b and 2.3.2.1a H5N1 Avian Influenza Viruses in Nepal in 2023
Samples collected from two avian influenza outbreaks in Bagmati Province in central Nepal between January and March 2023 were positive for H5N1. Full genomes were generated for both viruses, which revealed that one of the viruses was very similar to clade 2.3.4.4b H5N1 identified in Bangladesh in 2021/2022. The second virus was a reassortant H5N1 virus consisting of four genes (HA, NA, NP, and M) originating from a clade 2.3.2.1a H5N1 and the remaining four genes (NS, PB1, PB2, and PA) originating from a 2.3.4.4b H5N1. Notably, this second virus had a high identity with 2.3.2.1a clade viruses identified in humans and cats in India in 2024–2025. These are the first full genome sequences of H5N1 avian influenza viruses from Nepal and given the recent human infections by 2.3.2.1a H5N1 viruses in the region, these data will be of interest to both public health and veterinary authorities.
Journal Article
Seasonal Changes in Bird Species and Feeding Guilds along Elevational Gradients of the Central Himalayas, Nepal
The Himalayas are a global hotspot for bird diversity with a large number of threatened species, but little is known about seasonal changes in bird communities along elevational gradients in this region. We studied the seasonality of bird diversity in six valleys of the Central Himalayas, Nepal. Using 318 plots with a 50 m radius, located from 2200 to 3800 m a.s.l., and repeated sampling during different seasons (mainly pre-monsoon, monsoon, and post-monsoon), we analyzed 3642 occurrences of 178 species. Birds classified in the literature as resident were more species-rich than migratory birds (140 vs. 38 species). In all six valleys and within the studied elevation range, species richness of all birds showed a peak at mid-elevation levels of 2600 or 3000 m a.s.l. Similar patterns were found for the most species-rich feeding guilds of insectivores (96 species) and omnivores (24 species), whereas the species richness of herbivores (37 species including frugivores) increased towards higher elevations. Among these feeding guilds, only species richness of insectivores showed pronounced seasonal changes with higher species numbers during post-monsoon season. Similarly, individual bird species showed distinct spatio-temporal distribution patterns, with transitions from species dominated by elevational differences to those characterized by strong seasonal changes. In an era of climate change, the results demonstrate that individual bird species as well as feeding guilds might greatly differ in their responses to climate warming and changes in the seasonality of the precipitation regime, two aspects of climate change which should not be analyzed independently.
Journal Article
Snow Leopard and Himalayan Wolf: Food Habits and Prey Selection in the Central Himalayas, Nepal
Top carnivores play an important role in maintaining energy flow and functioning of the ecosystem, and a clear understanding of their diets and foraging strategies is essential for developing effective conservation strategies. In this paper, we compared diets and prey selection of snow leopards and wolves based on analyses of genotyped scats (snow leopards n = 182, wolves n = 57), collected within 26 sampling grid cells (5×5 km) that were distributed across a vast landscape of ca 5000 km2 in the Central Himalayas, Nepal. Within the grid cells, we sampled prey abundances using the double observer method. We found that interspecific differences in diet composition and prey selection reflected their respective habitat preferences, i.e. snow leopards significantly preferred cliff-dwelling wild ungulates (mainly bharal, 57% of identified material in scat samples), whereas wolves preferred typically plain-dwellers (Tibetan gazelle, kiang and argali, 31%). Livestock was consumed less frequently than their proportional availability by both predators (snow leopard = 27%; wolf = 24%), but significant avoidance was only detected among snow leopards. Among livestock species, snow leopards significantly preferred horses and goats, avoided yaks, and used sheep as available. We identified factors influencing diet composition using Generalized Linear Mixed Models. Wolves showed seasonal differences in the occurrence of small mammals/birds, probably due to the winter hibernation of an important prey, marmots. For snow leopard, occurrence of both wild ungulates and livestock in scats depended on sex and latitude. Wild ungulates occurrence increased while livestock decreased from south to north, probably due to a latitudinal gradient in prey availability. Livestock occurred more frequently in scats from male snow leopards (males: 47%, females: 21%), and wild ungulates more frequently in scats from females (males: 48%, females: 70%). The sexual difference agrees with previous telemetry studies on snow leopards and other large carnivores, and may reflect a high-risk high-gain strategy among males.
Journal Article
Climate‐driven decline in the habitat of the endemic spiny babbler (Turdoides nipalensis)
Climate change could amplify the extinction risk of endemic species, and the risk is even greater for species occupying high elevations and mountain ranges. In this study, we assessed the climatically suitable habitat of the only endemic Nepalese bird species, the spiny babbler (Turdoides nipalensis), and predicted the extent of the future (2050 and 2070) habitat of this species under two climate change scenarios (SSP2‐4.5 and SSP5‐8.5). We used georeferenced occurrence points alongside ecologically meaningful climatic and topographic variables to develop an ensemble suitable habitat model using different species distribution modeling algorithms in BIOMOD2. We identified 22,488.83 km2 (15%) of Nepal's total land area as suitable habitat for this endemic species, where the nonprotected regions incorporated the largest extent of suitable habitat (88%), with a majority of this suitable area within the central Mid‐Hill region. Under the SSP2‐4.5 scenario, 21.58% and 34.08% of the current suitable habitat range are projected to be lost by 2050 and 2070, respectively. Whereas under the SSP5‐8.5 scenario, our projections suggest that 40.45% and 52.18% of habitat will be lost by 2050 and 2070, respectively. Habitat suitability increased with a rise in warmest quarter precipitation (above 1000 mm), coldest quarter precipitation between 50 and 100 mm, and warmest quarter temperature between 20 and 30°C. Given our results, it is crucial to review the conservation policy of nonprotected areas and formulate a spiny babbler‐specific conservation action plan with a special focus on protecting their primary habitat in human‐dominated landscapes and nonprotected areas.
Journal Article
Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics
Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases. A One Health approach is essential to address this urgent issue, recognizing the interconnectedness of human, animal, and environmental health. This study investigated the prevalence and transmission of AMR in a temporary settlement in Kathmandu, Nepal. By employing shotgun metagenomics, we analyzed a diverse range of samples, including human fecal samples, avian fecal samples, and environmental samples. Our analysis revealed a complex interplay of pathogenic bacteria, virulence factors (VF), and antimicrobial resistance genes (ARGs) across these different domains. We identified a diverse range of bacterial species, including potential pathogens, in both human and animal samples. Notably,
Prevotella spp.
was the dominant gut bacterium in human samples. Additionally, we detected a wide range of phages and viruses, including Stx-2 converting phages, which can contribute to the virulence of Shiga toxin-producing
E. coli
(STEC) strains. Our analysis revealed the presence of 72 virulence factor genes and 53 ARG subtypes across the studied samples. Poultry samples exhibited the highest number of ARG subtypes, suggesting that the intensive use of antibiotics in poultry production may contribute to the dissemination of AMR. Furthermore, we observed frequent horizontal gene transfer (HGT) events, with gut microbiomes serving as key reservoirs for ARGs. This study underscores the critical role of a One Health approach in addressing AMR. By integrating human, animal, and environmental health perspectives, we can better understand the complex dynamics of AMR and develop effective strategies for prevention and control. Our findings highlight the urgent need for robust surveillance systems, judicious antibiotic use, and improved hygiene practices to mitigate the impact of AMR on public health.
Journal Article
Surveillance of Influenza A Virus and Its Subtypes in Migratory Wild Birds of Nepal
Nepal boarders India and China and all three countries lie within the Central Asian Flyway for migratory birds. Novel influenza A H7N9 caused human fatalities in China in 2013. Subclinical infections of influenza A H7N9 in birds and the potential for virus dispersal by migratory birds prompted this study to assess avian H7N9 viral intrusion into Nepal. Surveillance of influenza A virus in migratory birds was implemented in early 2014 with assistance from the Food and Agricultural Organization (FAO). Of 1811 environmental fecal samples collected from seven wetland migratory bird roosting areas, influenza A H9N2 was found in one sample from a ruddy shelduck in Koshi Tappu Wildlife Reserve located in southern Nepal. Avian H7N9 and other highly pathogenic avian influenza viruses were not detected. This study provides baseline data on the status of avian influenza virus in migratory bird populations in Nepal.
Journal Article
The Population Decline of Gyps Vultures in India and Nepal Has Slowed since Veterinary Use of Diclofenac was Banned
Populations of oriental white-backed vulture (Gyps bengalensis), long-billed vulture (Gyps indicus) and slender-billed vulture (Gyps tenuirostris) crashed during the mid-1990s throughout the Indian subcontinent. Surveys in India, initially conducted in 1991-1993 and repeated in 2000, 2002, 2003 and 2007, revealed that the population of Gyps bengalensis had fallen by 2007 to 0.1% of its numbers in the early 1990s, with the population of Gyps indicus and G. tenuirostris combined having fallen to 3.2% of its earlier level. A survey of G. bengalensis in western Nepal indicated that the size of the population in 2009 was 25% of that in 2002. In this paper, repeat surveys conducted in 2011 were analysed to estimate recent population trends. Populations of all three species of vulture remained at a low level, but the decline had slowed and may even have reversed for G. bengalensis, both in India and Nepal. However, estimates of the most recent population trends are imprecise, so it is possible that declines may be continuing, though at a significantly slower rate. The degree to which the decline of G. bengalensis in India has slowed is consistent with the expected effects on population trend of a measured change in the level of contamination of ungulate carcasses with the drug diclofenac, which is toxic to vultures, following a ban on its veterinary use in 2006. The most recent available information indicates that the elimination of diclofenac from the vultures' food supply is incomplete, so further efforts are required to fully implement the ban.
Journal Article
Ciconiiformes Nesting on Trees in Cereal-Dominated Farmlands: Importance of Scattered Trees for Heronries in Lowland Nepal
Cereal farming is on the increase globally, and trees on these agricultural landscapes are selectively removed by farmers. Waterbird populations, supported on many cereal farmlands, need trees to place heronries and can be impacted by farmers' habits. In a cereal-dominated landscape in lowland Nepal, a landscape-scale field design was used to quantify characteristics of existing trees (density, species, girth, height), and contrasted against heronry trees to understand how choice of nest trees by select Ciconiiformes species was affected by farmers' habits. Tree density was patchy and tree species richness low, dominated by two tree species that had direct utility to farmers (Dalbergia sissoo – timber; Mangifera indica – fruits). Heronries were preferentially located on two wild tree species that were 8% of available trees and were either revered in local religion (Ficus religiosa; 36% of all heronries) or favored for agroforestry (Bombax ceiba; 42%). Heronries were preferentially located on larger trees. Availability of suitable trees for heronries was reduced by farmers' habits, but religious beliefs and agroforestry continued to support multi-functionality of cereal-dominated cropfields in lowland Nepal.
Journal Article