What makes bats important reservoirs of zoonotic viruses like Nipah 

At the same time, environmental changes, such as deforestation in regions like the Amazon and Southeast Asia, as well as permafrost thaw, may expose previously sequestered pathogens and expand opportunities for viruses to encounter new hosts.

Pigs as amplifying hosts of Nipah

Nipah virus was first identified in 1998 during an outbreak among pig farmers in Malaysia, and was named after a village called Kampung Sungai Nipah. Fatalities among patients were reported to be as high as nearly 50–55 per cent. SARS-CoV-2 virus has shown around 1 per cent fatality in the general population.

Affected farm animals exhibited respiratory distress, coughing, tremors, and sudden collapse. Illness in pigs became popularly known as the “one-mile barking cough”, as its spread could be detected across nearby farms. 

Initially, the outbreak was misdiagnosed as Japanese encephalitis, but observation of the cultured virus in monkey kidney cell lines under electron microscopy provided the first indication of a novel pathogen.

Subsequent investigations identified pigs as amplifying hosts. And fruit bats of the genus Pteropus – including the flying fox (Pteropus hypomelanus) and the large flying fox (Pteropus vampyrus) – were recognised as the probable natural reservoirs, supported by high antibody prevalence and viral detection in bat excreta. 

Epidemiological tracing suggested that partially eaten or contaminated fruits (such as jambu air or water apple) dropped into pig enclosures facilitated transmission from bats to pigs. In response, the Malaysian government ordered the culling of approximately 1.1 million pigs and the relocation of farms away from fruit trees. 

Outbreaks of the virus in Bangladesh, India

Nipah later appeared in Bangladesh, but this time there were no pigs. The virus appeared to play hide and seek, as there were several outbreaks, and intermittent emergence of new infection clusters, causing a fatality rate of 74 per cent. Evidence suggested the Indian flying fox (Pteropus medius) as the reservoir. 

Consumption of fresh date palm sap was identified as a major risk factor, as the sap is frequently contaminated by bat saliva, urine, or feces. Outbreaks of Nipah virus consistently occurred in seasons and places where the consumption of date palm sap was common. 

In India, outbreaks have been documented in West Bengal – in Siliguri in 2001 and in Nadia in 2007. More recently, it was reported in Kerala with recurrent events since 2018, and occasional detections in eastern India. Two cases had been reported in West Bengal since December 2025, but the Union Health Ministry clarified that all the contacts linked to them tested negative.

Pteropus bat populations have been identified as the primary reservoir of the virus, with surveillance studies reporting substantial seroprevalence (23-65%) and detecting viral RNA in their tissues.

How viruses are classified 

Viruses can be broadly classified based on the type of genetic material they carry and the mechanisms by which it is replicated to produce progeny. DNA viruses possess DNA as their genetic material, which may be either double-stranded (e.g., adenoviruses and many bacteriophages) or single-stranded (e.g., parvoviruses). RNA viruses, in contrast, carry their genetic information in RNA, which may likewise be single-stranded (e.g., coronaviruses such as SARS-CoV-2) or double-stranded (e.g., rotavirus). 

Because nucleic acid strands are complementary and directionally polar (5′→3′), single-stranded RNA viruses (and also single stranded DNA viruses) are further classified as positive-sense or negative-sense. In RNA viruses, it depends on whether their genome can be directly translated or must first be transcribed into a complementary strand. 

A third major group, retroviruses, replicates through both RNA and DNA intermediates using reverse transcription during their replication cycle within host cells. The genetic material of Nipah virus is a single-stranded negative-sense RNA genome, and it is therefore classified as an RNA virus. 

Viruses occupy a debated position at the boundary of life, yet under Leslie Orgel’s broader definition – CITREONS (Complex Information-Transforming Reproductive Objects that Evolve by Natural Selection) – viruses qualify as evolving biological entities because they generate heritable variation and undergo natural selection within their hosts. 

Host–virus interactions

Viruses are obligatory parasites and completely depend on their host for replication and survival. Generally, viruses are specific to a single host, but viruses, due to their high mutation rate, can jump host occasionally to infect new organisms causing zoonosis. 

There are, however, certain rules of thumb: 

* Closer phylogenetic distance between two organisms increases the chances of zoonosis.

* To become endemic in a population of a new host, the virus should achieve a reasonable rate of transmission capability between the individuals. 

During early spillover events, infections may be severe due to limited host adaptations. But over time, evolutionary pressures tend to favour variants that optimise transmission, often leading to more stable host–virus interactions.

Why RNA viruses like Nipah are of particular concern 

RNA viruses like Nipah are a special concern due to their high rate of mutation. This stems from the enzyme RNA-dependent RNA polymerase (RdRp), which is highly error prone and lacks proof-reading activity (error correction property), unlike DNA polymerases. 

RNA viruses can quickly generate mutations that can help them establish in new hosts. But the same phenomenon can risk mutational meltdown, or error catastrophe, due to the accumulation of large numbers of deleterious mutations within a few cycles of replication. Thus, high rates of mutation impose a practical limit on the genome size of RNA viruses. 

Nipah virus possesses a relatively large (approximately 18 kb), non-segmented negative-sense RNA genome – near the upper range for paramyxoviruses. This suggests that its replication fidelity is sufficient to maintain additional regulatory and accessory genes, while still remaining constrained by the mutation-driven error threshold typical of RNA viruses.

Mutational variability

Structural features such as RNA secondary structures and mutational buffering at the protein level can provide partial robustness, allowing RNA viruses to tolerate a degree of replication error. Variations in mutational frequency in RNA viruses range from 10-² – 10-⁵ substitutions per site per year, with most occurring near the median 10-³ substitutionss per site per year. This is higher than DNA viruses, which have the value 10-⁸ substitution per site per year. 

One specific reason behind this mutational variability is host-cell differences. But it is the differences in viral generation time (replication rate), and specifically the time it takes to go from infected cell to another infected cell, that explain most of the variance in substitution rates. 

Finally, a small fraction of mutations, largely in deeper phylogenetic branches, establish high frequency in populations and get fixed. The rest are terminal and are ultimately lost. Overall, RNA viruses appear to be shaped by evolutionary pressures that balance replication speed with fidelity, as they must continually evade host innate and adaptive immune responses while maintaining viable genomes. 

This trade-off imposes an upper ceiling on tolerable mutation rates; exceeding it is deleterious, which is why mutagenic antivirals such as ribavirin and 5-fluorouracil can act by pushing viral populations toward lethal mutagenesis.

Ecological traits of bats, and viral transmission 

Bats are now recognised as important natural reservoirs for numerous zoonotic viruses. Evidence suggests bats evolved nearly 52-50 million years ago, coinciding with a significant rise in global temperature and zoonotic viruses, like henipaviruses such as Nipah and Hendra virus and lyssaviruses responsible for rabies. This suggests a very long history of host-virus co-speciation. 

Ecological traits of bats, such as seasonal or partial migration, mixed-species roosting, large colony sizes, and unusually long lifespans for small mammals, facilitate viral maintenance and transmission within and between populations. Transplacental transmission of viruses in bats leads to acquired virus in offspring. 

Although this is not well established, there may be effects of temperature and viral titres in bat blood, which indicate persistent infection and continuous viruses shedding from bats through saliva and urine. Rigorous scientific investigation, such as Bats: important reservoir hosts of emerging viruses by Charles H. Calisher and others, has already identified over 6o virus species belonging at least 18 different families, and the list is growing. 

But it is important to remember that bats play a unique ecological role, such as in controlling insects and supporting agriculture. Therefore, attempts to eliminate them can disrupt ecosystems, while doing little to reduce the already low incidence of virus transmission by bats.

Post read questions

Discuss the ecological and evolutionary factors that make bats important reservoirs of emerging zoonotic diseases, with special reference to Nipah virus.

Explain the concept of zoonotic spillover. Why do changing human–animal interfaces increase the risk of diseases such as Nipah virus infection?

RNA viruses pose unique challenges to global health security. Examine this statement with reference to mutation rates and viral evolution.

How do ecological disruption, agricultural intensification, and wildlife–human interactions contribute to the emergence of infectious diseases? Illustrate using Nipah virus outbreaks.

Public health responses to zoonotic diseases must balance disease prevention with biodiversity conservation. Discuss with reference to bats and Nipah virus.

(Dr. Arunangshu Das is the Principal Project Scientist at the Centre for Atmospheric Sciences, Indian Institute of Technology, Delhi.)

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