Widespread SARS-CoV-2 infection in free-ranging Neotropical bats suggests repeated human-to-bat spillback
- 1Centro de Biotecnología, Universidad Nacional de Loja, Loja, Ecuador; Grupo de Investigación en Genética y Biología Molecular, Universidad Nacional de Loja, Loj
Abstract
Bats harbor exceptional coronavirus diversity and are considered ancestral sources of several human pathogens. As SARS-CoV-2 transitioned from pandemic emergence to global endemicity in humans, concern has shifted from wildlife-to-human spillover toward reverse zoonosis. However, infection of free-ranging bat populations under natural conditions has not previously been demonstrated. Here, we report widespread detection of SARS-CoV-2 RNA in wild Neotropical bats sampled across Andean and Amazonian ecosystems of Southern Ecuador. RT-qPCR screening of 126 individuals, representing nine taxa, detected SARS-CoV-2 RNA in 34.12% of bats across multiple sites. Partial to near-complete viral genomes recovered from five individuals showed >99% nucleotide identity to contemporary human SARS-CoV-2 lineages and clustered within multiple global phylogenetic clades. Mixed-effects modeling revealed pronounced species-level heterogeneity, a positive association between elevation and infection probability, and higher infection probability in females compared with males. The close phylogenetic affinity of bat-derived genomes to circulating human variants and their distribution across multiple lineages suggest repeated anthropogenic spillback rather than sustained bat-specific circulation. These results expand current understanding of the ecological footprint of the COVID-19 pandemic and highlight the importance of integrating wildlife surveillance into long-term One Health strategies for emerging infectious diseases.
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BibTeX
@misc{armijosrivera2026widespread,
title = {{Widespread SARS-CoV-2 infection in free-ranging Neotropical bats suggests repeated human-to-bat spillback}},
author = {J. Armijos-Rivera and G. Parra and M. Bravo-Bonilla and M. Gonzalez-Maldonado and D. Roman-Caceres and A. Vasquez-Tituana and J. Valdivieso and F. Tinoco and A. Villavicencio and N. Aguirre and R. Cisneros-Vidal and V. Romero and J. Garces and D. de Mora and A. Bruno and A. Moreno and C. Tolini and L. Bavagnoli and L. M. Gomulski and F. Scolari and E. Crespan},
howpublished = {bioRxiv},
year = {2026},
month = aug,
doi = {10.64898/2026.08.27.741511},
url = {https://www.biorxiv.org/content/10.64898/2026.08.27.741511v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Widespread SARS-CoV-2 infection in free-ranging Neotropical bats suggests repeated human-to-bat spillback
AU - J. Armijos-Rivera
AU - G. Parra
AU - M. Bravo-Bonilla
AU - M. Gonzalez-Maldonado
AU - D. Roman-Caceres
AU - A. Vasquez-Tituana
AU - J. Valdivieso
AU - F. Tinoco
AU - A. Villavicencio
AU - N. Aguirre
AU - R. Cisneros-Vidal
AU - V. Romero
AU - J. Garces
AU - D. de Mora
AU - A. Bruno
AU - A. Moreno
AU - C. Tolini
AU - L. Bavagnoli
AU - L. M. Gomulski
AU - F. Scolari
AU - E. Crespan
PY - 2026
DA - 2026/08/27
PB - bioRxiv
DO - 10.64898/2026.08.27.741511
UR - https://www.biorxiv.org/content/10.64898/2026.08.27.741511v1
AB - Bats harbor exceptional coronavirus diversity and are considered ancestral sources of several human pathogens. As SARS-CoV-2 transitioned from pandemic emergence to global endemicity in humans, concern has shifted from wildlife-to-human spillover toward reverse zoonosis. However, infection of free-ranging bat populations under natural conditions has not previously been demonstrated. Here, we report widespread detection of SARS-CoV-2 RNA in wild Neotropical bats sampled across Andean and Amazonian ecosystems of Southern Ecuador. RT-qPCR screening of 126 individuals, representing nine taxa, detected SARS-CoV-2 RNA in 34.12% of bats across multiple sites. Partial to near-complete viral genomes recovered from five individuals showed >99% nucleotide identity to contemporary human SARS-CoV-2 lineages and clustered within multiple global phylogenetic clades. Mixed-effects modeling revealed pronounced species-level heterogeneity, a positive association between elevation and infection probability, and higher infection probability in females compared with males. The close phylogenetic affinity of bat-derived genomes to circulating human variants and their distribution across multiple lineages suggest repeated anthropogenic spillback rather than sustained bat-specific circulation. These results expand current understanding of the ecological footprint of the COVID-19 pandemic and highlight the importance of integrating wildlife surveillance into long-term One Health strategies for emerging infectious diseases.
ER -