Insights from a mobile healthcare clinic in Madagascar: Diversity and dynamics of viruses from febrile individuals in rural subsistence communities
- 1Arizona State University
Abstract
Communities living in biodiversity hotspots are at increased risk of pathogen exposure and spread due to insufficient access to nutrition, clean water, and sanitation. Viruses, in particular, have high epidemic and spillover potential, and widespread health impacts, yet, viral diversity and dynamics remain understudied in many high-risk regions. In Madagascar, a hotspot with unparalleled biodiversity, socioeconomic constraints, and a heavy burden of infectious diseases, ongoing healthcare initiatives provide opportunities to survey circulating viral diversity. Here, we used a metagenomic workflow to characterize the viromes of oral/nasal swabs from febrile individuals visiting a mobile healthcare clinic in southeastern Madagascar, of which 49% were malaria-positive (Plasmodium falciparum). We characterized sequences of human-infecting viruses from twelve families (Adenoviridae, Anelloviridae, Orthoherpesviridae, Papillomaviridae, Polyomaviridae, Astroviridae, Coronaviridae, Matonaviridae, Orthomyxoviridae, Paramyxoviridae, Picornaviridae, and Sedoreoviridae). These viral sequences generally showed high similarity to known lineages circulating globally, but multiple viruses considered rare or emerging were identified (e.g. enterovirus C105, enterovirus C117). While we did not detect a significant association between malaria status and pathogenic virus presence, younger individuals had higher odds of having a pathogenic virus. Nonpathogenic viruses in Anelloviridae were prevalent and diverse with richness ranging from 0 to 70. Individuals with P. falciparum or a pathogenic virus tended to share more anelloviruses. We also detected viruses that are protist-associated, plant-infecting, or with unknown hosts. Overall, our work documents extensive viral diversity in Madagascar, highlighting how metagenomic workflows can be used to build viral genomic resources for pathogen surveillance in regions with high infectious disease burden.
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BibTeX
@misc{paietta2026insights,
title = {{Insights from a mobile healthcare clinic in Madagascar: Diversity and dynamics of viruses from febrile individuals in rural subsistence communities}},
author = {E. N. Paietta and A. Tsirimanana and R. A. Johnston and T. F. Razafiarimihoby and O. Ravaoharimbola and S. Kraberger and C. M. M. DeSisto and E. Silva Orozco and M. Anahtar and B. McAdoo and E. Baitchman and S. Burza and M. Scotch and A. Varsani},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.07.757397},
url = {https://www.biorxiv.org/content/10.64898/2026.10.07.757397v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - Insights from a mobile healthcare clinic in Madagascar: Diversity and dynamics of viruses from febrile individuals in rural subsistence communities
AU - E. N. Paietta
AU - A. Tsirimanana
AU - R. A. Johnston
AU - T. F. Razafiarimihoby
AU - O. Ravaoharimbola
AU - S. Kraberger
AU - C. M. M. DeSisto
AU - E. Silva Orozco
AU - M. Anahtar
AU - B. McAdoo
AU - E. Baitchman
AU - S. Burza
AU - M. Scotch
AU - A. Varsani
PY - 2026
DA - 2026/10/07
PB - bioRxiv
DO - 10.64898/2026.10.07.757397
UR - https://www.biorxiv.org/content/10.64898/2026.10.07.757397v1
AB - Communities living in biodiversity hotspots are at increased risk of pathogen exposure and spread due to insufficient access to nutrition, clean water, and sanitation. Viruses, in particular, have high epidemic and spillover potential, and widespread health impacts, yet, viral diversity and dynamics remain understudied in many high-risk regions. In Madagascar, a hotspot with unparalleled biodiversity, socioeconomic constraints, and a heavy burden of infectious diseases, ongoing healthcare initiatives provide opportunities to survey circulating viral diversity. Here, we used a metagenomic workflow to characterize the viromes of oral/nasal swabs from febrile individuals visiting a mobile healthcare clinic in southeastern Madagascar, of which 49% were malaria-positive (Plasmodium falciparum). We characterized sequences of human-infecting viruses from twelve families (Adenoviridae, Anelloviridae, Orthoherpesviridae, Papillomaviridae, Polyomaviridae, Astroviridae, Coronaviridae, Matonaviridae, Orthomyxoviridae, Paramyxoviridae, Picornaviridae, and Sedoreoviridae). These viral sequences generally showed high similarity to known lineages circulating globally, but multiple viruses considered rare or emerging were identified (e.g. enterovirus C105, enterovirus C117). While we did not detect a significant association between malaria status and pathogenic virus presence, younger individuals had higher odds of having a pathogenic virus. Nonpathogenic viruses in Anelloviridae were prevalent and diverse with richness ranging from 0 to 70. Individuals with P. falciparum or a pathogenic virus tended to share more anelloviruses. We also detected viruses that are protist-associated, plant-infecting, or with unknown hosts. Overall, our work documents extensive viral diversity in Madagascar, highlighting how metagenomic workflows can be used to build viral genomic resources for pathogen surveillance in regions with high infectious disease burden.
ER -