Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response

Shruti Gupta; Rohit Sharma; Adeline E. Williams; Irma Sanchez-Vargas; Noah H. Rose; Chao Zhang; Alexander Crosbie-Villaseca; Margarita Kyza-Karavioti; Zheng Zhu; Gargi Dayama; Andrea Gloria-Soria; Doug E. Brackney; Jessica Manning; Sarah S. Wheeler; Angela Caranci; Trinidad Reyes; Massamba Sylla; Athanase Badolo; Jewelna Akorli; Ogechukwu B. Aribodor; Diego Ayala; Wei Liang Liu; Chun Hong Chen; Chalmers Vasquez; Cassandra Gonzalez Acosta; Alongkot Ponlawat; Tereza Magalhaes; Brendan H. Carter; Dawn M. Wesson; Darred Surin; Meg A. Younger; Andre Luis Costa-da-Silva; Matthew DeGennaro; Alexander Bergman; Louis Lambrechts; Carolyn S. McBride; Ken E. Olson; Eric Calvo; Nelson C. Lau

doi:10.1038/s41467-026-71964-1

Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response

Shruti Gupta
, Rohit Sharma
, Adeline E. Williams
, Irma Sanchez-Vargas
, Noah H. Rose
, Chao Zhang
, Alexander Crosbie-Villaseca
, Margarita Kyza-Karavioti
, Zheng Zhu
, Gargi Dayama
, Andrea Gloria-Soria
, Doug E. Brackney
, Jessica Manning
, Sarah S. Wheeler
, Angela Caranci
, Trinidad Reyes
, Massamba Sylla
, Athanase Badolo
, Jewelna Akorli
, Ogechukwu B. Aribodor

Diego Ayala, Wei Liang Liu, Chun Hong Chen, Chalmers Vasquez, Cassandra Gonzalez Acosta, Alongkot Ponlawat, Tereza Magalhaes, Brendan H. Carter, Dawn M. Wesson, Darred Surin, Meg A. Younger, Andre Luis Costa-da-Silva, Matthew DeGennaro, Alexander Bergman, Louis Lambrechts, Carolyn S. McBride, Ken E. Olson, Eric Calvo, Nelson C. Lau

Research output: Contribution to journal › Article › peer-review

Abstract

We report a global survey of viral small RNAs (vsmRNAs) from >200 Aedes aegypti samples to identify many mosquito viruses that actively infect this prominent arboviral vector. Ae. aegypti viruses in the Americas are abundant, with some displaying geographical boundaries. Viruses infecting Asian Ae. aegypti are similar to those in the Americas and reveal the first wild example of dengue vsmRNAs. African Ae. aegypti display vsmRNAs from viruses unique to these African strains. Academic lab colonies generally lack viruses, yet two commercial strains are deeply infected by a tombus-like virus that is related to plant viruses. Comparing matched viral long RNAs to vsmRNAs reveal viral transcripts evading the mosquito RNA interference (RNAi) pathway. By infecting mosquito cells with Ae. aegypti homogenates, we generate stably infected cell lines which produce vsmRNAs that were comparable to native mosquito vsmRNA patterns. Lastly, we demonstrate that these stably infected mosquito cells producing vsmRNAs can exert gene silencing of reporters bearing viral sequence segments, providing a potential explanation for how Ae. aegypti can resist viral infections. This vsmRNA genomics approach in Ae. aegypti can add to existing vector surveillance approaches by discovering new viruses that persist in mosquito populations.

Original language	English (US)
Article number	3658
Journal	Nature communications
Volume	17
Issue number	1
DOIs	https://doi.org/10.1038/s41467-026-71964-1
State	Published - Dec 2026

All Science Journal Classification (ASJC) codes

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General
General Physics and Astronomy

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10.1038/s41467-026-71964-1

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Gupta, S., Sharma, R., Williams, A. E., Sanchez-Vargas, I., Rose, N. H., Zhang, C., Crosbie-Villaseca, A., Kyza-Karavioti, M., Zhu, Z., Dayama, G., Gloria-Soria, A., Brackney, D. E., Manning, J., Wheeler, S. S., Caranci, A., Reyes, T., Sylla, M., Badolo, A., Akorli, J., ... Lau, N. C. (2026). Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response. Nature communications, 17(1), Article 3658. https://doi.org/10.1038/s41467-026-71964-1

@article{cd24e917b9a14daa98e037e0de9b371a,

title = "Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response",

abstract = "We report a global survey of viral small RNAs (vsmRNAs) from >200 Aedes aegypti samples to identify many mosquito viruses that actively infect this prominent arboviral vector. Ae. aegypti viruses in the Americas are abundant, with some displaying geographical boundaries. Viruses infecting Asian Ae. aegypti are similar to those in the Americas and reveal the first wild example of dengue vsmRNAs. African Ae. aegypti display vsmRNAs from viruses unique to these African strains. Academic lab colonies generally lack viruses, yet two commercial strains are deeply infected by a tombus-like virus that is related to plant viruses. Comparing matched viral long RNAs to vsmRNAs reveal viral transcripts evading the mosquito RNA interference (RNAi) pathway. By infecting mosquito cells with Ae. aegypti homogenates, we generate stably infected cell lines which produce vsmRNAs that were comparable to native mosquito vsmRNA patterns. Lastly, we demonstrate that these stably infected mosquito cells producing vsmRNAs can exert gene silencing of reporters bearing viral sequence segments, providing a potential explanation for how Ae. aegypti can resist viral infections. This vsmRNA genomics approach in Ae. aegypti can add to existing vector surveillance approaches by discovering new viruses that persist in mosquito populations.",

author = "Shruti Gupta and Rohit Sharma and Williams, \{Adeline E.\} and Irma Sanchez-Vargas and Rose, \{Noah H.\} and Chao Zhang and Alexander Crosbie-Villaseca and Margarita Kyza-Karavioti and Zheng Zhu and Gargi Dayama and Andrea Gloria-Soria and Brackney, \{Doug E.\} and Jessica Manning and Wheeler, \{Sarah S.\} and Angela Caranci and Trinidad Reyes and Massamba Sylla and Athanase Badolo and Jewelna Akorli and Aribodor, \{Ogechukwu B.\} and Diego Ayala and Liu, \{Wei Liang\} and Chen, \{Chun Hong\} and Chalmers Vasquez and Acosta, \{Cassandra Gonzalez\} and Alongkot Ponlawat and Tereza Magalhaes and Carter, \{Brendan H.\} and Wesson, \{Dawn M.\} and Darred Surin and Younger, \{Meg A.\} and Costa-da-Silva, \{Andre Luis\} and Matthew DeGennaro and Alexander Bergman and Louis Lambrechts and McBride, \{Carolyn S.\} and Olson, \{Ken E.\} and Eric Calvo and Lau, \{Nelson C.\}",

note = "Publisher Copyright: {\textcopyright} The Author(s) 2026.",

year = "2026",

month = dec,

doi = "10.1038/s41467-026-71964-1",

language = "English (US)",

volume = "17",

journal = "Nature communications",

issn = "2041-1723",

publisher = "Nature Research",

number = "1",

}

Gupta, S, Sharma, R, Williams, AE, Sanchez-Vargas, I, Rose, NH, Zhang, C, Crosbie-Villaseca, A, Kyza-Karavioti, M, Zhu, Z, Dayama, G, Gloria-Soria, A, Brackney, DE, Manning, J, Wheeler, SS, Caranci, A, Reyes, T, Sylla, M, Badolo, A, Akorli, J, Aribodor, OB, Ayala, D, Liu, WL, Chen, CH, Vasquez, C, Acosta, CG, Ponlawat, A, Magalhaes, T, Carter, BH, Wesson, DM, Surin, D, Younger, MA, Costa-da-Silva, AL, DeGennaro, M, Bergman, A, Lambrechts, L, McBride, CS, Olson, KE, Calvo, E & Lau, NC 2026, 'Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response', Nature communications, vol. 17, no. 1, 3658. https://doi.org/10.1038/s41467-026-71964-1

TY - JOUR

T1 - Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response

AU - Gupta, Shruti

AU - Sharma, Rohit

AU - Williams, Adeline E.

AU - Sanchez-Vargas, Irma

AU - Rose, Noah H.

AU - Zhang, Chao

AU - Crosbie-Villaseca, Alexander

AU - Kyza-Karavioti, Margarita

AU - Zhu, Zheng

AU - Dayama, Gargi

AU - Gloria-Soria, Andrea

AU - Brackney, Doug E.

AU - Manning, Jessica

AU - Wheeler, Sarah S.

AU - Caranci, Angela

AU - Reyes, Trinidad

AU - Sylla, Massamba

AU - Badolo, Athanase

AU - Akorli, Jewelna

AU - Aribodor, Ogechukwu B.

AU - Ayala, Diego

AU - Liu, Wei Liang

AU - Chen, Chun Hong

AU - Vasquez, Chalmers

AU - Acosta, Cassandra Gonzalez

AU - Ponlawat, Alongkot

AU - Magalhaes, Tereza

AU - Carter, Brendan H.

AU - Wesson, Dawn M.

AU - Surin, Darred

AU - Younger, Meg A.

AU - Costa-da-Silva, Andre Luis

AU - DeGennaro, Matthew

AU - Bergman, Alexander

AU - Lambrechts, Louis

AU - McBride, Carolyn S.

AU - Olson, Ken E.

AU - Calvo, Eric

AU - Lau, Nelson C.

PY - 2026/12

Y1 - 2026/12

N2 - We report a global survey of viral small RNAs (vsmRNAs) from >200 Aedes aegypti samples to identify many mosquito viruses that actively infect this prominent arboviral vector. Ae. aegypti viruses in the Americas are abundant, with some displaying geographical boundaries. Viruses infecting Asian Ae. aegypti are similar to those in the Americas and reveal the first wild example of dengue vsmRNAs. African Ae. aegypti display vsmRNAs from viruses unique to these African strains. Academic lab colonies generally lack viruses, yet two commercial strains are deeply infected by a tombus-like virus that is related to plant viruses. Comparing matched viral long RNAs to vsmRNAs reveal viral transcripts evading the mosquito RNA interference (RNAi) pathway. By infecting mosquito cells with Ae. aegypti homogenates, we generate stably infected cell lines which produce vsmRNAs that were comparable to native mosquito vsmRNA patterns. Lastly, we demonstrate that these stably infected mosquito cells producing vsmRNAs can exert gene silencing of reporters bearing viral sequence segments, providing a potential explanation for how Ae. aegypti can resist viral infections. This vsmRNA genomics approach in Ae. aegypti can add to existing vector surveillance approaches by discovering new viruses that persist in mosquito populations.

AB - We report a global survey of viral small RNAs (vsmRNAs) from >200 Aedes aegypti samples to identify many mosquito viruses that actively infect this prominent arboviral vector. Ae. aegypti viruses in the Americas are abundant, with some displaying geographical boundaries. Viruses infecting Asian Ae. aegypti are similar to those in the Americas and reveal the first wild example of dengue vsmRNAs. African Ae. aegypti display vsmRNAs from viruses unique to these African strains. Academic lab colonies generally lack viruses, yet two commercial strains are deeply infected by a tombus-like virus that is related to plant viruses. Comparing matched viral long RNAs to vsmRNAs reveal viral transcripts evading the mosquito RNA interference (RNAi) pathway. By infecting mosquito cells with Ae. aegypti homogenates, we generate stably infected cell lines which produce vsmRNAs that were comparable to native mosquito vsmRNA patterns. Lastly, we demonstrate that these stably infected mosquito cells producing vsmRNAs can exert gene silencing of reporters bearing viral sequence segments, providing a potential explanation for how Ae. aegypti can resist viral infections. This vsmRNA genomics approach in Ae. aegypti can add to existing vector surveillance approaches by discovering new viruses that persist in mosquito populations.

UR - https://www.scopus.com/pages/publications/105036410553

UR - https://www.scopus.com/pages/publications/105036410553#tab=citedBy

U2 - 10.1038/s41467-026-71964-1

DO - 10.1038/s41467-026-71964-1

M3 - Article

C2 - 42026069

AN - SCOPUS:105036410553

SN - 2041-1723

VL - 17

JO - Nature communications

JF - Nature communications

IS - 1

M1 - 3658

ER -

Small RNA genomics of Aedes aegypti mosquitoes discovers infectious viruses that trigger an RNA interference response

Abstract

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