Mosquito-borne diseases have been an ongoing concern in tropical climates around the world. Mosquito-borne viruses are gradually making their way from tropical regions in Africa and Asia to Latin America and other areas of the world through insect migration and global travel/commerce, with more than 80 countries now reporting mosquito-borne diseases. The hurricane season brings an increase in rainfall and standing water where mosquitos often lay their eggs, generating spikes in reported cases of infection. (1)

Mosquito-Borne Diseases

Malaria is a parasitic infection transmitted by the female Anopheles mosquito associated with fever, headache and chills. There were approximately 219 million cases of malaria in 87 countries and 435,000 deaths reported in 2017, up slightly from 2015 numbers. More than 90% of cases and deaths were reported in Africa, with 61% of deaths occurring in children under the age of five. Malaria is curable, but it can take 7 to 15 days for symptoms to appear and treatment within 24-48 hours of symptoms is critical (7).

The Dengue virus is transmitted by the Aedes aegyptis mosquito. Up to 50-100 million Dengue infections are estimated annually in over 100 countries, resulting in more than 24,000 deaths. Thought there is no specific treatment, a Dengue vaccine is now available. Early detection and general medical care can significantly reduce fatalities (6,10).

The Chikungunya virus, Zika virus, and Yellow Fever, are also carried by the Aedes aegyptis mosquito. While the Chikungunya and Zika viruses were originally associated with temporary fever, rash, and joint pain, the discovery of a link between Zika virus and Guillain-Barre syndrome and microcephaly, a congenital brain abnormality, has increased concerns. Because Zika can also be sexually transmitted and can potentially remain in the bloodstream and semen for months, pregnant women (or women who may become pregnant) are at particular risk from persons visiting regions where Zika is present. There is currently no specific treatment or vaccine for the Chikungunya and Zika viruses (5,9). The strong similarity between symptoms of infection for the Dengue, Chikungunya, and Zika viruses and the presence of multiple viruses in certain areas frequently leads to misdiagnosis. Highly selective, rapid point-of-care tests are needed to quickly identify and treat infection (8).

Application of Aptamers in Mosquito-Borne Disease

Accessible detection assays, treatments, and vaccines are lacking for many of the WHOs neglected mosquito-borne diseases. Because aptamers are highly selective, quickly and easily selected against specific strains of viruses and viral proteins, and very temperature-stable, they are ideal candidates for the development of new diagnostic tests and potential therapeutics for tropical diseases.

Researchers in Hong Kong completed feasibility testing of two aptamer-based colorimetric tests for the detection of malaria in whole blood lysates. Researchers explored both a syringe test using filter paper and a plate-based format using aptamer-functionalized magnetic beads. While the syringe test yielded better sensitivity and a broader dynamic range, more sample pre-treatment was required to remove interference from hemoglobin. The plate-based assay showed sufficient sensitivity and proved to be more user-friendly. Both formats showed selectivity for malaria and yielded semi-quantitative colorimetric results visible without instrumentation. Through lyophilization of detection reagents, the researchers generated an assay with extended stability at high temperatures (4).

In 2015, researchers in Taiwan developed DNA aptamers to the dengue virus by selecting against domain III of the flavivirus envelope protein (ED3). They identified an aptamer with anti-viral activity against all four serotypes of the dengue virus. (2) In 2016, researchers in Brazil selected DNA aptamers against the 5’-UTR region of the dengue virus. The aptamers prevented translation of viral proteins involved in infection. (3). In 2017, a research team in Korea discovered a truncated 2’fluoro RNA aptamer to Dengue virus that inhibits methyltransferase activity of Dengue virus serotypes 2 and 3, preventing viral replication (10). 

In 2019, researchers in Florida reported on a microfluidic assay for detection of Zika and Chikungunya viruses utilizing aptamers discovered by Base Pair. While the aptamers were selected for detection of Zika and Chikungunya envelope proteins in mosquito saliva as part of a joint effort with the University of Central Florida and the Gates Foundation to enhance tracking and surveillance of infected mosquitos, detection was demonstrated in serum and defibrinated blood. The limit of detection for the aptamer-based sandwich assay was 1 pM (50 pg/mL) in PBS and 10 pM (500 pg/mL) in 10% serum (11). Selective binding, nuclease resistance, reproducible chemical synthesis and inherently low immunogenicity make aptamers attractive as viral therapeutics, but also useful as diagnostic agents. 

Ongoing Initiatives in Mosquito-Borne Disease

Improved efforts to reduce standing water near homes and populated areas; use of mosquito netting, protective clothing, and mosquito repellant; and support of municipal efforts to reduce mosquito populations can help reduce the number of infections, but they will not eliminate mosquito-borne disease. Researchers continue to explore the application of aptamers to generate simple point-of-care diagnostics and specific treatments for mosquito-borne diseases.

Base Pair Aptamers to Dengue, Zika, and Chikungunya

View Dengue Virus Type 2 NS1 Protein Aptamers

Additional aptamer clones are available for evaluation in research, diagnostic, and therapeutic applications. Contact Base Pair for more information.

View Zika Virus Envelope Protein Aptamers

Additional aptamer clones are available for evaluation in research, diagnostic, and therapeutic applications. Contact Base Pair for more information.

Chikungunya Virus E1 Envelope Protein Aptamers

Two natural DNA aptamers to the chikungunya E1 envelop protein are coming soon to the on-line catalog, but are curretly available for special purchase, including an aptamer utilized in a self-sandwich microfluidic assay by the University of Central Florida. Aptamers are available for evaluation in research, diagnostic, and therapeutic applications. Contact Base Pair for more information.


  1. CDC. Mosquitos and Hurricanes. Accessed September 25, 2017. 
  2. Chen, H. et al. Selection and characterization of DNA aptamers targeting all four serotypes of dengue viruses. PLoS ONE. 2015. 10(6): e0131240. Doi:10.1371/jpurnal.pone.0131240. 
  3. Cnossen, E.J.N., et al. Characterization of oligonucleotide aptamers targeting the 5´-UTR from dengue virus. Future Med. Chem. 2017. 9(6):541-552.
  4. Dirkswager, R.M. et al. Development of aptamer-based point-of-care diagnostic devices for malaria using three-dimensional printing rapid prototyping. Sensors. 2016. 1(4):420-426. 
  5. WHO. Chikingunya. Accessed May 16, 2019. 
  6. WHO. Dengue control. Accessed May 16, 2019. 
  7. WHO. Malaria. Accessed May 16, 2019. 
  8. WHO. Neglected tropical diseases. Accessed September 25, 2017
  9. WHO. Zika virus. Accessed May 16, 2019.
  10. Jun, J.I., et al. 2017. Development of RNA aptamer that inhibits methyltransferase activity of dengue virus. Biotechnology Letters. 40(2):315-324.
  11. Saraf, N. et al. Multiplex viral detection platform based on a aptamers-integrated microfluidic channel. ACS Omega. 2019. 4:2234-2240.