The Epidemiology and Genetic Diversity of Coxsackievirus A16 in Peru

By Caleb Sooknanan


These are the most likely trees of coxsackievirus A16 isolates based on the full-length VP1 and VP4 sequences.

            Coxsackievirus A16 (CVA16) is an RNA virus that often affects young children and causes rashes and ulcerating blisters. The epidemiology of CVA16 is mostly unknown. Dr. Gladys Carrion and researchers from US Naval Medical Research Unit No. 6 — along with the Peruvian institutions La Universidad Nacional San Agustín, El Centro de Salud de Pachitea, and El Instituto de Medicina Tropical Daniel Alcides Carrión — studied molecular epidemiology of seven different CVA16 strains in Peru. This would enable researchers to more effectively characterize CVA16 in this country and understand CVA16 outbreaks in other regions of the world.


The study used CVA16 samples from nasopharyngeal swabs. The cells were cultured and then underwent immunofluorescence and reverse transcription polymerase chain reaction (RT-PCR). Since CVA16 has been classified into genotypes A, B, or C based on the VP1 sequence, the researchers amplified full-length VP1 sequences of the seven strains. These sequences would then be examined to determine genetic diversity and create phylogenetic trees for the different strains. The researchers successfully obtained full-length sequences for all strains.

According to the VP1 sequences, six strains were clustered in the same lineage and were separate from Australian, European, and Asian strains. These strains were classified as genotype C, while one divergent strain — found in Iquitos — was not clustered in any of the three genotypes. Thus, the molecular epidemiology of CVA16 in Peru was inferred to have a circulation pattern consisting primarily of genotype C.

Limitations of the study include the possibility that the molecular epidemiology of CVA16 may have been specific to certain regions within Peru, such as the Amazon basin. Also, the divergent strain may have been introduced independently into Iquitos by foreign travelers. Therefore, obtaining more isolate strains would be useful in understanding CVA16 epidemiology and genetic diversity within Peru and neighboring South America countries.



  1. “Department of Health.” Hand, Foot and Mouth Disease (Coxsackie Viral Infection). N.p., Oct. 2011. Web. 20 Nov. 2016.
  2. Carrion, et al., Molecular epidemiology of coxsackievirus A16 strains from four sentinel surveillance sites in Peru. International Journal of Infectious Diseases 52, 83-85 (2016). doi: 10.1016/j.ijid.2016.10.003
  3. Image retrieved from:

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