Cryptic circulation, persistence, and positive selection of yellow fever virus in Colombia

The Acute Febrile Illness (AFI) is defined as a sudden increase in temperature, accompanied by other symptoms caused by a wide variety of pathogens. Fever has multiple etiologies, including in South America infections caused by the protozoan parasite Plasmodium falciparum, which causes malaria; infection caused by the dengue virus, Leptospira spp., Rickettsia spp., typhoid fever, chikungunya, and Zika, as well as a wide range of other parasites, viruses, and bacteria. For this reason, it is common for people to seek medical attention.Given the wide range of pathogens that may be responsible for febrile illness, detecting the etiology is challenging with only a few diagnostic tests, increasing the risk that the illness will progress to become potentially fatal due to the absence of appropriate treatment. However, advances in genome sequencing, such as next-generation metagenomic sequencing, are emerging as promising tools to address the challenge of identifying fever etiologies by enabling unbiased detection of infectious agents in a biological sample. It is worth noting that detecting these pathogens can assist in designing targeted diagnostics and improving epidemiological surveillance in low- and middle-income countries such as Colombia.The metagenomic approach has been successful in detecting pathogens for which traditional detection methods fail. With this goal in mind, a characterization with a metagenomic approach is intended to be carried out for potential pathogens associated with undifferentiated febrile syndrome in different municipalities of Colombia.