Via NEJM: Autochthonous Japanese Encephalitis with Yellow Fever Coinfection in Africa. Excerpt:
Japanese encephalitis virus and yellow fever virus are mosquito-borne flaviviruses that circulate in disjunct geographic areas with different mosquito vectors. Japanese encephalitis is endemic to most of Asia and the Western Pacific, whereas yellow fever occurs in tropical areas of Africa and South America.
Both viruses lead to a wide spectrum of disease severities that include asymptomatic infection and mild illness with influenza-like symptoms. However, severe yellow fever disease can be fatal in 20 to 60% of cases, whereas symptomatic Japanese encephalitis virus can progress to severe encephalitis, with case fatality rates of up to 30%. Survivors often have long-term neuropsychological sequelae.
In March 2016, during the yellow fever outbreak in Angola, a 19-year-old man was admitted to the Cunene Provincial Hospital with a 5-day history of fever, headache, and jaundice. The patient, who survived, worked in the capital city of Luanda at the onset of disease and had not traveled abroad. A blood sample was obtained, and a test for yellow fever virus was positive.
The sample was later processed for high-throughput RNA sequencing. Because the protocol followed made use of randomly primed cDNA synthesis, it provided a comprehensive and quantitative view of all RNA present in the sample, thus enabling the characterization of potential coinfecting viruses.
Surprisingly, de novo assembly of the sample reads revealed a Japanese encephalitis virus genome (GenBank accession number, KX945367) in addition to the expected yellow fever virus genome (GenBank accession number, KX982182). Phylogenetic analysis revealed that this Japanese encephalitis virus variant belongs to genotype III, clustering closely with variants sampled in Asia.
The yellow fever virus sequence was closely related to both a sequence from the 1971 yellow fever virus outbreak in Angola and the recently reported yellow fever virus sequence detected in a sample from a Chinese traveler returning from Angola.