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Journal Articles Emerging Infectious Diseases Year : 2018

Visceral Leishmaniasis in Traveler to Guyana Caused by Leishmania siamensis , London, UK

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Abstract

to BLAST analyses (https://blast.ncbi.nlm.nih.gov/Blast. cgi). The YFV Uganda 2016 strain envelope sequence was aligned with reference YFV genomes by using MAFFT through the EMBL-EBI server (http://www.ebi.ac.uk), and phylogenies were generated with BEAST 1.8.4 (9), as previously described (7). BLAST analyses determined that the highest percentage identity (95%) is shared between the Uganda 2016 strain and strains from South Sudan 2003 in the envelope region (the only region for which data from the Sudan strain are available) versus 83% with Angola 2016 strains from the same region. Furthermore, the Uganda 2016 sequences corresponding to the NS genes NS3 and NS5 have the highest percentage identities (94% and 95%, respectively) with a Uganda 1948 strain relative to 85% and 84% with the Angola 2016 strains in the same regions. Together these BLAST analyses indicate that the Uganda 2016 YFV is most similar to strains in the East African genotype. Phylogenetic analyses confirm the BLAST analyses and place the Uganda 2016 YFV in a well-supported clade along with these East African genotype strains, whereas the Angola 2016 strains group with an Angola 1971 YFV (Figure), indicating that the Uganda outbreak in 2016 was not seeded by the Angola outbreak. These findings reiterate the endemicity of YFV throughout the tropical regions of Africa because at least 2 concurrent yellow fever outbreaks of independent origins were identified in 2016. Our findings also highlight the importance of assessing the molecular epidemiology of the virus in outbreak investigations. These data improve our understanding of YFV epidemiology in Africa and support the previous studies of Mutebi and colleagues (2). In addition, removal of contaminating ribosomal RNA proved to be an effective method for unbiased enrichment of viral RNA in degraded samples to enhance sequencing sensitivity.
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hal-03115084 , version 1 (19-01-2021)

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Jérôme Depaquit, Matthieu Kaltenbach, Frédérick Gay. Visceral Leishmaniasis in Traveler to Guyana Caused by Leishmania siamensis , London, UK. Emerging Infectious Diseases, 2018, 24 (8), pp.1599-1600. ⟨10.3201/eid2408.172147⟩. ⟨hal-03115084⟩
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