Chapare virus, a newly discovered arenavirus isolated from a fatal hemorrhagic fever case in Bolivia

Abstract

A small focus of hemorrhagic fever (HF) cases occurred near Cochabamba, Bolivia, in December 2003 and January 2004. Specimens were available from only one fatal case, which had a clinical course that included fever, headache, arthralgia, myalgia, and vomiting with subsequent deterioration and multiple hemorrhagic signs. A non-cytopathic virus was isolated from two of the patient serum samples, and identified as an arenavirus by IFA staining with a rabbit polyvalent antiserum raised against South American arenaviruses known to be associated with HF (Guanarito, Machupo, and Sabiá). RT-PCR analysis and subsequent analysis of the complete virus S and L RNA segment sequences identified the virus as a member of the New World Clade B arenaviruses, which includes all the pathogenic South American arenaviruses. The virus was shown to be most closely related to Sabiá virus, but with 26% and 30% nucleotide difference in the S and L segments, and 26%, 28%, 15% and 22% amino acid differences for the L, Z, N, and GP proteins, respectively, indicating the virus represents a newly discovered arenavirus, for which we propose the name Chapare virus. In conclusion, two different arenaviruses, Machupo and Chapare, can be associated with severe HF cases in Bolivia.

Figure 1. Map of Bolivia showing location of the Chapare virus-associated HF case relative to the Beni region where Machupo virus-associated HF cases originate.

The Beni Department boundary is depicted by the checkered line. Multiple Machupo isolates have been recorded from the Beni Department. The single Latino and Chapare virus locations are labeled and represented as dots.

Figure 2. Phylogenetic analysis of the complete S and L RNA segments of New World arenaviruses.

Complete S and L segments for New World arenaviruses were analyzed by Bayesian inference of phylogeny (MrBayes3.1.2) using the sequence of Pichindé virus as the outgroup. Multiple strains are grouped with small brackets and large brackets group the arenavirus Clades: A, A/Rec, B, and C. The Genbank accession numbers for the S segment analysis include: Allpahuayo (AY012686), Amapari (AF485256), Bear Canyon (AY924392), Catarina (DQ865245), Chapare (EU260463), Cupixi (AF512832), Flexal (AF485257), Guanarito (NC_005077), Junín (AY619641, NC_005081, AY746353), Latino (AF512830), Machupo (AY924208, AY619645, AY924202, NC_005078), Oliveros (U34248), Paraná (AF485261), Pichindé (NC_006447), Pirital (NC_005894), Sabiá (NC_006317), Tacaribe (NC_004293), Tamiami (AF485263), and Whitewater Arroyo (AF485264). The Genbank accession numbers used for the L segment analysis include: Allpahuayo (NC_010249), Amapari (AY924389), Bear Canyon (AY924390), Chapare (EU260464), Cupixi (NC_010252), Guanarito (NC_005082), Junín (NC_005080, AY819707, AY619640), Machupo (AY624354, NC_005079, AY619644), Oliveros (NC_010250), Pichindé (NC_006439), Pirital (NC_005897), Sabiá (NC_006313), Tacaribe (NC_004292), Tamiami (AY924393), and Whitewater Arroyo (AY924395).