Chapare Hemorrhagic Fever and Virus Detection in Rodents in Bolivia in 2019

Abstract

Background: In June 2019, the Bolivian Ministry of Health reported a cluster of cases of hemorrhagic fever that started in the municipality of Caranavi and expanded to La Paz. The cause of these cases was unknown.

Methods: We obtained samples for next-generation sequencing and virus isolation. Human and rodent specimens were tested by means of virus-specific real-time quantitative reverse-transcriptase-polymerase-chain-reaction assays, next-generation sequencing, and virus isolation.

Results: Nine cases of hemorrhagic fever were identified; four of the patients with this illness died. The etiologic agent was identified as Mammarenavirus Chapare mammarenavirus, or Chapare virus (CHAPV), which causes Chapare hemorrhagic fever (CHHF). Probable nosocomial transmission among health care workers was identified. Some patients with CHHF had neurologic manifestations, and those who survived had a prolonged recovery period. CHAPV RNA was detected in a variety of human body fluids (including blood; urine; nasopharyngeal, oropharyngeal, and bronchoalveolar-lavage fluid; conjunctiva; and semen) and in specimens obtained from captured small-eared pygmy rice rats (Oligoryzomys microtis). In survivors of CHHF, viral RNA was detected up to 170 days after symptom onset; CHAPV was isolated from a semen sample obtained 86 days after symptom onset.

Conclusions: M. Chapare mammarenavirus was identified as the etiologic agent of CHHF. Both spillover from a zoonotic reservoir and possible person-to-person transmission were identified. This virus was detected in a rodent species, O. microtis. (Funded by the Bolivian Ministry of Health and others.).

Figure 1.. Chapare Virus in Bolivia.

This map of South America shows the location of Bolivia and the distribution of the possible rodent reservoir of Chapare virus (CHAPV), small-eared pygmy rice rats (Oligoryzomys microtis). The inset shows the history of transmission of Bolivian hemorrhagic fever and Chapare hemorrhagic fever (CHHF) and the locations of CHAPV transmission in 2019.

Figure 2.. Transmission Chains Indicating Epidemiologic Linkages of Probable and Confirmed CHHF Cases in 2019.

Figure 3.. Detection of CHAPV by an Indirect Immunofluorescence Assay and Electron Microscopy.

In Panel A, an indirect immunofluorescence assay shows CHAPV Bolivia 2019 isolate obtained from Patient S1-2 (passage 1 in Vero E6 cells, 7 days after inoculation). In Panel B, electron microscopy of CHAPV Bolivia 2019 isolate shows typical arenavirus morphologic features with pleomorphic virions containing ribosomes. The virus isolate was obtained from Patient S1-4 (passage 2 in Vero E6 cells, 7 days after inoculation). The arrow indicates a budding viral particle. The scale bar represents 200 nm.

Figure 4.. Phylogenetic Analysis of New World Mammarenaviruses, Including Chapare mammarenavirus Species.

The phylogenetic tree shows relatedness between representative New World mammarenavirus S segments (Panels A and B) and L segments (Panels C and D) from clades A, B, and C, and 2019 Chapare virus sequences obtained from seven patients and two rodents (Oligoryzomys microtis) in the 2019 CHHF outbreak in Bolivia. The GenBank accession numbers of the sequences used in the phylogenetic analysis are listed in parentheses after the patient number and the location and date of specimen collection. The GenBank numbers of other viruses follow the virus names. The scale bars denote the genetic distance in nucleotide substitutions per site. The arrows in Panels A and C indicate the expanded sections shown in Panels B and D.