Novel paramyxovirus associated with severe acute febrile disease, South Sudan and Uganda, 2012

Abstract

In 2012, a female wildlife biologist experienced fever, malaise, headache, generalized myalgia and arthralgia, neck stiffness, and a sore throat shortly after returning to the United States from a 6-week field expedition to South Sudan and Uganda. She was hospitalized, after which a maculopapular rash developed and became confluent. When the patient was discharged from the hospital on day 14, arthralgia and myalgia had improved, oropharynx ulcerations had healed, the rash had resolved without desquamation, and blood counts and hepatic enzyme levels were returning to reference levels. After several known suspect pathogens were ruled out as the cause of her illness, deep sequencing and metagenomics analysis revealed a novel paramyxovirus related to rubula-like viruses isolated from fruit bats.

Keywords: Paramyxoviridae; Sosuga virus; South Sudan; Uganda; bats; diagnostics; metagenomics; rash; rubula-like virus; viruses; zoonosis.

Figure 1

A) Maculopapular eruption observed on the back and arms of 25-year-old female wildlife biologist infected with a novel paramyxovirus related to rubula-like viruses isolated from fruit bats, on hospitalization day 2. B) Bone marrow biopsy sample showing macrocytic hemophagocytosis (possible granulocyte infiltration).

Figure 2

A) Organization of the viral genome of novel paramyxovirus related to rubula-like viruses isolated from fruit bats was determined from the full-length sequence. B) Localization of the predicted viral genes and open reading frames (ORFs). The V/P edition site is predicted from the similarity to Tuhoko virus 3. C) Terminal sequences were determined by standard rapid amplification of cDNA ends (RACE) methods. The complementarity of terminal sequences is shown in vRNA and vcRNA sense. D) Amino acid sequences of the nucleocapsid (N) protein of 22 representative paramyxovirus sequences were aligned by using the MUSCLE algorithm (CLC Genomics Workbench version 6.0.1; CLC bio, Cambridge, MA, USA). The phylogenetic analysis was conducted with a Bayesian algorithm (Mr.Bayes, Geneious version 6.1.5, www.geneious.com/). NP sequences were extracted from the complete genomic sequences in GenBank: KF774436 (Sosuga virus [SosV]), GU128082 (Tuhoko virus 3 ), GU128081 (Tuhoko virus 2), GU128080 (Tuhoko virus 1), AF298895 (Tioman virus), NC_007620 (Menangle virus), JX051319 (Achimota virus 1), JX051320 (Achimota virus 2), NC_003443 (human parainfluenza virus type 2), AF052755 (simian parainfluenza virus 5), HQ660095 (bat paramyxovirus Epo_spe/AR1/DRC/2009), NC_002200 (mumps virus), NC_009489 (Mapuera virus), NC_009640 (porcine rubulavirus), NC_001498 (measles virus), NC_006296 (rinderpest virus), NC_001921 (canine distemper virus), NC_001552 (Sendai virus), NC_003461 (human parainfluenza virus type 1), NC_002728 (Nipah virus), NC_001906 (Henra virus), NC_002617 (Newcastle disease virus). vcRNA, viral complementary RNA; N, nucleocapsid protein; V/P, V protein; M, matrix protein; F, fusion protein; HN, hemagglutinin-neuraminidase; L, molecular weight DNA ladder; CDS, coding sequence; nt pos. nucleotide position; vRNA, viral RNA.

Figure 3

A) Virus isolation confirmed by reverse transcription PCR. SosV was isolated after intracranial and intraperitoneal inoculation into 2-day-old suckling mice. A specific reverse transcription PCR designed to amplify 2,188 bp of the SosV genome was performed by using RNA from brains (Br), liver (Lv), and spleen (Sp) of the euthanized animals. Viral RNA was found only in the brain, not in liver or spleen. B) Propagation of SosV in cell culture. Homogenized tissues (brain, liver, and spleen) were used to infect H292 cells. Fixed monolayers were stained with convalescent-phase serum from the patient and anti-human AlexaFluor 488 antibody (Invitrogen, Grand Island, NY, USA). C) Sosuga virus particle. Virus morphologic appearance was examined by taking supernatants from infected Vero-E6 cells, clarifying by slow-speed centrifugation, and depositing on grids for negative staining and examination by transmission electron microscopy. Pleomorphic virions can be observed. Neg.ctrl, negative control; Se, serum; SosV, Sosuga virus.