Lujo virus, a new hemorrhagic fever virus from Southern Africa

lujo-virus-treeA new member of the arenavirus family, Lujo virus, has been identified in patients who died during an outbreak of hemorrhagic fever in late 2008. Sequence analysis reveals that Lujo is a new arenavirus, genetically distinct from other members of the family which includes Lassa virus.

A patient with unexplained hemorrhagic fever was identified in Zambia in September 2008. After transfer to Sandton for further care, four health care workers involved with the case also became ill. The first four patients died, and the fifth survived after treatment with ribavirin.

Sequence analysis of total liver and serum RNA from the patients revealed the presence of a new member of the arenavirus family. The virus has been provisionally named Lujo based on its origin in Lusaka, Zambia, and Johannesburg, South Africa. Phylogenetic trees were prepared from the viral genome sequences (example at left). These trees show that Lujo virus branches off the root of the Old World arenaviruses. This analysis suggests that Lujo virus is a member of a novel genetic lineage, and is distinct from previously characterized viruses in this family.

It’s not clear how the index case was infected by Lujo virus. Most arenavirus infections are acquired by contact with infected rodent excreta, by inhalation of dust or aerosolized virus-containing particles, or ingestion of contaminated foods. At least one arenavirus might be transmitted from bats, and this possibility should not be ruled out for Lujo virus. The index patient likely transmitted the infection to the four health care workers via aerosols or infected body fluids.

There are several noteworthy aspects of this emerging story. First, it is clear that pyrosequencing can be used to rapidly identify new pathogens. In this case, sequences were obtained within 72 hours of receipt of clinical specimens. Lujo virus appears to be highly lethal in humans, based on the deaths of 4 out of 5 of the infected patients. However the number of infections identified so far is small, and the lethality ratio might fall as additional infections are studied. Now that the sequence of Lujo virus is known, reagents can be produced which will enable rapid identification of new cases by more conventional diagnostic approaches such as polymerase chain reaction. Lujo is a new member of the arenavirus family and is genetically distinct from both Old and New World arenaviruses. Why it has just appeared in humans is not known, but possible reasons include the more frequent contact between humans and wild animal species, and better and more aggressive detection methods. It is likely that a virus closely related to Lujo is present in either rodents or bats but has not been previously detected. As we have said many times before, the zoonotic pool is very deep.

I am struck by similarities between the events surrounding the discovery of Lujo virua and Lassa virus in 1969. In both outbreaks, Columbia University Medical center was involved, and a nurse who was infected by the index patient survived as a consequence of antiviral therapy.

Briese, T., Paweska, J., McMullan, L., Hutchison, S., Street, C., Palacios, G., Khristova, M., Weyer, J., Swanepoel, R., Egholm, M., Nichol, S., & Lipkin, W. (2009). Genetic Detection and Characterization of Lujo Virus, a New Hemorrhagic Fever–Associated Arenavirus from Southern Africa PLoS Pathogens, 4 (5) DOI: 10.1371/journal.ppat.1000455

Integration of arenavirus DNA into the cell genome

retrotransposonIs that title correct? Arenaviruses have an RNA genome which is not known to be copied into DNA at any stage of the replication cycle. How could a DNA copy of this virus be produced and be inserted into the host genome?

The RNA genome of retroviruses is converted to a DNA form during viral replication by the viral enzyme reverse transcriptase. The viral DNA then integrates into the host’s genome, becoming a permanent part of the cell. These events have no counterparts during replication of arenaviruses. The RNA genomes of these viruses are copied via an RNA intermediate, entirely in the cytoplasm of the cell. Nevertheless, the authors of a recent study found a DNA copy of the RNA genome of lymphocytic choriomeningitis virus (LCMV), a commonly studied arenavirus, integrated into host cell DNA.

This unusual story began in 1979 with the report that DNA complementary to the RNA genome of LCMV can be detected in about 1 in 103 to 104 infected cells. The authors speculated that retroviruses were involved but did not provide mechanistic evidence. Eighteen years later, the authors subcloned these cells to produce cell lines containing LCMV DNA. They then used polymerase chain reaction to isolate LCMV DNA from the cloned cells, including the cellular sequence flanking the viral genome. Nucleotide sequence analysis revealed that both cell lines contain a copy of the viral glycoprotein (GP) gene joined to cellular sequences encoding an IAP (intracisternal A type) retrotransposon. The authors identified LCMV integration both in cultured cells and infected mice.

Retrotransposons are sequences related to retroviruses that are found in the genome of many organisms. The gene content and arrangement are similar to retroviruses, but they lack an extracellular phase: they do not encode an env gene. Retrotransposons may be retroviral progenitors, or degenerate forms of these viruses. They are amazingly abundant: 42% of the human genome is made up of retrotransposons.

Based on their experimental results, the authors proposed that the following events occurred in a cell infected with LCVM. During copying of the retrotransposon RNA into a cDNA copy by reverse transcriptase, the enzyme switched templates and began copying the LCMV GP RNA. This hybrid DNA – retrotransposon linked to LCVM sequences –  then integrated into the host genome.

The results reported in this paper have enormous implications for evolution and for human gene therapy. Because retrotransposons transpose most efficiently in the thymus and testicles, the recombination events described could lead to transmission of RNA virus genes in the germline. Therefore the contribution of non-retroviral RNA viruses to evolution of the mammalian genome might be greater than previously believed. In addition, it is possible that RNA virus vectors used for gene therapy could integrate into the human genome via the mechanism described in this study. Such integration could lead to undesired mutation such as activation of oncogenes. Therefore the ability of specific RNA virus vectors to integrate into the human genome should be carefully tested before the vectors are approved for use in humans.

Rolf M. Zinkernagel, Paul Klenerman, Hans Hengartner (1997). A non-retroviral RNA virus persists in DNA form Nature, 390 (6657), 298-301 DOI: 10.1038/36876

M. B. Geuking, J. Weber, M. Dewannieux, E. Gorelik, T. Heidmann, H. Hengartner, R. M. Zinkernagel, L. Hangartner (2009). Recombination of Retrotransposon and Exogenous RNA Virus Results in Nonretroviral cDNA Integration Science, 323 (5912), 393-396 DOI: 10.1126/science.1167375