Widespread Recombination, Reassortment, and Transmission of Unbalanced Compound Viral Genotypes in Natural Arenavirus InfectionsMark D. Stenglein, Elliott R. Jacobson, Li-Wen Chang, Chris Sanders, Michelle G. Hawkins, David S-M. Guzman, Tracy Drazenovich, Freeland Dunker, Elizabeth K. Kamaka, Debbie Fisher, Drury R. Reavill, Linda F. Meola, Gregory Levens, Joseph L. DeRisi
PLoS, 2015Abstract: Arenaviruses are one of the largest families of human hemorrhagic fever viruses and are
known to infect both mammals and snakes. Arenaviruses package a large (L) and small
(S) genome segment in their virions. For segmented RNA viruses like these, novel genotypes
can be generated through mutation, recombination, and reassortment. Although it is
believed that an ancient recombination event led to the emergence of a new lineage of
mammalian arenaviruses, neither recombination nor reassortment has been definitively
documented in natural arenavirus infections. Here, we used metagenomic sequencing to
survey the viral diversity present in captive arenavirus-infected snakes. From 48 infected
animals, we determined the complete or near complete sequence of 210 genome segments
that grouped into 23 L and 11 S genotypes. The majority of snakes were multiply infected,
with up to 4 distinct S and 11 distinct L segment genotypes in individual animals. This S/L
imbalance was typical: in all cases intrahost L segment genotypes outnumbered S genotypes,
and a particular S segment genotype dominated in individual animals and at a population
level. We corroborated sequencing results by qRT-PCR and virus isolation, and
isolates replicated as ensembles in culture. Numerous instances of recombination and
reassortment were detected, including recombinant segments with unusual organizations featuring 2 intergenic regions and superfluous content, which were capable of stable replication
and transmission despite their atypical structures. Overall, this represents intrahost
diversity of an extent and form that goes well beyond what has been observed for arenaviruses
or for viruses in general. This diversity can be plausibly attributed to the captive intermingling
of sub-clinically infected wild-caught snakes. Thus, beyond providing a unique
opportunity to study arenavirus evolution and adaptation, these findings allow the investigation
of unintended anthropogenic impacts on viral ecology, diversity, and disease potential.
