Molecular characterization of a new highly divergent Mobala related arenavirus isolated from Praomys sp. rodents

Abstract

Arenaviruses represent a family of viruses that are naturally present in rodents belonging to subfamily Murinae, Neotominae or Sigmodontinae. Except for Lassa virus, little information is available on other Old-World arenaviruses. Here, we describe strain AnRB3214, a virus isolated from a presumed Praomys sp. rodent in the Central African Republic in 1981 and assigned to Ippy virus based on antigenic similarity. The strain was simultaneously sequenced on Illumina NovaSeq 6000 and MinION Mk1B devices and analysed with various bioinformatics tools. We show that the best genome coverage and depth were obtained with the Kaiju and Minimap2 classification and identification tools, on either the MinION or the Illumina reads. The genetic analysis of AnRB3214 fragments showed 68% to 79% similarity with the Mobala and Gairo mammarenaviruses at the nucleic acid level. Strain AnRB3214 had a truncated nucleoprotein smaller than that of other Old World arenaviruses. Molecular clock analysis suggests that this strain diverged from Mobala virus at least 400 years ago. Finally, this study illustrates the importance of genomics in the identification of archived viruses and expands on the diversity of African arenaviruses, because strain AnRB3214 is either a variant or a close relative of Mobala virus, and not Ippy virus.

Predicting the evolution of the Lassa virus endemic area and population at risk over the next decades

“…As reported for other mammarenaviruses, the virus may only be present in the M. natalensis subtaxon A-I 36 , 37 . Records of Lassa virus infection in M. natalensis subtaxon A-II 76 and in other rodent species including M. erythroleucus or Hylomyscus pamfi 77 suggest, however, that susceptibility to Lassa virus infection may not be species or subtaxon specific. Other possible explanatory factors include intra-host competition between different viruses 38 , 78 , or cross-immunity due to the circulation of closely related viruses 40 , 41 .…”

“…As most other old world arenaviruses that circulate in M. natalensis are found only in East Africa 12 , 36 , 37 , there is little data to assess these two mechanisms based on field data. Only in Mayo-Ranewo (Taraba state, eastern Nigeria), rodent trapping studies have identified a Mobala-like virus in M. natalensis 76 , 79 , which does not seem to effectively restrict the transmission of Lassa virus, as human infections are often reported in that state of Nigeria 80 .…”

“…In addition, some factors may hinder virus dispersal following a hypothetical introduction into a new ecologically suitable region. First, in our analyses, as there is evidence that Lassa virus infection may not be species or subtaxon-specific 76 , 77 , we considered the entire M. natalensis species to be susceptible to Lassa virus infection. It is, however, possible that the virus spreads less (or more) efficiently in a different subtaxon of M. natalensis .…”