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

Huguette Simo Tchetgna,Jean-Claude Manuguerra,Benjamin Selekon,Antoine Gessain,Aurelia Kwasiborski,Nicolas Berthet,Emmanuel Nakouné,Stephane Descorps-Declère,Valérie Caro,Mathias Vandenbogaert

doi:10.1038/s41598-021-88046-5

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.

Highlights

Arenaviruses are enveloped, single-stranded RNA viruses belonging to family Arenaviridae, order Bunyavirales
Taxonomic assignments showed that the percentage of reads from the AnRB-3214-Illumina dataset assigned as belonging to the Arenaviridae family ranged from 0.02 to 0.4% whereas for reads belonging to the AnRB-3214-MinION dataset, taxonomic assignment percentages were 0.01% and 0.88% for Centrifuge[32] and Kaiju[31], respectively (Table 1)
We demonstrated that strain AnRB3214 is distinct from the only other Ippy strain described to date, strain DakAnB188d, which originates from the Central African Republic (CAR)

Summary

Introduction

Arenaviruses are enveloped, single-stranded RNA viruses belonging to family Arenaviridae, order Bunyavirales. With approximately 43 species, arenaviruses are subdivided into four genera (Antennavirus, Hartmanivirus, Reptarenavirus and Mammarenavirus) that infect fishes, snakes or mammals[1]. Arenaviruses typically have ambisense, bisegmented RNA genomes. Each RNA segment encodes two non-overlapping open reading frames (ORFs) of opposite polarity. The small (S) 3500 nt genomic segment encodes the nucleocapsid protein (NP) and a glycoprotein precursor (GPC), which later matures into two membrane glycoproteins, GP1 and GP2. The large (L) ~ 7000 nt genomic segment codes for the RNA-dependent RNA polymerase (RdRp) and exceptionally a zinc-binding protein (Z) in the Mammarenavirus and Reptarenavirus genera[2,3]. Antennavirus has a trisegmented RNA genome, with NP and GPC being on two distinct segments[4]

Methods

Results

Discussion

Conclusion