Complete genome sequence of Tacaribe virus

Abstract

Tacaribe virus (TCRV) is the prototype of the New World arenaviruses (also known as TCRV serocomplex viruses). While TCRV is not itself a human pathogen, many closely related members of this group cause hemorrhagic fever, and thus TCRV has long served as an important BSL2 system for research into diverse areas of arenavirus biology. Due to its widespread use, a coding-complete sequence for both the S and L segments of the bipartite genome has been publically available for almost 30 years. However, more recently, this sequence has been found to contain significant discrepancies compared to other samples of the same original strain (i.e., TRVL-11573). Further, it is incomplete with respect to the genome ends, which contain critical regulatory elements for RNA synthesis. In order to rectify these issues we now present the first complete genome sequence for this important prototype arenavirus. In addition to completing the S segment 5' end, we identified an apparent error in the L segment 3' end as well as substantial discrepancies in the S segment intergenic region likely to affect folding. Comparison of this sequence with existing partial sequences confirmed a 12-amino-acid deletion in GP, including putative glycosylation sites, and a 4-amino-acid exchange flanking the exonuclease domain of NP. Accounting for these corrections, the TRVL-11573 strain appears to be nearly identical to that isolated in Florida in 2012. The availability of this information provides a solid basis for future molecular and genetic work on this important prototype arenavirus.

Fig. 1

Analysis of Tacaribe virus non-coding sequences. (A) Schematic diagram of the genome, indicating discrepancies in non-coding regions. Open reading frames (colored boxes), terminal noncoding regions (grey boxes) and intergenic regions (hairpin) are all indicated. Arrowheads indicate the location of missing data and discrepancies. (B) Genome termini. Sequences determined in this study (TCRV-EXP, shown in bold) were compared to the reference sequences for strain TRVL-11573 (TCRV-REF) and the 2012 Florida strain (TCRV-Florida) as well as Junín virus (JUNV, strain Romero) and Machupo virus (MACV, strain Carvallo). Mismatches are shown in red, and missing data are indicated by dashes. Complementarity of the genome end sequences is shown with the promoter region at the 3’ end boxed. Missing data/discrepancies are shown in red. (C) Intergenic regions. Annotation is as described for (B). GenBank accession numbers are as follows: TCRV-EXP (S segment, MT081316; L segment, MT081317), TCRV-REF (S segment, M20304; L segment, J04340), TCRV-Florida (S segment, KF923400; L segment, KF923401). JUNV and MACV S and L segment sequences were as published in references [23] and [24], respectively

Fig. 2

Analysis of Tacaribe virus coding region sequences. Sequence discrepancies in the (A) nucleoprotein (NP) or (B) glycoprotein (GP) open reading frame. Arrowheads indicate the location of discrepancies, which are shown in red text in the respective sequences. Amino acid positions are indicated. Exonuclease catalytic site residues (in NP) and putative N-linked glycosylation sites (in GP) are boxed in black. GenBank accession numbers are as follows: TCRV-EXP (S segment, MT081316; L segment, MT081317), TCRV-REF (S segment, M20304; L segment, J04340), TCRV-Florida (S segment, KF923400; L segment, KF923401), TCRV-NP partial (KC329849), TCRV-GP partial (KP159416)