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. 2019 Feb 21;14(2):e0212585.
doi: 10.1371/journal.pone.0212585. eCollection 2019.

A new approach for Small Ruminant Lentivirus full genome characterization revealed the circulation of divergent strains

Barbara Colitti  1 , Elisabetta Coradduzza  2 , Giantonella Puggioni  2 , Maria Teresa Capucchio  1 , Ramsés Reina  3 , Luigi Bertolotti  1 , Sergio Rosati  1
Affiliations

A new approach for Small Ruminant Lentivirus full genome characterization revealed the circulation of divergent strains

Barbara Colitti et al. PLoS One. .

Abstract

Small Ruminant Lentiviruses (SRLV) include at least 4 viral highly divergent genotypes. Genotypes A and B are widely distributed and genotypes C and E have been recognized in restricted geographic areas. New phylogroups have been identified targeting conserved regions. However, this approach suffers from the potential risk to misamplify highly divergent strains. Pathogenic strains are easily adapted to fibroblastic cells, but non-pathogenic strains isolation may require a different approach. We developed a fast and effective method for SRLV full genome characterization after cell culture isolation. Spleen samples were collected during regular slaughter from sheep and goats in northwestern Italy. Spleen-derived macrophage cultures were monitored for reverse transcriptase activity and RNA was extracted from the supernatant of positive cultures. Using Illumina MiSeq platform 22 new full genome sequences were obtained. The success of this approach is based on the following features: spleen is one of the main target for SRLV persistence; red pulp is a reserve of resident macrophages, the main target for SRLV replication in vivo; RTA is a sensitive assay for any replicating retrovirus; de novo sequencing do not require genetic knowledge in advance.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Bayesian tree based on the full genome sequences alignment.
Newly characterized isolates are reported in bold. SRLV genotypes are reported. Posterior probability of each node is showed above branches.
Fig 2
Fig 2. Bayesian tree based on the partial gag sequence alignment.
Newly characterized isolates are reported in bold. SRLV subtypes are reported. Posterior probability of each node is showed above branches.
See this image and copyright information in PMC

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