Maximum-likelihood phylogenetic tree of nucleocapsid gene sequences depicting the phylogenetic relationships of Africa-1 Rabies Viruses originating from Cameroon with other Africa-1 from Africa.

<p>The phylogenetic tree was estimated from the alignment of 1040 nucleotides (nt) long sequence alignment (positions 41–1080 nucleotides according to the genome of the Rabies Virus strain RRV_ON-99-2) using a maximum-likelihood (ML) method under the general time-reversible (GTR) model of nucleotide substitution, with the rate of each substitution type estimated from the dataset using PHYML 3.0 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006041#pntd.0006041.ref055" target="_blank">55</a>]. The ML base frequencies, the proportion of invariable sites (I) and a gamma distribution of rate variation among sites (Γ with four rate categories) were estimated from the dataset. Newly sequenced Rabies Viruses are indicated with circles color-coded according to their respective regions of origin: CEN, Centre; EAS, East; NOW, North West; SOW, South West and WES, West. Their districts of origin are coded as specified by district codes provided in <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006041#pntd.0006041.t001" target="_blank">Table 1</a>. The districts of the Centre region, other than Yaounde, are specified in bold black. The years of origin of the studied viruses are provided by two digit numbers preceding the letter “V” in the virus name (10V-, 2010; 11V-, 2011; 12V-, 2012; 13V-, 2013; 14V-, 2014; 15V-, 2015, 16V-; 2016). Database available reference viruses are named with corresponding GenBank accession numbers followed by the country (CAR, Central African Republic) and year of origin, if known. Viruses from Central Africa are specifically highlighted with red-filed triangles; except those from Cameroon that are further distinguished by the indication of the regions (CEN, Centre) and district (OBA, Obala; MON, Monatélé; SAA, Sa’a; YAO, Yaounde) codes. Clades, subclades and lineages are designated as reported in a reference study based on the ML phylogeny of 321 RABV sequences from five concatenated genes [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0006041#pntd.0006041.ref021" target="_blank">21</a>]. The major clades, lineages and variants of the Rabies Virus commented in the main text are gathered in color-shaded boxes. Viruses displaying peculiar features, commented in the main text, are further highlighted by black arrows. ML bootstrap values (generated from 100 replicates) >60% are shown next to the nodes. Scale is shown at the left as substitutions per site.