Primers used for complete sequencing of the F and HN genes.

a<p>F, forward; R, reverse.</p>b<p>M, F, HN, and L matrix, fusion protein, hemagglutinin-neuraminidase, and polymerase genes, respectively.</p>c<p>primers designed on conserved sequences based on the alignment of the complete sequences of 219 F genes and 74 HN genes published in GenBank.</p

Characteristics of viruses analyzed in this study.

<p><b>-</b> *full genome sequence.</p

List of specific signatures on the F complete gene for genotypes and subsequent sub-genotype discrimination.

<p>The second column indicates the combination of specific amino (first line) and nucleic (second line) signatures that discriminate the genotypes. The fourth column shows the same for the sub-genotype discrimination and is applicable once the genotype has been assigned. Underlined amino or nucleic acids represent specific unique signatures.</p

Estimates of evolutionary distances between genotypes.

<p>Average intergenotype distance: 0.190.</p><p>Average intragenotype distance: 0.038.</p

Estimates of evolutionary distances between sub-genotypes.

<p>Average intra-subgenotype distance: 0.03.</p

Comparison of tree topology after phylogenetic reconstruction on the 741 complete F gene sequences using four phylogenetic methods: (a) Maximum Likelihood (ML), (b) Bayesian (MrBayes), (c) Maximum Parsimony (MP), and (d) Neighbor Joining (NJ).

<p>Branch support values correspond to 1000 bootstrap replicates for ML, MP, and NJ, and posterior probabilities estimated for 10,000 samples of the Markov chain for MrBayes. The area of the triangle is proportional to the number of isolates within the genotype.</p

Phylogenetic analysis of 1921 partial F gene sequences based on nucleotides from positions 1 to 372.

<p>Trees were constructed using Bayesian inference with 47,408,000 iterations and 1/1000 tree sampled in the chain. Minimal average ESS for all parameters was 88, and PSRF were between 1.00003 and 1.01335. A class I virus was used as an outgroup. Sequences from this study are 5 Malian strains (1 in sub-genotype XIVa, 3 in XIVb, and 1 in XIVc), 5 Ethiopian strains (VIf), and 4 Madagascar strains (XI). The complete list of the 1921 sequences, the corresponding multiple sequence alignments, and the tree in Newick and Figtree format can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076413#pone.0076413.s008" target="_blank">Table S8</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076413#pone.0076413.s007" target="_blank">Table S7</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076413#pone.0076413.s005" target="_blank">Figure S5I</a>, and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076413#pone.0076413.s009" target="_blank">Figure S9Q</a>, respectively.</p

Phylogenetic analysis of 110 complete genome sequences.

<p>Trees were constructed using Bayesian inference with 2,960,000 iterations and 1/1000 tree sampled in the chain Minimal average ESS for all parameters was 365, and PSRF were between 0.99978 and 1.0059. A class I virus was used as an outgroup. Sequences from this study are three Malian strains, one in each of sub-genotypes XIVa, b, and c. The complete list of the 110 sequences, the corresponding multiple sequence alignments, and the tree in Newick and Figtree format can be found in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076413#pone.0076413.s008" target="_blank">Table S8</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076413#pone.0076413.s007" target="_blank">Table S7</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076413#pone.0076413.s005" target="_blank">Figure S5H</a>and<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0076413#pone.0076413.s009" target="_blank">Figure S9P</a>, respectively.</p