Sequence and phylogenetic analysis
Nucleotide sequences were edited and assembled using BioEdit software,
then, using Clustal W, aligned against and compared with G gene
sequences of:
- The most commonly used subtype B vaccines (i.e. aMPV/B vaccine -
strain VCO3; aMPV/B vaccine - Strain 11/94; aMPV/B vaccine - strain 1062
and aMPV/B vaccine - strain PL21)
- 82 already available European aMPV B sequences (Table S1)
- 59 extra-European aMPV-B sequences retrieved from GenBank(Table S2).
Phylogenetic relationships among the aMPV-B strains were reconstructed
using the neighbor-joining algorithm implemented in MEGA X (Kumar et
al., 2018). The branch support was calculated by performing 1000
bootstrap replicates; only branches supported by bootstrap values ≥ 70%
were considered reliable. Complete deletion option was selected before
the analysis begins, to remove sites containing missing data or
alignment gaps. Within-group mean pairwise genetic p-distance was
estimated using MEGA X in order to evaluate the genetic heterogeneity of
aMPV population.