Discovery of a divergent HPIV4 from respiratory secretions using second and third generation metagenomic sequencing

Alquezar-Planas, David E.; Mourier, Tobias; Bruhn, Christian A. W.; Hansen, Anders J.; Vitcetz, Sarah Nathalie; Mørk, Søren; Gorodkin, Jan; Nielsen, Hanne Abel; Guo, Yan; Sethuraman, Anand; Paxinos, Ellen E.; Shan, Tongling; Delwart, Eric L.; Nielsen, Lars P.

having highest homology within the Circoviridae. The contigs had a local amino acid homology ranging between 59-69% (for local alignments covering at least 100 bp) with highest similarity to genomes recently characterized from reclaimed waste-water 12 . Members of the Circoviridae family represent the smallest replicating viral genomes known to infect eukaryotes. They comprise a group of circular ssDNA viruses known to be severely pathogenic in birds and swine 13, 14 . They were recently identified in human plasma and stool 15 ; however, their widespread biological significance remains poorly understood. Lysholm and colleagues also identified various circovirus-like reads, but attributed their presence to reagent-derived extraction kit contamination 5 . The same commercial extraction kit supplier was used in this study (see Methods), and therefore chose to exclude these samples from further analysis. pertussis, N. Pneumoniae, and C. Pneumoniae using PCR assay but resulted in no detection. Figure S11 : Primary sequence alignment of members within the Paramyxoviridae family showing the putative absence of the insert region in some HPIV4 strains as well as in non-Rubulavirus Paramyxoviridae. Produced with Clustalw2 with a gap opening score of Figure S12 : Alignment of translated HN nucleotide sequences from all five completely sequenced HPIV4 genomes. Alignment was performed using Geneious software. The differences and similarities described among the various HPIV4 strains are clearly visible.