S1 File. Virome sequence data information from the Parvoviridae and Papillomaviridae
families (with references and figures).
S1 Table. Neoromicia samples collected to investigate the South African Neoromicia virome.
S3 Table. Neoromicia samples pooled for molecular detection of selected viruses.
S4 Table. Alpha- and Betacoronavirus genera hemi-nested RT-PCR primers.
S5 Table. Pairwise similarities inferred from distance estimations of full length genomes
of the Circoviridae family. Sequence similarities of viruses in the Circoviridae family inferred
from estimated evolutionary divergence calculated from pairwise distances. Full genomes were
aligned and trimmed to 1075 overlapping positions. All ambiguous positions were removed
for each sequence pair. Analyses were conducted in MEGA7 [41].
S6 Table. Pairwise similarities inferred from distance estimations of an L gene region
between selected Bunyavirales. The table shows pairwise sequence similarities inferred from
evolutionary divergence estimates of 249 positions of compared Bunyavirales. The number of
base differences per site from between sequences were converted to percentage of similarities.
Standard errors for distance estimates are shown above the diagonal. Codon positions
included were 1±3 as well as noncoding. Ambiguous positions were removed for each
sequence pair as per pairwise deletion. Estimates were analysed in MEGA7 [41].
S7 Table. Pairwise similarities inferred from distance estimations of a 605bp conserved
segment of the coronavirus RNA dependent RNA polymerase gene. The table shows
pairwise sequence similarities inferred from evolutionary divergence estimates of 605 positions
of compared coronaviruses. The number of base differences per site from between
sequences were converted to percentage of similarities. The sequences from this study are
highlighted in grey and closest similarities to sequences from other studies are indicated in
bold. Standard errors for distance estimates are shown above the diagonal in grey text.
Codon positions included were 1±3 as well as noncoding and ambiguous positions were
removed for each sequence pair as per pairwise deletion. Estimates were analysed in MEGA
7 [41].
S8 Table. Genome annotation of BtCoVNeo5038 with similarities to compared lineage C
betacoronaviruses. The percentage similarities were inferred from pairwise distance estimates
of the base pair and amino acid differences per site for each gene and of the overall genome.
The estimates were calculated in MEGA7 [41] using pairwise deletion to treat gaps. All percentage
similarities are given in comparison to BtCoVNeoV5038. Accession number of compared
betacoronaviruses are listed in order: KC869678.4, KX574227, EF065505.1, EF065509.1,
JX869059.2, KF958702.1, KF917527.1, and KJ477102.1.
S9 Table. Pairwise similarities inferred from distance estimations between betacoronavirus
full genomes. The table shows pairwise similarities inferred from evolutionary divergence
estimates of betacoronavirus full genomes. The number of base differences per site
between sequences were converted to percentage similarities. Within lineage similarities are
indicated in shaded blocks. Standard errors for distance estimates are shown above the diagonal
in grey text. Codon positions included were 1±3 as well as noncoding and ambiguous positions
were removed for each sequence pair as per pairwise deletion. Estimates were analysed in
MEGA 7 [41].
S10 Table. Coronavirus strains and Genbank accession numbers of sequences used in the
full genome phylogeny.