Supplementary Results
Bat-origin caliciviruses (BtCalVs) across China and the first identification
of bat-origin noroviruses (BtNoVs) that are closely related to GII and GIV
human NoVs. The family Caliciviridae includes five genera (Lagovirus, Nebovirus,
Norovirus, Sapovirus, and Vesivirus) of small, non-enveloped viruses with linear,
positive-sense single-stranded RNA (7.5-8.5 kb in length). Noroviruses, sapoviruses,
and neboviruses are associated with enteric diseases in a range of mammals, including
humans.
Six BtCalVs were identified and sequenced in three bat species of two genera in
four provinces (Supplementary Table S2 and Figure S1). According to the
phylogenetic tree based on the polyproteins (Figure 4(A)), three BtCalVs identified in
three different bat species in three different locations (clade 1) could be assigned into
the genus sapovirus and formed three lineages closely related to a previously reported
lineage of sapoviruses identified in another bat species, Hipposideros pomona. Two
BtCalVs, BtRs-CalV-2/GX2012 and BtRs-CalV/YN2010, could be classified into the
genus Norovirus and were closely related to human NoVs. They shared 61.4%-63.4%
aa identities with the reported GII and GIV NoVs of humans and pigs, and less than
55.2% aa identity with other NoVs. Another BtCalV, BtMspp.-CaliciV/GD2012,
represented a separate clade that could not be assigned into any known genus. The aa
identities of the predicted polyproteins between these novel BtCalVs and other CalVs
are shown in Supplementary Table S9.
Bat-origin polyomaviruses (BtPyVs) across China. Members of the family
polyomaviridae are small, non-enveloped viruses with circular, double-stranded DNA
(~5 kb in length). They infect a variety of avian, rodent, and primate species, and
some of them are potentially oncogenic. BK and JC viruses are human pathogens, and
two recently reported PyVs, KI and WU, can be frequently detected in respiratory
samples from patients with respiratory symptoms.
Four novel BtPyVs were identified in two bat genera in Guangdong and Shanxi
provinces (Supplementary Table S2 and Figure S1). Phylogenetic analysis based on
the large T proteins was conducted (Figure 4(B)). Three BtPyVs form a separate clade
(clade 2) closely related to a previously reported bat PyV, Bat Ml PyV. The remaining
BtPyV, BtRp-PyV/GD2012, represented a separate clade distant from any other
known PyVs. The aa identities of the predicted large T proteins between these novel
BtPyVs and known PyVs are shown in Supplementary Table S10.
Bat-origin hepatitis E virus (BtHEV), rhabdovirus (BtRhaV), and
bunyavirus (BtBunyaV) identified in China. Hepatitis E virus (HEV), a virus
mainly transmitted by the oral-faecal route, is one of the most common causative
agents of human acute hepatitis in developing countries. HEVs are primarily
classified into 4 genotypes. Genotype 1 (G1) and G2 contain only human HEVs,
while G3 and G4 contain HEVs identified from humans and other animals, such as
pigs, rabbits, and wild boars. Only one novel BHEV, BtRf-HEV/SX2013, was
identified in Rhinolophus ferrumequinum from Shanxi province, China. The genome
sequence of this virus shared only 62.2% nucleotide (nt) identity with that of the
previously full-length sequenced BHEV strain, BatHEV/BS7/GE/2009, in E.
serotinus in Germany, and less than 55.9% nt identity with HEVs identified from
other hosts. The phylogenetic trees based on the complete nt sequences of ORF1 and
ORF2
were
used
to
describe
the
evolutionary
relationships
between
BtRf-HEV/SX2013 and other members in the family Hepeviridae (Figure 4(C)).
BtRf-HEV/SX2013 could be clustered together with BatHEV/BS7/GE/2009 and
distant from other clusters, and the two bat-borne HEVs had a common ancestor but
were distinct from HEVs of human and other nonhuman hosts. In ORF1, conserved
domains or motifs are predicted in Supplementary Table S19. The nt and deduced aa
sequence identities between BtRf-HEV/SX2013 and other HEVs are shown in
Supplementary Table S20.
The family Rhabdoviridae contains nine approved genera. Most of the
previously reported BtRhaVs were classified into the genus Lyssavirus and served as
the source of human rabies. However, until now, no BtRhaV under the genus
Lyssavirus has been identified in China. Only one BtRhaV, BtMp-RhaV/SX2013, was
identified in Myotis pequinius in Shanxi province. Based on the partially sequenced L
(RdRp) protein (less than 34% aa identity with known rhabdoviruses) of this virus,
phylogenetic
analysis
was
conducted
(Figure
4(D)).
The
clade
of
BtMp-RhaV/SX2013 represented a separate evolutionary lineage under the family
Rhabdoviridae.
Viruses in the family Bunyaviridae are enveloped viruses with segmented (S, M,
and L genome segments), negative-sense single-strand RNA. Members of four genera,
Hantavirus, Nairovirus, Orthobunyavirus, and Phlebovirus, can infect vertebrate
animals and are transmitted by arthropods. One bunyavirus, Rp-BunyaV/SAX2011,
was identified in Rhinolophus pearsoni from Shaanxi. The deduced aa sequence of the
L gene covered Pre-motif A of conserved motif III
(KNQHGGLREIYV-X5-RIVQ-X3-E-X3-R), which was a conserved motif in members
of the genus Phlebovirus. The partial L gene of Bat Rp-BunyaV/SAX2011 exhibited
40 - 45% nt and 26 - 32% aa identities with members of the genus Phlebovirus. A
phylogenetic tree was constructed based on the partial L proteins of
Rp-BunyaV/SAX2011 and other members of the family Bunyaviridae (Figure 4(E)).
The clade of Rp-BunyaV/SAX2011 was closely related to the genus Phlebovirus.
Bat origin orthoreovirus (BtORV) and rotavirus (BtRV) under the family
Reoviridae identified in China. Viruses in the family Reoviridae are non-enveloped,
segmented, double-stranded RNA viruses with 10-12 genome segments. Members
under the genera Orthoreovirus and Rotavirus belong to the subfamilies
Spinareovirinae and Sedoreovirinae separately. Rotaviruses, specifically group A
rotaviruses (RVA), are common cause of severe diarrhea among infants and young
children.
In this study, we found 1,080 reads of BtORV in Myotis bats and 657 reads of
BtRV in R. sinicus bats in Guangdong province. The assembled contigs of this BtORV,
BtMspp.-ORV/GD2012, showed very high sequence similarities (91%-98% aa
identities) with previously reported BtORV identified in European Bats. The
assembled contigs of this BtRV, BtRs-RV/GD2012, showed very high sequence
similarities (86%-99% aa identities) with members of RVA.