Supporting Information

Suid DNA and contamination

It is known to that lab reagents are often contaminated by DNA from various species including pig (Sus scrofa) (Leonard et al. 2007). We identified porcine , such as porcine circovirus, porcine parvovirus and, torque teno sus in our samples. The fact the we did not find these sequences in the negative controls argues against general pig DNA contamination. Moreover, Sus barbatus, an endemic pig species found in the region where leeches were sampled, was identified by metabarcoding (Axtner et al. 2019) as leech host in 3 (L7, L8, L37) out the 5 samples positive to porcine viruses. Furthermore, in order to understand if there was pig DNA contamination in our data, we mapped the reads from the samples which were positive for porcine viruses to the mitochondrial genomes of both Sus scrofa and Sus barbatus, since often mitochondrial genomes are obtained from capture experiments as byproducts, and we observed that the mitochondrial reads had higher identity to the Sus barbatus mitochondrial genome than to Sus scrofa. Finally, pig viruses were not identified in the water samples. This suggests that the porcine viruses found in the leech samples did not derive from pig, Sus scrofa, DNA contamination, but rather from bearded pigs the leech had fed on.

Supplementary Figure Legends

Suppl. Fig. 1. Application of viral capture on medical leeches fed with human blood spiked with four viruses, as positive control. All four viruses were detected, but enrichment efficiency (proportion of on-target viral reads) (bottom left) and target genome recovery (bottom right) varied among viruses. At the bottom right, the contigs recovered for each virus (black bars) are mapped to the reference genome together with the corresponding RNA olignonucleotide baits (blue bars). The adeno-associated virus (AAV) recovered by capture may have been present in the HeLa cell line in which HAdV was cultivated.

Suppl. Fig. 2. Evolutionary relationships of the partial L gene sequence of the rhabdoviruses identified in the leech bloodmeals (in red) with representatives of the family. The consensus sequences of the contigs found in leech samples were used as representative sequence. The main genera of the Rhabdoviridae family are indicated on the right. The tree was inferred using the maximum-likelihood method with the GTR+G+I model and node robustness assessed with 500 rapid bootstrap pseudoreplicates. The tree is scaled according to the number of nucleotide substitutions per site. The tree is rooted arbitrarily on one of two basal clades (genera Almendravirus and Bahiavirus) that comprise viruses isolated from mosquitoes. Abbreviations and accession numbers of reference sequences are reported in https://doi.org/10.1371/journal.ppat.1004664.s013 (Walker et al. 2015).

Suppl. Fig. 3. Genomic regions covered by the Vesiculovirus (A), Ephemerovirus (B) and Lyssavirus (C) contigs (black bars) identified in leech bloodmeals and corresponding RNA oligonucleotides bait (blue bars) positions. The sequences of the PCR primers and PCR products used to confirm the Lyssavirus contigs are shown in panel D.

Suppl. Fig. 4. Evolutionary relationships of the partial RNA-dependent RNA polymerase gene (orf1ab) sequence of the coronavirus identified in the leech bloodmeals (in red) with representatives of the family. The consensus of the 16 contigs found in leech samples was used as representative sequence. The four genera (Alpha-, Beta-, Gamma- and Delta-coronavirus) of the Coronaviridae family are indicated. The betacoronaviruses are further divided into four (a-d) subgroup clusters. The tree was inferred using the maximum-likelihood method with the GTR+G+I model and node robustness assessed with 500 rapid bootstrap pseudoreplicates. The tree is scaled according to the number of nucleotide substitutions per site. The tree is midpoint-rooted for purposes of clarity. CoV: coronavirus.

Suppl. Fig. 5. Genomic region covered by the Coronaviridae contigs (black bars) identified in leech bloodmeals and corresponding RNA oligonucleotides bait (blue bars) positions.

Suppl. Fig. 6. Genomic regions covered by contigs (black bars) of the three – Torque teno sus virus (A), giant panda anellovirus (C) and Paguma larvata torque teno virus (E) – identified in leech bloodmeals and corresponding RNA oligonucleotides bait (blue bars) positions. The sequences of the PCR primers and PCR products used to confirm the Torque teno sus virus, giant panda anellovirus and Paguma larvata torque teno virus contigs are shown in panels B, D and F, respectively.

Suppl. Fig. 7. Genomic regions covered by the porcine circovirus (A), porcine parvovirus (C) and feline foamy virus (D) contigs (black bars) identified in leech bloodmeals and corresponding RNA oligonucleotides bait (blue bars) positions. The sequences of the PCR primers and PCR products used to confirm the porcine circovirus contigs are shown in panels B.

Suppl. Fig. 8. Evolutionary relationships of the partial replicase (NS1) gene sequence of the parvovirus identified in the leech bloodmeals (in red) with representatives of the Parvovirinae subfamily ( family). The main genera (Ave-, Copi-, Dependo-, Erythro-, Proto-, and Tetra-parvovirus) of the Parvovirinae subfamily are indicated on the right. The tree was inferred using the maximum-likelihood method with the GTR+G+I model and node robustness assessed with 500 rapid bootstrap pseudoreplicates. The tree is scaled according to the number of nucleotide substitutions per site. The tree is midpoint-rooted for purposes of clarity. PV: parvovirus; AAV: adeno-associated virus.

Suppl. Fig. 9. Evolutionary relationships of the partial polymerase gene sequence of the foamy viruses identified in the leech bloodmeals (in red) with representatives of the Spumaretrovirinae subfamily (family Retroviridae). The four genera (Simii-, Equi-, Bovi- and Feli-spumavirus) of the Spumaretrovirinae subfamily are indicated on the right. The tree was inferred using the maximum- likelihood method with the GTR+G+I model and node robustness assessed with 500 rapid bootstrap pseudoreplicates. The tree is scaled according to the number of nucleotide substitutions per site. The tree is rooted on the clade of the sloth endogenous foamy viruses (SloEFV). FV: foamy virus.

Suppl. Fig. 10. Genomic regions covered by the Equid herpesvirus (EHV) contigs (red bars) identified in the water samples and corresponding RNA oligonucleotides bait (blue bars) positions. An enlargement of the three different regions covered is shown in panels B, C and D. The sequence of the product of the nested panherpes PCR targeting the DNA polymerase gene which was used to confirm the presence of EHV in the samples is shown in panels A and E (enlargement) in green. Suppl. Fig. 11. Genomic regions covered by the Retroviridae (A), (B) and (C) contigs (black bars) identified in sediment samples and corresponding RNA oligonucleotides bait (blue bars) positions. The sequence of the product of the PCR targeting the env gene which was used to confirm the presence of JSRV in sample SM3 is shown in light green (A).

Suppl. Fig. 12. Evolutionary relationships of the partial E1-E2 gene sequence of the papillomavirus identified in a sediment sample (in red) with representatives of the Papillomaviridae family. The main genera of the Papillomaviridae family are indicated on the right. The tree was inferred using the maximum-likelihood method with the GTR+G+I model and node robustness assessed with 500 rapid bootstrap pseudoreplicates. The tree is scaled according to the number of nucleotide substitutions per site. The tree is midpoint-rooted for purposes of clarity. PV: papillomavirus.

Supplementary References

Axtner, J., Crampton-Platt, A., Hörig, L. A., Mohamed, A., Xu, C. C., Yu, D. W., & Wilting, A. (2019). ‘An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies’, GigaScience, 8/4: giz029.

Leonard, J. A., Shanks, O., Hofreiter, M., Kreuz, E., Hodges, L., Ream, W., Wayne, R. K., et al. (2007). ‘Animal DNA in PCR reagents plagues ancient DNA research’, Journal of Archaeological Science, 34/9: 1361–6. DOI: https://doi.org/10.1016/j.jas.2006.10.023

S1. Walker, P.J., Firth, C., Widen, S.G., Blasdell, K.R., Guzman, H., et al. (2015). Evolution of Genome Size and Complexity in the Rhabdoviridae. PLOS Pathogens, 11(2): e1004664.

Supplementary Table Legends

Suppl. Tab. 1. Read counts for leech and waterhole samples with SRA accession numbers.

Suppl. Tab. 2. Primers used and amplification results obtained for the leech viral contigs confirmation PCRs.

Suppl. Tab. 3. Best BLAST hit for each viral contig identified in leech and waterhole samples.

Suppl. Tab. 4. Viral enrichment achieved by capture for each sample.

Suppl. Fig. 1

HAdV + BoHV + MeV + + iDNA InfA

LIBRARIES

Vertebrate virus DB BAITS

1 2,000 4,000 6,000 8,000 10,000 12,000 14,000 16,000 18,000 20,000 22,000 24,000 26,000 28,000 30,000 32,000 34,000 35,690 HAdV (KF268310) % VIRAL READS

1 10,000 20,000 30,000 40,000 50,000 60,000 70,000 80,000 90,000 100,000 110,000 120,000 134,896 BoHV BoHV (JX898220) MeV

1 1,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10,000 11,000 12,000 13,000 14,000 15,000 15,894 MeV (JF727649)

1 200 400 600 800 1,000 1,200 1,400 1,600 1,800 2,000 2,200 2,400 2,600 2,800 3,000 3,200 3,400 3,600 3,800 4,000 4,200 4,400 4,679 AAV (AF043303)

HAdV 1 100 200 300 400 500 600 700 800 900 1,000 1,100 1,200 1,300 1,400 1,500 1,600 1,695 AAV InfA-4 (KP459300)

1 100 200 300 400 500 600 700 800 900 1,000 1,100 1,200 1,300 1,400 1,540 InfA-5 (CY121393)

1 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 984 InfA-7 (KP881888)

1 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 851 InfA InfA-8 (CY031599) Suppl. Fig. 2

ABTV PTAMV Almendravirus MOUV 100 NMV 100 92 CNTV Sawgravirus 100 SAWV 100 BGV 100 HARV Bahiavirus MSV 99 L22 consensus L12-17-18-23-27-28-34-37-40-54-57-68 consensus 100 100 L64 consensus 94 L04 consensus 100 97 L04-26-51-55-58-62 consensus 92 L49-56-58 consensus IKOV WCBV 100 MOKV 100 LBV 90 74 SBV 60 LBV 49 100 100 IRKV OZEV Lyssavirus EBLV1 85 DUVV 98 RABV 95 ABLV 95 ARAV EBLV2 99 KHUV 100 GARV 100 SUNV Unassigned 100 KWAV 35 OVRV 100 NIAV 100 SRIV Sripuvirus 100 SMV 66 CHOV NORCV 75 DObSV 100 DMelSV Sigmavirus NKOV 100 NISV 100 FUKV 78 99 BARV 100 MEBV 100 OITAV Ledantevirus 100 100 FKRV 75 KOLEV KCV 46 100 KEUV 100 LDV SCRV 100 PRV Perhabdovirus 100 EVEX 70 L5-23-38-44-68 consensus 100 SVCV Sprivivirus 70 PFRV RADIV PERV 76 99 100 99 70 CHNV 51 ISFV JURV 97 38 MSPV CARV Vesiculovirus 100 VSNJV 100 MORV 100 VSIV 100 100 85 COCV 76 VSAV MARAV JOIV LJV 100 WONV 99 100 PCV 34 96 ORV MCOV 26 NGAV 32 GLOV Hapavirus 100 MANV 100 LJAV 100 MQOV 79 100 MOSV 100 KAMV 96 FLAV 100 HPV BASV 35 100 CPV 100 SWBV Tibrovirus 100 100 TIBV BAV 96 YATV 100 KOTV 100 KOOLV 100 KIMV 100 Ephemerovirus 100 BEFV 100 BRMV OBOV 100 ARV ARUV 100 INHV Unassigned 100 ITAV 100 IRIRV 100 CURV Curiovirus 65 RBUV 98 TUPV 100 KLAV Tupavirus DURV 0.4 Suppl. Fig. 3

A

1 500 1,000 1,500 2,000 2,500 3,000 3,500 4,000 4,500 5,000 5,500 6,000 6,500 7,000 7,500 8,000 8,500 9,000 9,500 10,000 10,500 11,134 Vesicular stomatitis Indiana nucleocapsid protein CDS phosphoprot... matrix prot... glycoprotein CDS polymerase protein CDS virus (KU296058)

L05 L68 L44 L38 L23

B

1 1,000 2,000 3,000 4,000 5,000 6,000 7,000 8,000 9,000 10,000 10,988 11,988 12,988 14,943 Bovine ephemeral fever N gene P gene M gene G gene GNS gene alpha ... bet... g... L gene virus (MH756623) N CDS P CDS M CDS G CDS GNS CDS a. a... bet... g... L CDS

L12 L22 L17 L37 L40 L57 L56 L68 L54 L27 L34 L58 L49 L23 L28 L18

C

1 500 1,000 1,500 2,000 2,500 3,000 3,500 4,000 4,500 5,000 5,500 6,000 6,500 6,998 7,493 7,986 8,486 8,986 9,486 9,986 10,486 10,986 11,486 12,003 Lagos bat virus N CDS P CDS M CDS G CDS L CDS (GU170202) N gene P gene M gene G gene L gene L12 + L58 L55 L51 L64 L04(1) L26 L62 L04(2)

D 1 50 100 150 200 250 300 350 400 450 500 550 600 650 700 750 800 850 900 950 1,000 1,059 Consensus L64 L04(1) L04(2) L26 L62 L51 L58 L55 L55-L58 PCR product primer Lagos_F1 primer Lagos_F2 primer Lagos_R1 primer Lagos_R2 Alpaca respiratory CoV (JQ410000) Suppl. Fig. 4 100 100 Camel CoV (KT253324) 100 Human CoV 229E (AF304460) Human CoV NL63 (AY567487) 0.3 100 Bat CoV HKU8 (EU420139) Mi Bat CoV (EU420138) Ro Bat CoV HKU10 (JQ989270) Sc Bat CoV (DQ648858) 100 92 100 � 100 PEDV (MF577027) My Bat CoV (KF430219) 100 Rh Bat CoV HKU2 (EF203064) 100 SADS (MF094681) FCoV (DQ848678) 100 TGEV (KX499468) 100 PRCV (DQ811787) Erinaceus CoV (KC545386) Bat CoV HKU5-1 (EF065509) 100 100 Bat CoV HKU4-1 (EF065505) c 100 93 Bat CoV/133/2005 (DQ648794_) MERS CoV (JX869059) Bat CoV HKU9-1 (EF065513) 94 79 Bat CoV HKU9-3 (EF065515) 63 97 Bat CoV HKU9-4 (EF065516) d 45 97 Bat CoV HKU9-2 (EF065514) Ro Bat CoV (KU762338) 96 Bat CoV/Zhejiang2013 (KF636752) Bat CoV kenya (KY352407) 100 Bat SARSr CoV HKU3-1 (DQ022305) Bat SARSr CoV Rf1 (DQ412042) 100 100 100 Bat SARSr CoV Rm1 (DQ412043) civet SARS CoV (AY304486) 84 100 SARS CoV (AY508724) b 100 Bat SARSr CoV WIV16 (KT444582) 100 100 59 Bat SARSr CoV WIV1 (KF367457) Bat SARSr CoV Rp3 (DQ071615) � 94 Bat SARS-like CoV (MG772934) 100 Bat SARS-like CoV (MG772933) 100 SARV CoV 2 (MN908947) 100 79 SARS CoV 2 (MT093631) Sambar deer CoV (FJ425188) 100 Waterbuck CoV (FJ425184) 100 Bovine CoV (AF391541) 99 46 Giraffe CoV (EF424622) 73 White-tailed deer CoV (FJ425187) Bovine CoV (AF220295) 100 100 Canine respiratory CoV (JX860640) Human CoV OC43 (AY391777) a 100 100 91 PHEV (DQ011855) 67 Equine CoV (LC061272) Rattus CoV HKU24 (KM349744) 100 MHV-A59 (AF029248) 100 99 MHV-1 (FJ647223) Human CoV HKU1 (MK167038) CoV from leech bloodmeals Avian infectious bronchitis virus (AJ311317) 99 Beluga whale CoV (EU111742) � Bulbul CoV HKU11 (FJ376619) 100 82 Munia CoV HKU13 (FJ376622) 100 Wigeon CoV HKU20 (JQ065048) � Night-heron CoV HKU19 (JQ065047) Suppl. Fig. 5

1 2,000 4,000 6,000 8,000 10,000 12,000 14,000 15,998 17,998 19,998 21,998 23,998 25,998 29,155 Bat coronavirus orf1ab gene N... M.. N gene N. (EF065516) S gene orf1ab CDS N... M.. N CDS N. S CDS L68 L38 L60 L25 L09 L14 L37 L15 L44 L40 L23 L01 L22 L03 L21 L30 Suppl. Fig. 6

A

1 100 200 299 399 498 598 698 798 898 998 1,098 1,198 1,298 1,398 1,498 1,598 1,698 1,798 1,898 1,998 2,098 2,198 2,298 2,398 2,498 2,598 2,698 2,860 Torque teno sus virus ORF2 protein CDS (KT174486) ORF3 protein CDS ORF1 protein CDS L08 L37

B 1 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 Consensus L37 L37 PCR product primer torq_2_fw primer torq_1_rev

C

1 100 200 294 387 485 585 685 785 885 985 1,085 1,185 1,285 1,385 1,485 1,585 1,685 1,785 1,885 1,985 2,096 Giant panda anellovirus ORF2 CDS ORF3 CDS (MF327544) ORF1 CDS L07 L39 L17 L36

D 1 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 373 Consensus L39 L36 L17 L17 PCR product L07 L07 PCR product primer torq_2_fw primer torq_1_rev

E

Paguma larvata torque 1 97 193 290 390 490 590 690 790 890 990 1,090 1,190 1,290 1,390 1,490 1,590 1,690 1,790 1,890 1,990 2,090 2,190 2,290 2,381 2,458 2,484 teno virus (LC387545) hypothetical protein CDS L25 L21 L39(1) L39(2) L39(3) L39(4) L39(5) L39(6)

F 1 20 40 60 80 100 120 140 160 180 200 220 240 260 280 300 320 340 360 380 400 420 440 460 480 500 520 540 560 588 Consensus L39(1) L39(2) L39(3) L39(4) L39(5) L39(6) L21 L25 L25 PCR product primer civet_2_fw primer civet_1_fw primer civet_1_rev Suppl. Fig. 7

A

Porcine circovirus 1 100 200 300 400 500 600 700 800 900 1,000 1,100 1,200 1,300 1,400 1,500 1,600 1,767 (KF742545) Rep CDS Cap CDS L07(1) + L07(2) L59

B 1 10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220 230 240 250 260 270 274 Consensus L7(1) L7(2) L59 L7 PCR product L59 PCR product primer circo_F1 primer circo_F2 primer circo_R1 primer circo_R2

C

Porcine parvovirus 1 196 396 596 795 995 1,195 1,395 1,588 1,785 1,980 2,178 2,378 2,578 2,768 2,968 3,168 3,366 3,563 3,763 3,963 4,163 4,363 4,563 4,758 4,950 5,150 5,345 5,552 (HM031135) replicase CDS ORF3 CDS capsid protein CDS L14(1) + L14(2) L08

D

1 500 1,000 1,499 1,999 2,499 2,999 3,499 3,999 4,499 4,999 5,499 5,996 6,496 6,996 7,496 7,996 8,494 8,994 9,494 9,994 10,494 10,994 11,700 Feline foamy virus gag CDS env CDS bel2 CDS (Y08851) U3 of 5' LTR pol CDS bel1 CDS U3 of 3'LTR gag gene env gene bel2 gene pol gene bel1 gene L64(1) L07 L64(2) L46 Suppl. Fig. 8

Porcine PV7 (MG543469) 100 Porcine PV7 (MK484100) ChappaPV Porcine PV1 (NC_001718) Mice minute virus (NC_001510) 100 100 93 Mouse PV3 (DQ196318) ProtoPV 67 Canine PV (NC_001539) Desmodus rotundus PV1 (MG745677) 98 Murine AAV2 (MF416384) Muscovy duck PV (KY069274) 100 82 100 Duck PV (KR075690) 64 65 Goose PV (JF926695) Marsupial AAV1 (MK026553) 58 Elephas maximus enAAV (LC372536) DependoPV 70 California sea lion AAV1 (JN420371) 68 Rhinolophus pusillus AAV1 (MF682926) 100 Endogenous Simian PV (LT963767) 49 Rhinolophus sinicus AAV1 (MF682927) 43 Porcine PV2 (GU938300) 100 Porcine PV2 (KM926355) 91 Porcine PV2 (KY018935) Eidolon helvum PV1 (JQ037753) 97 Porcine PV3 (KP768490) 54 Porcine PV3 (EU200677) 90 100 Ungulate TetraPV2 (MG365920) 95 L8 100 Ovine hokovirus 1 (JF504699) TetraPV 97 Bovine hokovirus 2 (MH814981) 100 Bovine hokovirus 1 (EU200669) 100 94 Ungulate TetraPV1 (KT225725) 25 Human PV4 (GU120196) 100 Human PV4 (AY622943) 74 60 100 Human PV4 (KU871314) Chimpanzee PV4 (HQ113143) Rodent TetraPV (MG745670) Turkey PV (KX084397) 100 Chicken PV (KX133427) Chicken PV (KU523900) 96 63 AvePV Chicken PV (MG602520) 36 100 Galliform avePV1 (KU569162) Simian PV (U26342) 100 Human PV B19 (AY386330) ErythroPV Bovine PV2 (KT148961) 100 Roe deer CopiPV (MK091524) 100 Porcine PV6 (NC_023860) 100 L14 (1) Porcine PV5 (JX896318) 100 100 Porcine PV5 (JX896320) Porcine PV4 (MK378283) CopiPV 70 85 Porcine PV4 (GQ387499) 47 Porcine PV4 (GU978968) 92 85 Porcine PV4 (HM031135) 0.2 L14 (2) Suppl. Fig. 9 Spider monkey SFV (NC_039027) 96 Yellow-breasted capuchin SFV (NC_039031) 100 0.2 98 White-tufted-ear marmoset SFV (NC_039030) Squirrel monkey SFV (NC_039028) Taiwanese macaque SFV (KF026286) 100 Rhesus macque SFV (NC_039238) 100 100 Japanese macaque SFV (NC_039026) 87 Guenon SFV (NC_043445) 100 SFVcae SFV (MF582544) 53 55 Grivet SFV (M74895) Simiispumavirus Western lowland gorilla SFV (NC_039029) 99 Western chimpanzee SFV (U04327) 99 100 Eastern chimpanzee SFV (NC_039025) 100 Human spumaretrovirus (M54978) 90 Human foamy virus (Y07725) Orangutan SFV (NC_039085) 89 Equine FV (LC381046) 100 Equine FV (AF201902) Equispumavirus 93 Bovine FV (JX307862) 100 Bovine FV (LC510606) 96 95 Bovine FV (AY134750) Bovispumavirus Bovine FV (LC510607) Feline FV (MH633393) 95 Feline FV (MH633423) 98 Feline FV (MH633347) 77 75 67 Feline FV (MH633380) 100 Feline FV (MH633376) 100 70 Feline FV (MH633369) Felispumavirus 51 Feline FV (MH633424) 100 Puma feline FV (NC_039022) 38 Feline syncytial virus (U78765) Feline FV (MH633407) 77 L46 65 71 L64 (2) 83 L64 (1) L07 Rhinolophus affinis FV (JQ814855) C. didactylus SloEFV (KR703337) 79 B. pygmaeus SloEFV (GQ169511) 100 C.hoffmanni SloEFV (GQ169514) 57 B. variegatus SloEFV (KR703287) 58 M. darwinii SloEFV (KR703432) Suppl. Fig. 10

A 1 5,000 10,000 15,000 20,000 25,000 29,999 34,999 39,999 44,999 49,999 54,999 59,999 64,999 69,999 74,999 79,999 84,998 89,998 94,998 99,998 104,998 109,998 114,998 119,998 124,998 129,998 134,998 139,998 147,469 Equid alphaherpesvirus 1 e... t.. r. O.. tegument pro... si... ma... e. tra... tra... (MF975656) D... m. o.

B

Equid 60,199 60,399 60,599 60,799 60,999 61,199 61,399 61,599 61,799 61,999 62,199 62,399 62,599 62,799 62,999 63,199 alphaherpesvirus 1 virion p... (MF975656) membraine glycoprotein B CDS WM20

C

82,199 82,249 82,299 82,349 82,399 82,449 82,499 82,549 82,599 82,649 82,699 82,749 82,799 82,848 82,898 82,948 82,998 83,048 83,098 83,148 83,198 83,248 83,298 Equid alphaherpesvirus 1 DNA packaging protein CDS (MF975656) ORF45 CDS WM3(1)

D

Equid 125,398 125,448 125,498 125,548 125,598 125,648 125,698 125,748 125,798 125,848 125,898 125,948 125,998 126,048 126,098 126,148 126,198 126,248 126,298 126,348 126,398 126,448 126,498 126,548 126,598 126,648 alphaherpesvirus 1 (MF975656) membrane glycoprotein G CDS WM3(2)

E

49,999 50,199 50,399 50,599 50,799 50,999 51,199 51,399 51,599 51,799 51,999 52,199 52,399 52,599 52,799 52,999 53,199 53,399 53,599 53,799 53,899 Equid ORF29 CDS alphaherpesvirus 1 (MF975656) DNA polymerase CDS WM20 PCR product WM3 PCR product Suppl. Fig. 11

A

1 496 996 1,496 1,996 2,496 2,996 3,496 3,996 4,496 4,996 5,496 5,996 6,496 6,996 7,939 JSRV (EF680296) 5'UTR 3'UTR pro CDS orf-x CDS env CDS pro gene orf-x gene env gene SM6(1)+PCR product SM6(2) SM6(3) SM6(4)

B

1 2,000 4,000 6,000 8,000 10,000 12,000 14,000 16,000 18,000 20,000 21,997 23,997 25,997 27,997 29,997 33,090 Equine adenovirus IX E1b g... IVa2... pol gene 52K ... pIIIa gene pV... p... dbp g... 100K gene p.. (KT160425) E1b ... pTP gene hypoth... IX E1b ... IVa2... pol CDS pIIIa CDS penton... pV... p... hexon capsid pro... p. dbp C... 100K CDS p.. fiber p... E... E... E1b ... 52K ... pTP CDS SM20

C

1 500 1,000 1,500 1,999 2,494 2,994 3,494 3,994 4,494 4,994 5,494 5,994 6,494 6,994 7,610 Equus caballus E6 CDS E1 CDS E4 C... L2 CDS L1 CDS papillomavirus E7 CDS E2 CDS (AF498323) E6 gene E1 gene E4 g... L2 gene L1 gene E7 gene E2 gene ST38 Suppl. Fig. 12 Psittacus erithacus PV1 (AF502599) Theta 100 Fringilla coelebs PV1 (AY057109) Eta Human PV5 (M17463) 100 Macaca fascicularis PV1 (EF028290) Beta 64 Capra hircus PV1 (DQ091200) Phi 98 Cervus elaphus PV2 (KT932712) 93 49 Bos taurus PV9 (AB331650) Xi 75 Erinaceus europaeus PV1 (FJ379293) Dyoeta Human PV4 (X70827) Gamma 100 Canis familiaris PV2 (AY722648) 96 Tau 66 Felis catus PV3 (JX972168) Apodemus sylvaticus PV1 (HQ625440) Pipa Erethizon dorsatum PV1 (AY684126) Sigma 100 100 Human PV41 (X56147) Nu 39 Human PV1 (V01116) Mu 98 Castor canadensis PV1 (KC020689) Dyosigma 95 97 Sylvilagus floridanus PV1 (K02708) Kappa Lynx rufus PV1 (AY904722) 100 Ailuropoda melanoleuca PV4 (MF327538) 96 Lambda 32 Enhydra lutris PV1 (KJ410351) Trichechus manatus PV3 (KP205502) Rho Rupicapra rupicapra PV1 (KC876045) Dyokappa 21 Ursus maritimus PV1 (EF536349) Omega Sus scrofa PV1 (EF395818) Dyodelta 19 73 69 Delphinus delphis PV1 (GU117620) Upsilon 100 Phocoena phocoena PV1 (GU117621) 47 Omikron Macaca fascicularis PV3 (EF558839) 100 14 100 Papio hamadryas PV1 (JF304764) Alpha Human PV16 (K02718) Eidolon helvum PV2 (KX276957) 45 Psi Eptesicus serotinus PV2 (KC858264) Dyoomega Felis catus PV2 (EU796884) Dyotheta 20 36 Canis familiaris PV3 (DQ295066) 100 Canis familiaris PV8 (HQ262536) Chi Peromyscus PV1 (JF755418) 18 100 Mastomys natalensis PV1 (U01834) Iota Equus ferus caballus PV7 (JX035935) Dyorho 15 61 ST38 75 Equus caballus PV1 (AF498323) 100 Zeta 59 Equus asinus PV2 (MH625918) Equus caballus PV2 (EU503122) Dyoiota 67 Equus asinus PV1 (KF741371) Dyochi 100 Cervus elaphus PV1 (KU350625) Epsilon 100 Camelus dromedarius PV1 (HQ912790) 96 Bos taurus PV13 (JQ798171) 99 Ovis aries PV1 (U83594) Delta 0.2 89 Odocoileus virginianus PV1 (M11910) 100 Alces alces PV1 (M15953)