Final CLOVERT bug fixes + hairball figure

(Recompiled with Rory's last additions)

Code_Dev/X_Hairballs.R

@@ -1,50 +1,69 @@
 
+library(magrittr)
 library(tidyverse)
+library(vroom)
+
 library(igraph)
 library(ggraph)
 library(graphlayouts)
 library(oaqc)
 
 vir <- vroom("Virion/Virion.csv.gz")
 
-clo <- read_csv("~/Github/clover/clover/Clover_v1.0_NBCIreconciled_20201218.csv")
+vir %<>% 
+  filter(HostNCBIResolved == TRUE,
+         VirusNCBIResolved == TRUE) %>%
+  select(Host,Virus,Database) %>% 
+  na.omit() %>% 
+  unique()
+
+vir %>%
+  filter(Database=="HP3") %>%
+  select(Host, Virus) %>% 
+  unique() -> hp3
 
-hp3 <- read_csv("~/Github/clover/data/source_databases/HP3_associations.csv")
+vir %>%
+  select(Host, Virus) %>% 
+  unique() -> vir 
 
-vir %>% select(Host,Virus) %>% na.omit() %>% unique() -> vir
+hp3$Source = 'HP3'
+vir$Source = 'VIRION'
 
-clo %>% select(Host, Virus) %>% 
-  mutate(Host = str_c(Host, '_clo'),
-         Virus = str_c(Virus, '_clo')) -> clo
+hp3 %<>% mutate(Virus = str_c(Virus,"_hp3"),
+                Host = str_c(Host, "_hp3"))
 
-hp3 %>% select(hHostNameFinal, vVirusNameCorrected) %>% 
-  rename(Virus = 'vVirusNameCorrected',
-         Host = 'hHostNameFinal') %>%
-  mutate(Host = str_c(Host, '_hp3'),
-         Virus = str_c(Virus, '_hp3')) -> hp3
+vir %>% bind_rows(hp3) -> vir
+vir %<>% na.omit()
 
-vir %>% bind_rows(clo) %>% bind_rows(hp3) -> vir
+net <- graph.data.frame(as.data.frame(vir), directed = FALSE)
 
-vir %>% unique -> clo
+sub_gs <- components(net)
+small_sub <- which(sub_gs$csize < 20)
+(rm_nodes <- which(sub_gs$membership %in% small_sub))
+net <- delete_vertices(net, rm_nodes)
 
-net <- graph.data.frame(as.data.frame(clo), directed = FALSE)
 
 net <- set_vertex_attr(net, 'Type', index = V(net), 
-                ifelse(V(net)$name %in% clo$Host, "Host", "Virus"))
+                ifelse(V(net)$name %in% vir$Host, "Host", "Virus"))
 
-net <- decompose.graph(net, min.vertices = 500)
-net <- union(net[[1]], net[[2]], net[[3]], byname = TRUE)
-V(net)$Type <- ifelse(is.na(V(net)$Type_1),
-                         ifelse(is.na(V(net)$Type_2), V(net)$Type_3, V(net)$Type_2),
-                      V(net)$Type_1)
+net <- set_vertex_attr(net, 'Source', index = V(net), 
+                       ifelse(str_detect(V(net)$name, "_hp3"), "HP3", "VIRION"))
 
 got_palette <- c("#325E9A", "#DD5D5D", "#325E9A", "#DD5D5D")
 
-ggraph(net, layout = "stress") + # layout = "centrality", cent = graph.strength(net)) +
-  geom_edge_link0(edge_colour = "grey50", alpha = 0.3) +
-  geom_node_point(aes(fill = Type), colour = "grey50", shape = 21, size = 1, stroke = 0.25) +
+ggraph(net, layout = "kk") + 
+  geom_edge_link(edge_colour = "grey80", alpha = 0.2) +
+  geom_node_point(aes(fill = Type), colour = "grey50", shape = 21, size = 1.1, stroke = 0.8, alpha = 0.5) +
   scale_fill_manual(values = got_palette) +
-  theme_graph() +
-  theme(legend.position = "none") # ,
-    #   panel.background = element_rect(fill = "#ADEADD"))
-
+  theme_bw() +
+  facet_nodes( ~ Source, scales = "free", shrink = TRUE) + 
+  theme(legend.position = "none",
+        strip.text = element_text(size = 20),
+        axis.title.x=element_blank(),
+        axis.text.x=element_blank(),
+        axis.ticks.x=element_blank(),
+        axis.title.y=element_blank(),
+        axis.text.y=element_blank(),
+        axis.ticks.y=element_blank(),
+        panel.background = element_rect(fill = "#ADEADD"),
+        plot.background = element_rect(fill = "#ADEADD"))

Intermediate/Formatted/CLOVERFormatted.csv

@@ -636,6 +636,7 @@ kareius bicoloratus,hirame novirhabdovirus,143345,1980915,TRUE,TRUE,kareius,pleu
 kareius bicoloratus,hirame novirhabdovirus,143345,1980915,TRUE,TRUE,kareius,pleuronectidae,pleuronectiformes,actinopteri,kareius bicoloratus,NA,novirhabdovirus,rhabdoviridae,mononegavirales,monjiviricetes,hirame novirhabdovirus,NA,NA,Isolation/Observation,Isolation,Shaw,Shaw et al. 2020 Mol Ecol,NA,ViPR,NA,NA,NA,NA,NA,NA,NA,NA
 kareius bicoloratus,infectious pancreatic necrosis virus,143345,11002,TRUE,TRUE,kareius,pleuronectidae,pleuronectiformes,actinopteri,kareius bicoloratus,NA,aquabirnavirus,birnaviridae,NA,NA,infectious pancreatic necrosis virus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2013,"Kim WS, 2013, J Vet Diagn Invest, 25",24081931,NA,NA,NA,NA,NA,NA,NA
 labroides dimidiatus,santee-cooper ranavirus,241309,198068,TRUE,TRUE,labroides,labridae,labriformes,actinopteri,labroides dimidiatus,NA,ranavirus,iridoviridae,pimascovirales,megaviricetes,santee-cooper ranavirus,NA,NA,PCR/Sequencing,NCBI Nucleotide,EID2,Wardeh et al. 2015 Sci Data,NA,NCBI Nucleotide,NA,227071953,2009,NA,NA,NA,NA,NA
+labroides dimidiatus,santee-cooper ranavirus,241309,198068,TRUE,TRUE,labroides,labridae,labriformes,actinopteri,labroides dimidatus,NA,ranavirus,iridoviridae,pimascovirales,megaviricetes,santee-cooper ranavirus,NA,NA,Isolation/Observation,Isolation,Shaw,Shaw et al. 2020 Mol Ecol,1995,"Hedrick RP, 1995, Vet Res, 26",8581016,NA,NA,NA,NA,NA,NA,NA
 labrus mixtus,piscine novirhabdovirus,508554,1980916,TRUE,TRUE,labrus,labridae,labriformes,actinopteri,labrus mixtus,NA,novirhabdovirus,rhabdoviridae,mononegavirales,monjiviricetes,oncorhynchus 2 novirhabdovirus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2015,"Munro ES, 2015, J Fish Dis, 38",24661037,NA,NA,NA,NA,NA,NA,NA
 lagocephalus lunaris,redspotted grouper nervous necrosis virus,204814,43763,TRUE,TRUE,lagocephalus,tetraodontidae,tetraodontiformes,actinopteri,lagocephalus lunaris,NA,betanodavirus,nodaviridae,nodamuvirales,magsaviricetes,redspotted grouper nervous necrosis virus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2008,"Gomez DK, 2008, J Vet Diagn Invest, 20",18182506,NA,NA,NA,NA,NA,NA,NA
 lagocephalus spadiceus,infectious spleen and kidney necrosis virus,435151,180170,TRUE,TRUE,lagocephalus,tetraodontidae,tetraodontiformes,actinopteri,lagocephalus spadiceus,NA,megalocytivirus,iridoviridae,pimascovirales,megaviricetes,infectious spleen and kidney necrosis virus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2007,"Wang YQ, 2007, Arch Virol, 152",17131065,NA,NA,NA,NA,NA,NA,NA
@@ -1796,7 +1797,6 @@ zanclus cornutus,redspotted grouper nervous necrosis virus,75044,43763,TRUE,TRUE
 zebrasoma flavescens,redspotted grouper nervous necrosis virus,175439,43763,TRUE,TRUE,zebrasoma,acanthuridae,acanthuriformes,actinopteri,zebrasoma flavescens,NA,betanodavirus,nodaviridae,nodamuvirales,magsaviricetes,redspotted grouper nervous necrosis virus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2006,"Gomez DK, 2006, J Vet Sci, 7",17106229,NA,NA,NA,NA,NA,NA,NA
 zeus faber,redspotted grouper nervous necrosis virus,64108,43763,TRUE,TRUE,zeus,zeidae,zeiformes,actinopteri,zeus faber,NA,betanodavirus,nodaviridae,nodamuvirales,magsaviricetes,redspotted grouper nervous necrosis virus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2008,"Gomez DK, 2008, J Vet Diagn Invest, 20",18182506,NA,NA,NA,NA,NA,NA,NA
 zoarces gillii,redspotted grouper nervous necrosis virus,762048,43763,TRUE,TRUE,zoarces,zoarcidae,perciformes,actinopteri,zoarces gillii,NA,betanodavirus,nodaviridae,nodamuvirales,magsaviricetes,redspotted grouper nervous necrosis virus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2008,"Gomez DK, 2008, J Vet Diagn Invest, 20",18182506,NA,NA,NA,NA,NA,NA,NA
-labroides dimidiatus,santee-cooper ranavirus,241309,198068,TRUE,TRUE,labroides,labridae,labriformes,actinopterygii,labroides dimidatus,NA,ranavirus,iridoviridae,pimascovirales,megaviricetes,santee-cooper ranavirus,NA,NA,Isolation/Observation,Isolation,Shaw,Shaw et al. 2020 Mol Ecol,1995,"Hedrick RP, 1995, Vet Res, 26",8581016,NA,NA,NA,NA,NA,NA,NA
 acris crepitans,frog virus 3,317300,10493,TRUE,TRUE,acris,hylidae,anura,amphibia,acris crepitans,NA,ranavirus,iridoviridae,pimascovirales,megaviricetes,frog virus 3,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2012,"Hoverman JT, 2012, Ecohealth, 9",22173292,NA,NA,NA,NA,NA,NA,NA
 agalychnis callidryas,frog virus 3,197464,10493,TRUE,TRUE,agalychnis,hylidae,anura,amphibia,agalychnis callidryas,NA,ranavirus,iridoviridae,pimascovirales,megaviricetes,frog virus 3,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,NA,http://dx.doi.org/10.13128/Acta_Herpetol-13516,NA,NA,NA,NA,NA,NA,NA,NA
 alytes obstetricans,frog virus 3,8443,10493,TRUE,TRUE,alytes,alytidae,anura,amphibia,alytes obstetricans,NA,ranavirus,iridoviridae,pimascovirales,megaviricetes,frog virus 3,NA,NA,PCR/Sequencing,NCBI Nucleotide,EID2,Wardeh et al. 2015 Sci Data,NA,NCBI Nucleotide,NA,190358099,2008,NA,NA,NA,NA,NA
@@ -11978,11 +11978,11 @@ rissa tridactyla,tyuleniy virus,75485,40004,TRUE,TRUE,rissa,laridae,charadriifor
 rissa tridactyla,tyuleniy virus,75485,40004,TRUE,TRUE,rissa,laridae,charadriiformes,aves,rissa tridactyla,NA,flavivirus,flaviviridae,amarillovirales,flasuviricetes,tyuleniy virus,NA,NA,Antibodies,Antibodies,Shaw,Shaw et al. 2020 Mol Ecol,NA,ArboCat,NA,NA,NA,NA,NA,NA,NA,NA
 rissa tridactyla,uukuniemi uukuvirus,75485,2749936,TRUE,TRUE,rissa,laridae,charadriiformes,aves,rissa tridactyla,NA,uukuvirus,phenuiviridae,bunyavirales,ellioviricetes,uukuniemi phlebovirus,NA,NA,Isolation/Observation,Isolation,Shaw,Shaw et al. 2020 Mol Ecol,1984,"Eley SM, 1984, J Hyg (Lond), 93",6501877,NA,NA,NA,NA,NA,NA,NA
 rupicola rupicola,avian orthoavulavirus 1,81879,2560319,TRUE,TRUE,rupicola,cotingidae,passeriformes,aves,rupicola rupicola,NA,orthoavulavirus,paramyxoviridae,mononegavirales,monjiviricetes,newcastle disease virus,NA,NA,Isolation/Observation,Histopathology,Shaw,Shaw et al. 2020 Mol Ecol,NA,http://link.springer.com/chapter/10.1007/978-1-4613-1759-3_12,NA,NA,NA,NA,NA,NA,NA,NA
-rupornis magnirostris,avian coronavirus,2709556,694014,TRUE,TRUE,NA,accipitridae,accipitriformes,aves,buteo magnirostris,NA,gammacoronavirus,coronaviridae,nidovirales,pisoniviricetes,avian coronavirus,NA,NA,PCR/Sequencing,NCBI Nucleotide,EID2,Wardeh et al. 2015 Sci Data,NA,NCBI Nucleotide,NA,283510354,2010,NA,NA,NA,NA,NA
-rupornis magnirostris,avian coronavirus,2709556,694014,TRUE,TRUE,NA,accipitridae,accipitriformes,aves,buteo magnirostris,NA,gammacoronavirus,coronaviridae,nidovirales,pisoniviricetes,avian coronavirus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2011,"Cardoso TC, 2011, Vector Borne Zoonotic Dis, 11",21142971,NA,NA,NA,NA,NA,NA,NA
-rupornis magnirostris,avian coronavirus,2709556,694014,TRUE,TRUE,NA,accipitridae,accipitriformes,aves,buteo magnirostris,NA,gammacoronavirus,coronaviridae,nidovirales,pisoniviricetes,avian coronavirus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,NA,ViPR,NA,NA,NA,NA,NA,NA,NA,NA
-rupornis magnirostris,murine coronavirus,2709556,694005,TRUE,TRUE,NA,accipitridae,accipitriformes,aves,buteo magnirostris,NA,betacoronavirus,coronaviridae,nidovirales,pisoniviricetes,murine coronavirus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2015,"Dur�es-Carvalho R, 2015, J Mol Evol, 81",26250156,NA,NA,NA,NA,NA,NA,NA
-rupornis magnirostris,murine coronavirus,2709556,694005,TRUE,TRUE,NA,accipitridae,accipitriformes,aves,buteo magnirostris,NA,betacoronavirus,coronaviridae,nidovirales,pisoniviricetes,murine coronavirus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,NA,ViPR,NA,NA,NA,NA,NA,NA,NA,NA
+rupornis magnirostris,avian coronavirus,2709556,694014,TRUE,TRUE,rupornis,accipitridae,accipitriformes,aves,buteo magnirostris,NA,gammacoronavirus,coronaviridae,nidovirales,pisoniviricetes,avian coronavirus,NA,NA,PCR/Sequencing,NCBI Nucleotide,EID2,Wardeh et al. 2015 Sci Data,NA,NCBI Nucleotide,NA,283510354,2010,NA,NA,NA,NA,NA
+rupornis magnirostris,avian coronavirus,2709556,694014,TRUE,TRUE,rupornis,accipitridae,accipitriformes,aves,buteo magnirostris,NA,gammacoronavirus,coronaviridae,nidovirales,pisoniviricetes,avian coronavirus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2011,"Cardoso TC, 2011, Vector Borne Zoonotic Dis, 11",21142971,NA,NA,NA,NA,NA,NA,NA
+rupornis magnirostris,avian coronavirus,2709556,694014,TRUE,TRUE,rupornis,accipitridae,accipitriformes,aves,buteo magnirostris,NA,gammacoronavirus,coronaviridae,nidovirales,pisoniviricetes,avian coronavirus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,NA,ViPR,NA,NA,NA,NA,NA,NA,NA,NA
+rupornis magnirostris,murine coronavirus,2709556,694005,TRUE,TRUE,rupornis,accipitridae,accipitriformes,aves,buteo magnirostris,NA,betacoronavirus,coronaviridae,nidovirales,pisoniviricetes,murine coronavirus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,2015,"Dur�es-Carvalho R, 2015, J Mol Evol, 81",26250156,NA,NA,NA,NA,NA,NA,NA
+rupornis magnirostris,murine coronavirus,2709556,694005,TRUE,TRUE,rupornis,accipitridae,accipitriformes,aves,buteo magnirostris,NA,betacoronavirus,coronaviridae,nidovirales,pisoniviricetes,murine coronavirus,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,NA,ViPR,NA,NA,NA,NA,NA,NA,NA,NA
 sagittarius serpentarius,avian orthoavulavirus 1,56258,2560319,TRUE,TRUE,sagittarius,sagittariidae,accipitriformes,aves,sagittarius serpentarius,NA,orthoavulavirus,paramyxoviridae,mononegavirales,monjiviricetes,newcastle disease virus,NA,NA,Isolation/Observation,Isolation,Shaw,Shaw et al. 2020 Mol Ecol,1976,"Chu HP, 1976, Avian Pathol, 5",18777349,NA,NA,NA,NA,NA,NA,NA
 sagittarius serpentarius,avian orthoavulavirus 1,56258,2560319,TRUE,TRUE,sagittarius,sagittariidae,accipitriformes,aves,sagittarius serpentarius,NA,orthoavulavirus,paramyxoviridae,mononegavirales,monjiviricetes,newcastle disease virus,NA,NA,Isolation/Observation,Isolation,Shaw,Shaw et al. 2020 Mol Ecol,NA,DOI:10.1080/03079457608418189,NA,NA,NA,NA,NA,NA,NA,NA
 saltator maximus,saint louis encephalitis virus,460219,11080,TRUE,TRUE,saltator,thraupidae,passeriformes,aves,saltator maximus,NA,flavivirus,flaviviridae,amarillovirales,flasuviricetes,st. louis encephalitis virus,NA,NA,PCR/Sequencing,NCBI Nucleotide,EID2,Wardeh et al. 2015 Sci Data,NA,NCBI Nucleotide,NA,305431366,2010,NA,NA,NA,NA,NA
@@ -48653,10 +48653,10 @@ leontocebus fuscicollis,cowpox virus,9487,10243,TRUE,TRUE,leontocebus,cebidae,pr
 leontocebus fuscicollis,cowpox virus,9487,10243,TRUE,TRUE,leontocebus,cebidae,primates,mammalia,saguinus fuscicollis,NA,orthopoxvirus,poxviridae,chitovirales,pokkesviricetes,cowpox virus,NA,NA,Isolation/Observation,Isolation,Shaw,Shaw et al. 2020 Mol Ecol,NA,ViPR,NA,NA,NA,NA,NA,NA,NA,NA
 leontocebus fuscicollis,hepatovirus a,9487,12092,TRUE,TRUE,leontocebus,cebidae,primates,mammalia,saguinus fuscicollis,NA,hepatovirus,picornaviridae,picornavirales,pisoniviricetes,hepatovirus a,NA,NA,Antibodies,Antibodies,Shaw,Shaw et al. 2020 Mol Ecol,1992,"Balayan MS, 1992, Vaccine, 10 Suppl 1",1335654,NA,NA,NA,NA,NA,NA,NA
 leontocebus fuscicollis,lymphocytic choriomeningitis mammarenavirus,9487,11623,TRUE,TRUE,leontocebus,cebidae,primates,mammalia,saguinus fuscicollis,NA,mammarenavirus,arenaviridae,bunyavirales,ellioviricetes,lymphocytic choriomeningitis mammarenavirus,NA,NA,Isolation/Observation,Histopathology,Shaw,Shaw et al. 2020 Mol Ecol,NA,http://www.jstor.org/stable/20094936,NA,NA,NA,NA,NA,NA,NA,NA
-leontocebus nigricollis,lymphocytic choriomeningitis mammarenavirus,9489,11623,TRUE,TRUE,leontocebus,callitrichidae,primates,mammalia,saguinus nigricollis,NA,mammarenavirus,arenaviridae,bunyavirales,ellioviricetes,lymphocytic choriomeningitis mammarenavirus,NA,NA,Isolation/Observation,Histopathology,Shaw,Shaw et al. 2020 Mol Ecol,NA,http://www.jstor.org/stable/20094936,NA,NA,NA,NA,NA,NA,NA,NA
-leontocebus nigricollis,pegivirus a,9489,1307800,TRUE,TRUE,leontocebus,callitrichidae,primates,mammalia,saguinus nigricollis,NA,pegivirus,flaviviridae,amarillovirales,flasuviricetes,gb virus a,NA,NA,PCR/Sequencing,PCR,HP3,Olival et al. 2017 Nature,1997,Bukh & Apga 1997,NA,NA,NA,NA,NA,NA,NA,NA
-leontocebus nigricollis,pegivirus a,9489,1307800,TRUE,TRUE,leontocebus,callitrichidae,primates,mammalia,saguinus nigricollis,NA,pegivirus,flaviviridae,amarillovirales,flasuviricetes,pegivirus a,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,1997,"Bukh J, 1997, Virology, 229",9126255,NA,NA,NA,NA,NA,NA,NA
-leontocebus nigricollis,pegivirus a,9489,1307800,TRUE,TRUE,leontocebus,callitrichidae,primates,mammalia,saguinus nigricollis,NA,pegivirus,flaviviridae,amarillovirales,flasuviricetes,pegivirus a,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,NA,ViPR,NA,NA,NA,NA,NA,NA,NA,NA
+leontocebus nigricollis,lymphocytic choriomeningitis mammarenavirus,9489,11623,TRUE,TRUE,leontocebus,cebidae,primates,mammalia,saguinus nigricollis,NA,mammarenavirus,arenaviridae,bunyavirales,ellioviricetes,lymphocytic choriomeningitis mammarenavirus,NA,NA,Isolation/Observation,Histopathology,Shaw,Shaw et al. 2020 Mol Ecol,NA,http://www.jstor.org/stable/20094936,NA,NA,NA,NA,NA,NA,NA,NA
+leontocebus nigricollis,pegivirus a,9489,1307800,TRUE,TRUE,leontocebus,cebidae,primates,mammalia,saguinus nigricollis,NA,pegivirus,flaviviridae,amarillovirales,flasuviricetes,gb virus a,NA,NA,PCR/Sequencing,PCR,HP3,Olival et al. 2017 Nature,1997,Bukh & Apga 1997,NA,NA,NA,NA,NA,NA,NA,NA
+leontocebus nigricollis,pegivirus a,9489,1307800,TRUE,TRUE,leontocebus,cebidae,primates,mammalia,saguinus nigricollis,NA,pegivirus,flaviviridae,amarillovirales,flasuviricetes,pegivirus a,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,1997,"Bukh J, 1997, Virology, 229",9126255,NA,NA,NA,NA,NA,NA,NA
+leontocebus nigricollis,pegivirus a,9489,1307800,TRUE,TRUE,leontocebus,cebidae,primates,mammalia,saguinus nigricollis,NA,pegivirus,flaviviridae,amarillovirales,flasuviricetes,pegivirus a,NA,NA,PCR/Sequencing,PCR,Shaw,Shaw et al. 2020 Mol Ecol,NA,ViPR,NA,NA,NA,NA,NA,NA,NA,NA
 leontopithecus chrysomelas,lymphocytic choriomeningitis mammarenavirus,57374,11623,TRUE,TRUE,leontopithecus,cebidae,primates,mammalia,leontopithecus chrysomelas,NA,mammarenavirus,arenaviridae,bunyavirales,ellioviricetes,lymphocytic choriomeningitis mammarenavirus,NA,NA,Isolation/Observation,Histopathology,Shaw,Shaw et al. 2020 Mol Ecol,NA,http://www.jstor.org/stable/20094936,NA,NA,NA,NA,NA,NA,NA,NA
 leontopithecus chrysomelas,simian foamy virus,57374,11642,TRUE,TRUE,leontopithecus,cebidae,primates,mammalia,leontopithecus chrysomelas,NA,spumavirus,retroviridae,ortervirales,revtraviricetes,simian foamy virus,NA,NA,Antibodies,Antibodies,Shaw,Shaw et al. 2020 Mol Ecol,2015,"Muniz CP, 2015, Retrovirology, 12",26576961,NA,NA,NA,NA,NA,NA,NA
 leontopithecus chrysomelas,torque teno virus,57374,68887,TRUE,TRUE,leontopithecus,cebidae,primates,mammalia,leontopithecus chrysomelas,NA,NA,anelloviridae,NA,NA,torque teno virus,NA,NA,PCR/Sequencing,PCR,HP3,Olival et al. 2017 Nature,2008,Catroxo et al. 2008,NA,NA,NA,NA,NA,NA,NA,NA