Archive for July, 2013

1793 viruses!

Tuesday, July 30th, 2013

In case you missed it, I spent ten days in hospital this past May (2013).

When they took the skin biopsy from my arm, I got them to take 2 samples. One of them, along with a throat and skin swab was later sent to the virologists I do some work with in the Viroscience Lab at the Erasmus Medical Center (EMC).

I got the sequence data back about a week ago and have been looking at them, firstly via BLAST and then using a bunch of code I’ve been writing lately. There are 115K reads from 6 preparations (RNA and DNA protocols for each of the 3 samples). These come from a “next generation” sequencer, a Roche 454. The next generation sequencing involves using random primers to indiscriminately match genetic material. My BLAST output files are about 82Mb in total (this is relatively small, some of my other data sets are about 30Gb). I BLASTed against a viral subset alias nucleotide database that I made from the full NCBI Nucleotide Database, excluding all bacteriophage viruses. There are about 1.3M viral sequences in the subset db.

I wont go into details, but wanted to dump a bit of data that’s pretty amusing / interesting. Just to give the EMC folks an idea of the scale of diversity I am seeing, I grepped out all “complete genome” hits from all the BLAST output. I chucked out suffixes in the sequence titles that matched the regex (nearly )?complete genome|isolate|strain|subtype).* and then stripped the titles of any text beyond the string “virus” in the title (this step collapses a lot of virus strain information that should really be kept). Then, do a unique sort and…. it turns out I have reads matching at least 1793 viruses.

I feel like the subject of a metagenomics study. At the hospital, once the chickenpox tests had come back negative, they threw a ton of tests at my samples and everything was negative. Otherwise, I’d really be worried :-)

Given the list of sequence matches, it feels like the only plausible explanation is that I’m actually dead and that this is all just a simulation.

Here’s the sorted list of virus names (read counts omitted). I find it pretty amazing. I don’t know what it all means, but I’m planning to find out more by writing more code and learning more.

Abalone herpesvirus
Abalone shriveling syndrome-associated virus
Abelson murine leukemia virus
Abutilon mosaic virus
Acanthamoeba castellanii mamavirus
Acanthamoeba polyphaga mimivirus
Acanthamoeba polyphaga moumouvirus
Acanthocystis turfacea Chlorella virus
Acheta domestica densovirus
Achimota virus
Acidianus bottle-shaped virus
Acidianus filamentous virus
Acidianus filamentus virus
Acidianus spindle-shaped virus
Aconitum latent virus
Acute bee paralysis virus
Adelaide River virus
Adeno-associated virus
Adenovirus
Adoxophyes honmai enomopoxvirus
Adoxophyes honmai nucleopolyhedrovirus
Adoxophyes orana granulovirus
Adoxophyes orana nucleopolyhedrovirus
Aedes aegypti densovirus
Aedes flavivirus
Aedes taeniorhynchus iridescent virus
Aeropyrum pernix K1 DNA
Aeropyrum spring-shaped virus
African cassava mosaic Burkina Faso virus
African cassava mosaic virus
African green monkey polyomavirus
African oil palm ringspot virus
African swine fever virus
Ageratum enation alphasatellite
Ageratum enation virus
Ageratum leaf curl virus
Ageratum yellow vein China virus
Ageratum yellow vein Singapore alphasatellite
Ageratum yellow vein virus
Agropyron mosaic virus
Agrotis ipsilon multiple nucleopolyhedrovirus
Agrotis segetum granulovirus
Agrotis segetum nucleopolyhedrovirus
Aichi virus
Aleutian mink disease parvovirus
Alfuy virus
Algerian watermelon mosaic virus
Alkhumra hemorrhagic fever virus
Allium virus
Alpaca respiratory coronavirus
Alphavirus
Alstroemeria virus
Alternanthera mosaic virus
Alternanthera yellow vein virus
Ambystoma tigrinum stebbensi virus
American hop latent virus
Amphotropic murine leukemia virus
Amsacta moorei entomopoxvirus
Anatid herpesvirus
Andean potato latent virus
Andean potato mild mottle virus
Anguillid herpesvirus
Anopheles gambiae densonucleosis virus
Antheraea pernyi nucleopolyhedrovirus
Anticarsia gemmatalis nucleopolyhedrovirus
Aotine herpesvirus
Aphid lethal paralysis virus
Apium virus
Apocheima cinerarium nucleopolyhedrovirus
Apodemus sylvaticus papillomavirus
Apple chlorotic leaf spot virus
Apple green crinkle associated virus
Apple stem grooving virus
Apple stem pitting virus
Apricot latent virus
Apricot pseudo-chlorotic leaf spot virus
Aravan virus
Archaeal BJ1 virus
Arctic ground squirrel hepatitis B virus
Armigeres subalbatus virus
Arracacha mottle virus
Artemisia virus
Artibeus jamaicensis parvovirus
Asclepias asymptomatic virus
Asian prunus virus
Asparagus virus
Astrovirus
Ateles paniscus polyomavirus
Ateline herpesvirus
Atlantic salmon paramyxovirus
Atlantic salmon swim bladder sarcoma virus
Aurantiochytrium single-stranded RNA virus
Australian bat lyssavirus
Autographa californica nucleopolyhedrovirus
Avastrovirus
Avian adeno-associated virus
Avian adenovirus
Avian bornavirus
Avian carcinoma virus
Avian encephalomyelitis virus
Avian endogenous retrovirus
Avian gyrovirus
Avian hepatitis E virus
Avian infectious bronchitis virus
Avian leukemia virus
Avian leukosis virus
Avian metapneumovirus
Avian myelocytomatosis virus
Avian nephritis virus
Avian paramyxovirus
Avian pneumovirus
B19 virus
BK polyomavirus
Babanki virus
Baboon endogenous virus
Baboon enterovirus
Bacillus virus
Bagaza virus
Bamboo mosaic virus
Baminivirus
Banana bract mosaic virus
Banana mild mosaic virus
Banana streak CA virus
Banana streak GF virus
Banana streak IM virus
Banana streak Imove virus
Banana streak Mys virus
Banana streak Mysore virus
Banana streak UA virus
Banana streak UI virus
Banana streak UL virus
Banana streak UM virus
Banana streak virus
Bandicoot papillomatosis carcinomatosis virus
Barbel circovirus
Barley dwarf virus
Barley yellow dwarf virus
Barmah Forest virus
Basella rugose mosaic virus
Bat Paramyxovirus
Bat SARS CoV Rs672/2006
Bat SARS coronavirus
Bat adenovirus
Bat betaherpesvirus
Bat circovirus
Bat coronavirus
Bat hepatitis virus
Bat hepevirus
Bat picornavirus
Bat polyomavirus
Bat sapovirus
Bathycoccus sp. RCC1105 virus
Beak and feather disease virus
Bean common mosaic necrosis virus
Bean common mosaic virus
Bean leafroll virus
Bean yellow mosaic virus
Beauveria bassiana RNA virus
Bebaru virus
Beet black scorch virus
Beet chlorosis virus
Beet curly top Iran virus
Beet curly top virus
Beet mild curly top virus
Beet mild yellowing virus
Beet mosaic virus
Beet severe curly top virus
Beet soil-borne mosaic virus
Beet western yellows virus
Beet yellows virus
Beilong virus
Bell pepper endornavirus
Bell pepper mottle virus
Berrimah virus
Betacoronavirus
Bettongia penicillata papillomavirus
Bhendi yellow vein Bhubhaneswar virus
Bhendi yellow vein mosaic betasatellite
Bhendi yellow vein mosaic virus
Bidens mottle virus
Black raspberry virus
Blackberry virus
Blackeye cowpea mosaic virus
Blattella germanica densovirus
Blue squill virus
Blueberry latent virus
Blueberry red ringspot virus
Blueberry scorch virus
Blueberry virus
Bluegill picornavirus
Bocavirus
Bokeloh bat lyssavirus
Bombyx mandarina nucleopolyhedrovirus
Bombyx mori Macula-like virus
Bombyx mori NPV
Bombyx mori densovirus
Bombyx mori nuclear polyhedrosis virus
Border disease virus
Borna disease virus
Bos grunniens papillomavirus
Botryotinia fuckeliana totivirus
Botrytis virus
Bougainvillea spectabilis chlorotic vein-banding virus
Bovine adeno-associated virus
Bovine adenovirus
Bovine astrovirus
Bovine coronavirus
Bovine enterovirus
Bovine ephemeral fever virus
Bovine foamy virus
Bovine herpesvirus
Bovine hungarovirus
Bovine kobuvirus
Bovine leukemia virus
Bovine papillomavirus
Bovine papular stomatitis virus
Bovine parainfluenza virus
Bovine parvovirus
Bovine polyomavirus
Bovine respiratory coronavirus
Bovine respiratory syncytial virus
Bovine rhinovirus
Bovine syncytial virus
Bovine viral diarrhea virus
Brassica yellows virus
Breda virus
Brevicoryne brassicae picorna-like virus
Bromus catharticus striate mosaic virus
Brugmansia mosaic virus
Brugmansia suaveolens mottle virus
Budgerigar fledgling disease polyomavirus
Buggy Creek virus
Bulbul coronavirus
Bundibugyo ebolavirus
Bussuquara virus
Butterbur mosaic virus
Cacao swollen shoot virus
Cactus mild mottle virus
Cactus virus
Cafeteria roenbergensis virus
Caladenia virus
Calf-giraffe coronavirus
Calibrachoa mottle virus
Calicivirus
California sea lion anellovirus
California sea lion polyomavirus
Callitrichine herpesvirus
Camelpox virus
Camelus dromedarius papillomavirus
Canary circovirus
Canary polyomavirus
Canarypox virus
Canine adenovirus
Canine bocavirus
Canine circovirus
Canine coronavirus
Canine distemper virus
Canine kobuvirus
Canine minute virus
Canine oral papillomavirus
Canine papillomavirus
Canine parvovirus
Canine picodicistrovirus
Canine picornavirus
Canine respiratory coronavirus
Canine vesivirus
Canna Yellow Streak Virus from United Kingdom
Capra hircus papillomavirus
Caprine arthritis encephalitis virus
Caprine arthritis-encephalitis virus
Cardioderma polyomavirus
Cardiospermum yellow leaf curl virus
Caretta caretta papillomavirus
Carnation etched ring virus
Carnation mottle virus
Carrot mottle mimic umbravirus
Carrot mottle virus
Carrot necrotic dieback virus
Carrot red leaf virus
Carrot yellow leaf virus
Cassava brown streak virus
Cassava common mosaic virus
Cassava latent virus
Cassava vein mosaic virus
Catharanthus yellow mosaic virus
Cauliflower mosaic virus
Cavally virus
Caviid herpesvirus
Cebus albifrons polyomavirus
Cedar virus
Celery mosaic virus
Cercopithecine herpesvirus
Cercopithecus erythrotis polyomavirus
Cercopithicine herpesvirus
Cereal yellow dwarf virus
Cervus elaphus papillomavirus
Cestrum yellow leaf curling virus
Chaerephon polyomavirus
Chaetoceros lorenzianus DNA Virus DNA
Chaetoceros salsugineum DNA virus
Chaetoceros tenuissimus DNA virus
Chandipura virus
Chaoyang virus
Chayote mosaic tymovirus
Chelonia mydas papillomavirus
Chenopodium leaf curl virus
Chenopodium mosaic virus
Cherry green ring mottle virus
Cherry mottle leaf virus
Cherry necrotic rusty mottle virus
Cherry rusty mottle associated virus
Cherry virus
Chiba virus
Chicken anemia virus
Chicken astrovirus
Chicken parvovirus
Chickpea chlorosis Australia virus
Chickpea chlorosis virus
Chickpea chlorotic dwarf virus
Chickpea chlorotic stunt virus
Chickpea redleaf virus
Chickpea yellows mastrevirus
Chikungunya virus
Chilli leaf curl India virus
Chilli leaf curl virus
Chilli ringspot virus
Chilli veinal mottle virus
Chilo iridescent virus
Chiltepin yellow mosaic virus
Chimeric Tick-borne encephalitis virus
Chimpanzee adenovirus
Chimpanzee alpha-1 herpesvirus
Chimpanzee polyomavirus
Chimpanzee stool associated circular ssDNA virus
Chimpanzee stool avian-like circovirus
Chinese yam necrotic mosaic virus
Chlamys acute necrobiotic virus
Chloris striate mosaic virus
Choristoneura biennis entomopoxvirus
Choristoneura fumiferana MNPV polyhedrin
Choristoneura fumiferana defective nucleopolyhedrovirus
Choristoneura occidentalis granulovirus
Choristoneura rosaceana entomopoxvirus
Chrysanthemum virus
Chrysodeixis chalcites nucleopolyhedrovirus
Circoviridae bovine stool/BK/KOR/2011
Circovirus
Circulifer tenellus virus
Citrus chlorotic dwarf associated virus
Citrus leaf blotch virus
Citrus sudden death-associated virus
Citrus tatter leaf virus
Citrus tristeza virus
Citrus yellow mosaic virus
Citrus yellow vein clearing virus
Clanis bilineata nucleopolyhedrosis virus
Classical swine fever virus
Clerodendron yellow mosaic virus
Clitocybe odora virus
Clitoria yellow mottle virus
Cloning vector pEAV030 containing cDNA of Equine arteritis virus
Clostera anachoreta granulovirus
Coastal Plains virus
Cocal virus
Cocksfoot mild mosaic virus
Cocksfoot mottle virus
Cocksfoot streak virus
Coconut foliar decay virus
Coleus vein necrosis virus
Colobus guereza papillomavirus
Colombian datura virus
Columbid circovirus
Common chimpanzee papillomavirus
Common marmoset foamy virus
Common midwife toad ranavirus
Common-moorhen coronavirus
Cordyline virus
Coronavirus
Cote d'Ivoire ebolavirus
Cotesia congregata virus
Cotia virus
Cotton leaf curl Burewala betasatellite
Cotton leaf curl Burewala virus
Cotton leaf curl Gezira alphasatellite
Cotton leaf curl Gezira virus
Cotton leaf curl Kokhran virus
Cotton leaf curl Multan betasatellite
Cotton leaf curl Multan virus
Cotton leaf curl Shadadpur virus
Cotton leafroll dwarf virus
Cottontail rabbit (Shope) papillomavirus
Cottontail rabbit papillomavirus
Cowpea aphid-borne mosaic virus
Cowpox virus
Coxsackievirus
Crassocephalum yellow vein virus
Crocuta crocuta papillomavirus
Croton yellow vein mosaic virus
Croton yellow vein virus
Crow polyomavirus
Cryphonectria hypovirus
Cryptophlebia leucotreta granulovirus
Cucumber fruit mottle mosaic virus
Cucumber green mottle mosaic virus
Cucumber mottle virus
Cucumber necrosis virus
Cucumber vein yellowing virus
Cucurbit aphid-borne yellows virus
Culex flavivirus
Culex nigripalpus baculovirus
Culex originated Tymoviridae-like virus
Culex tritaeniorhynchus rhabdovirus
Curtovirus
Cutthroat trout virus
Cycad leaf necrosis virus
Cyclovirus
Cydia pomonella granulovirus
Cygnus olor circovirus
Cymbidium mosaic virus
Cynomolgus macaque cytomegalovirus
Cyprinid herpesvirus
DG-75 Murine leukemia virus
Dahlia common mosaic virus
Dahlia mosaic virus
Daphne mosaic virus
Deer papillomavirus
Deerpox virus
Deformed wing virus
Delphinus delphis papillomavirus
Dendrolimus punctatus densovirus
Dengue Virus Type 2
Dengue type 3 virus
Dengue virus
Diaporthe ambigua RNA virus
Diascia yellow mottle virus
Diatraea saccharalis densovirus
Digitaria ciliaris striate mosaic virus
Digitaria didactyla striate mosaic virus
Digitaria streak virus
Dioscorea bacilliform virus
Diplodia scrobiculata RNA virus
Diuris virus
Dolichos yellow mosaic virus
Donggang virus
Dracaena mottle virus
Dragonfly circularisvirus
Dragonfly cyclicusvirus
Dragonfly cyclovirus
Dragonfly orbiculatusvirus
Dragonfly-associated circular virus
Dragonfly-associated mastrevirus
Drosophila A virus
Drosophila C virus
Drosophila melanogaster sigma virus
Drosophila melanogaster totivirus
Drosophila obscura sigma virus
Duck astrovirus
Duck circovirus
Duck coronavirus
Duck egg-drop syndrome virus
Duck enteritis virus
Duck flavivirus
Duck hepatitis A virus
Duck hepatitis B Virus DNA
Duck hepatitis B virus
Duck hepatitis virus
Duck picornavirus
Dulcamara mottle virus
Duvenhage virus
Dweet mottle virus
East African cassava mosaic virus
East Asian Passiflora virus
Eastern equine encephalitis virus
Ebola virus
Echovirus
Eclipta yellow vein virus
Ecotropis obliqua NPV
Ectocarpus siliculosus virus
Ectromelia virus
Eel Virus European X
Eidolon helvum parvovirus
Eidolon polyomavirus
Eimeria brunetti RNA virus
Elephant endotheliotropic herpesvirus
Elephantid herpesvirus
Eliat virus
Emilia yellow vein virus
Encephalomyocarditis (EMC) virus
Encephalomyocarditis virus
Entebbe bat virus
Enterovirus
Enzootic nasal tumour virus
Epinotia aporema granulovirus
Epiphyas postvittana nucleopolyhedrovirus
Epizootic haematopoietic necrosis virus
Epstein-Barr virus
Equid herpesvirus
Equine Pegivirus
Equine adenovirus
Equine arteritis virus
Equine coronavirus
Equine foamy virus
Equine herpesvirus
Equine infectious anemia virus
Equine papillomavirus
Equine polyomavirus
Equine rhinitis A virus
Equine rhinovirus
Equinus papillomavirus
Equus caballus papillomavirus
Equus ferus caballus papillomavirus
Eragrostis curvula streak virus
Eragrostis minor streak virus
Eragrostis streak virus
Erethizon dorsatum papillomavirus
Erysimum latent virus
Erythrovirus
Eupatorium vein clearing virus
Eupatorium yellow vein virus
Euphorbia leaf curl Guangxi virus
Euproctis pseudoconspersa nucleopolyhedrovirus
Euprosterna elaeasa virus
European bat lyssavirus
European elk papillomavirus
European hedgehog papillomavirus
European sheatfish virus
Farmington virus
Feldmannia species virus
Felid herpesvirus
Feline bocavirus
Feline calicivirus
Feline coronavirus
Feline foamy virus
Feline immunodeficiency virus
Feline infectious peritonitis virus
Feline leukemia virus
Feline morbillivirus
Feline papillomavirus
Feline picornavirus
Felis domesticus papillomavirus
Fenneropenaeus chinensis hepatopancreatic densovirus
Fer-de-lance virus
Ferret hepatitis E virus
Fig badnavirus
Fig fleck-associated virus
Finch circovirus
Finch polyomavirus
Flavivirus
Foot-and-mouth disease virus
Fort Morgan virus
Fowl adenovirus
Fowlpox virus
Foxtail mosaic virus
Francolinus leucoscepus papillomavirus
Frangipani mosaic virus
Freesia mosaic virus
French bean severe leaf curl virus
Friend murine leukemia virus
Friend spleen focus-forming virus
Fringilla coelebs papillomavirus
Frog adenovirus
Frog virus
Fujinami sarcoma virus
Furcraea necrotic streak virus
Fusarium graminearum dsRNA mycovirus
Fusarium graminearum hypovirus
Fusellovirus
GB virus
Galinsoga mosaic virus
Gallid herpesvirus
Gammapapillomavirus
Gammaretrovirus
Garlic common latent virus
Garlic virus
Gastropod associated circular ssDNA virus
Gayfeather mild mottle virus
Gentian Kobu-sho-associated virus
Geobacillus virus
Getah virus
Giardia canis virus
Giardia lamblia virus
Gibbon leukemia virus
Gill-associated virus
Giraffe coronavirus
Glomus sp. RF1 medium virus
Glossina pallidipes salivary gland hypertrophy virus
Goatpox virus
Goose adenovirus
Goose circovirus
Goose hemorrhagic polyomavirus
Goose paramyxovirus
Goose parvovirus
Gooseberry vein banding virus
Gorilla gorilla gorilla polyomavirus
Grapevine Pinot gris virus
Grapevine Rupestris stem pitting associated virus
Grapevine Rupestris stem pitting virus
Grapevine Syrah Virus-1
Grapevine berry inner necrosis virus
Grapevine endophyte endornavirus
Grapevine fleck virus
Grapevine geminivirus
Grapevine leafroll-associated virus
Grapevine rupestris stem pitting-associated virus
Grapevine vein-clearing virus
Grapevine virus
Grass carp rhabdovirus
Gremmeniella abietina RNA virus
Gremmeniella abietina mitochondrial RNA virus
Gremmeniella abietina type B RNA virus
Ground squirrel hepatitis virus
Grouper iridovirus
Gryllus bimaculatus nudivirus
Gull circovirus
Gyrovirus
HBV genotype A1
HBV genotype A2
HBV genotype B DNA
HBV genotype C DNA
HBV genotype D, serotype ayw3
HBV genotype D3
HBV genotype D4
HBV genotype E
HBV genotype F2
HBV genotype F4
HBV genotype G DNA
HBV genotype H DNA
HIV-1
HIV-1 92BR025 from Brazil
HIV-1 CRF03_AB
HIV-1 CRF04_cpx clone 94CY032-3 from Cyprus
HIV-1 E9 from the USA
HIV-1 G829 from Ghana
HIV-1 M_02CD.KS069 proviral
HIV-1 M_02CD.LBTB032 proviral
HIV-1 M_02CD.LBTB084 proviral
HIV-1 M_02CD.MBTB047 proviral
HIV-1 M_97CD.KFE267 proviral
HIV-1 M_97CD.KTB119 proviral
HIV-1 M_97CD.MBFE250 proviral
HIV-1 chimpanzee C455
HIV-1 chimpanzee C499
HIV-1 clone 00PTHDE10 from Portugal
HIV-1 clone 309 from China
HIV-1 clone 341 from China
HIV-1 clone 90cf402 from the Central African Republic
HIV-1 clone 92ug037 from Uganda
HIV-1 clone 93th253 from Thailand
HIV-1 clone 96TZ-BF061 from Tanzania
HIV-1 clone 96TZ-BF071 from Tanzania
HIV-1 clone 96TZ-BF110 from Tanzania
HIV-1 clone 98PTHEM103 from Portugal
HIV-1 clone C.96BW06.H51 from Botswana
HIV-1 clone C.96BW06.J4 from Botswana
HIV-1 clone C.96BW06.J7 from Botswana
HIV-1 clone C.96BW06.K18 from Botswana
HIV-1 clone C1P from USA
HIV-1 clone D24 from India
HIV-1 clone ES1-16 from USA
HIV-1 clone ES1-20 from USA
HIV-1 clone ES10-53 from USA
HIV-1 clone ES4-24 from USA
HIV-1 clone ES8-17 from USA
HIV-1 clone ES8-43 from USA
HIV-1 clone I-1 from USA
HIV-1 clone I-2 from USA
HIV-1 clone MJ4 from Botswana
HIV-1 clone N-1 from USA
HIV-1 clone N-2 from USA
HIV-1 clone S61D1 from Spain
HIV-1 clone S61D15 from Spain
HIV-1 clone S61G1 from Spain
HIV-1 clone S61G7 from Spain
HIV-1 clone XJDC6431-2 from China
HIV-1 clone XJDC6441 from China
HIV-1 clone XJN0084 from China
HIV-1 clone ZAM184-5.6 from Zambia
HIV-1 clone p05MYKL045.1 from Malaysia
HIV-1 clone pBD6.15 from Cameroon
HIV-1 clone pCM235-2 from Thailand
HIV-1 clone pCM235-4 from USA
HIV-1 clone pCMO2.3 from Cameroon
HIV-1 clone pCMO2.5 from Cameroon
HIV-1 clone pIIIB from USA
HIV-1 clone pWCML249 from Kenya
HIV-1 clone pZAC from South Africa
HIV-1 genotype CRF05_DF
HIV-1 patient WCIPR sample 1985 clone 4
HIV-1 patient WCIPR sample 1985 clone 46
HIV-1 patient WCIPR sample 1985 clone 5
HIV-1 patient WCIPR sample 1985 clone 52
HIV-1 patient WCIPR sample 1985 clone 54
HIV-1 patient WCIPR sample 1990 clone 11
HIV-1 patient WCIPR sample 1990 clone 18
HIV-2
HIV-l from Greece
HMO Astrovirus
HPIV-1
Halastavi arva RNA virus
Haloarcula hispanica icosahedral virus
Haloarcula hispanica pleomorphic virus
Halogeometricum pleomorphic virus
Halorubrum pleomorphic virus
Halovirus
Hamster polyomavirus
Hana virus
Hardenbergia mosaic virus
Hardenbergia virus
Helicobasidium mompa endornavirus
Helicoverpa armigera NPV
Helicoverpa armigera NPV NNg1 DNA
Helicoverpa armigera densovirus
Helicoverpa armigera granulovirus
Helicoverpa armigera multiple nucleopolyhedrovirus
Helicoverpa armigera nuclear polyhedrosis virus
Helicoverpa zea nudivirus
Helicoverpa zea single nucleocapsid nucleopolyhedrovirus
Heliocoverpa armigera nucleopolyhedrovirus
Heliothis virescens ascovirus
Heliothis zea virus
Helleborus net necrosis virus
Hemorrhagic enteritis virus
Hendra virus
Hepataitis E virus
Hepatitis A virus
Hepatitis B Virus
Hepatitis B virus
Hepatitis C virus
Hepatitis D Virus genotype 3, clone 010-OBC Cl11
Hepatitis D Virus genotype 3, clone 010-OBCCl2
Hepatitis D Virus genotype 3, clone BR2-ENB
Hepatitis D virus
Hepatitis E virus
Hepatitis G virus
Hepatitis GB virus
Hepatitis delta virus
Hepatopancreatic parvovirus
Heron hepatitis B virus
Herpes simplex virus
Heterocapsa circularisquama RNA virus
Heterosigma akashiwo RNA virus
Hibiscus chlorotic ringspot virus
Hibiscus latent Singapore virus
Highlands J virus
Hippeastrum mosaic virus
Hipposideros bat coronavirus
Hirame rhabdovirus
His1 virus
His2 virus
Hog cholera virus
Hollyhock leaf crumple virus
Hollyhock leaf curl virus
Hollyhock yellow vein mosaic virus
Homalodisca coagulata virus
Honeysuckle ringspot virus
Honeysuckle yellow vein Kagoshima virus
Honeysuckle yellow vein beta-[Japan:Fukui:2001] DNA
Honeysuckle yellow vein beta-[Japan:Masuda:2003] DNA
Honeysuckle yellow vein mosaic beta-[Japan:Kumamoto:1998] DNA
Honeysuckle yellow vein mosaic beta-[Japan:Miyizaki:2001] DNA
Honeysuckle yellow vein mosaic disease associated satellite DNA beta-[Ibaraki] DNA
Honeysuckle yellow vein mosaic disease associated satellite DNA beta-[Nara] DNA
Honeysuckle yellow vein mosaic virus
Honeysuckle yellow vein virus
Hop latent virus
Hop mosaic virus
Hordeum mosaic virus
Horsepox virus
Horseradish latent virus
Huma Immunodeficiency Virus Isolate D205
Human Bocavirus
Human Coronavirus
Human JC virus
Human Papillomavirus
Human Respiratory syncytial virus
Human T Cell Lymphotropic Virus I
Human T-cell lymphotropic virus
Human T-lymphotropic virus
Human TMEV-like cardiovirus
Human adenovirus
Human astrovirus
Human betacoronavirus
Human bocavirus
Human calicivirus
Human circular dsDNA virus
Human coronavirus
Human coxsackievirus
Human cytomegalovirus
Human echovirus
Human endogenous retrovirus
Human enteric coronavirus
Human enterovirus
Human foamy virus
Human group 1 coronavirus
Human gyrovirus
Human hepatitis A virus
Human hepatitis virus
Human herpesvirus
Human immunodeficiency virus
Human lymphadenopathy virus
Human metapneumovirus
Human papillomavirus
Human papillomoavirus
Human parainfluenza virus
Human parechovirus
Human parvovirus
Human poliovirus
Human polyomavirus
Human respiratory syncytial virus
Human rhinovirus
Human spumaretrovirus
Hybrid snakehead virus
Hydrangea chlorotic mottle virus
Hydrangea ringspot virus
Hyperthermophilic Archaeal Virus 1
Hyperthermophilic Archaeal Virus 2
Hyphantria cunea nucleopolyhedrovirus
Ia io picornavirus
Ictalurid herpesvirus
Igbo Ora virus
Iguape virus
Ikoma lyssavirus
Ilheus virus
Indian cassava mosaic virus
Indian citrus ringspot virus
Infectious bronchitis virus
Infectious flacherie virus
Infectious haematopoietic necrosis virus
Infectious hematopoietic necrosis virus
Infectious hypodermal and hematopoietic necrosis virus
Infectious spleen and kidney necrosis virus
Influenza A virus
Ipomoea yellow vein virus
Iranian johnsongrass mosaic virus
Iranian maize mosaic nucleorhabdovirus
Irkut virus
Israel acute paralysis virus
Israeli acute paralysis virus
J-virus
JC polyomavirus
JC virus
Jaagsiekte sheep retrovirus
Japanese encephalitis SA-14 virus
Japanese encephalitis virus
Japanese iris necrotic ring virus
Japanese yam mosaic virus
Jembrana disease virus
Jurona virus
KI polyomavirus
Kakugo virus
Kalanchoe latent virus
Kalanchoe top-spotting virus
Karshi virus
Kashmir bee virus
Kedougou virus
Kelp fly virus
Kennedya yellow mosaic virus
Keunjorong mosaic virus
Khujand lyssavirus
Kimberley virus
Koala retrovirus
Kobuvirus
Koi herpesvirus
Kokobera virus
Konjac mosaic virus
Kotonkan virus
Kyasanur forest disease virus
Kyuri green mottle mosaic virus
Lactate dehydrogenase-elevating virus
Lagenorhynchus acutus papillomavirus
Lagos bat virus
Lake Victoria marburgvirus
Lamium leaf distortion associated virus
Langat virus
Large yellow croaker iridovirus
Lausannevirus
Leek yellow stripe virus
Leishmania RNA virus
Lelystad virus
Leporid herpesvirus
Lettuce necrotic yellows virus
Lettuce virus
Lettuce yellow mottle virus
Leucania separata nuclear polyhedrosis virus
Ligustrum necrotic ringspot virus
Lily mottle virus
Lily symptomless virus
Lisianthus necrosis virus
Little cherry virus
Ljungan virus
Lloviu virus
Lolium latent virus
Lordsdale virus
Louping ill virus
Lucerne transient streak virus
Lucky bamboo bacilliform virus
Ludwigia yellow vein virus
Lumpy skin disease virus
Lupine mosaic virus
Lygus lineolaris virus
Lymantria dispar nucleopolyhedrovirus
Lymantria xylina MNPV
Lymphocystis disease virus
Lynx rufus papillomavirus
Lyssavirus
MW polyomavirus
Macaca fascicularis papillomavirus
Macaca fascicularis polyomavirus
Macaca fuscata rhadinovirus
Macaca mulatta rhadinovirus
Macacine herpesvirus
Macaque simian foamy virus
Macrobrachium rosenbergii Taihu virus
Magnaporthe oryzae virus
Magpie-robin coronavirus
Maize chlorotic dwarf virus
Maize chlorotic mottle virus
Maize dwarf mosaic virus
Maize fine streak virus
Maize mosaic virus
Maize necrotic streak virus
Maize rayado fino virus
Maize streak Reunion virus
Maize streak virus
Maize white line mosaic virus
Malakal virus
Malpais Spring virus
Malvastrum leaf curl Guangdong virus
Malvastrum yellow mosaic virus
Malvastrum yellow vein Yunnan virus
Malvastrum yellow vein virus
Mamastrovirus
Mamestra brassicae MNPV
Mamestra brassicae multiple nucleopolyhedrovirus
Mamestra configurata NPV-A
Mamestra configurata nucleopolyhedrovirus
Mapuera virus
Maraba virus
Maracuja mosaic virus
Marburg marburgvirus
Marine RNA virus
Marseillevirus
Maruca vitrata MNPV
Mason-Pfizer monkey virus
Mastadenovirus
Mastomys coucha papillomavirus
Mastomys polyomavirus
Mavirus
Mayaro virus
Measles virus
Megavirus
Melanoplus sanguinipes entomopoxvirus
Meleagrid herpesvirus
Melon aphid-borne yellows virus
Melon necrotic spot virus
Menangle virus
Mengo virus
Meno virus
Merkel cell polyomavirus
Mesta yellow vein mosaic virus
Micro Torque teno virus
Micromonas sp. RCC1109 virus
Microvirus
Midway virus
Miniopterus polyomavirus
Miniopterus schreibersii papillomavirus
Miniopterus schreibersii picornavirus
Mink astrovirus
Mink calicivirus
Mink coronavirus
Mint virus
Minute virus
Mirabilis jalapa mottle virus
Mirabilis mosaic virus
Miscanthus streak virus
Mokola virus
Molluscum contagiosum virus
Moloney murine leukemia virus
Moloney murine sarcoma virus
Monkey B-lymphotropic papovavirus
Monkeypox virus
Morelia spilota papillomavirus
Moroccan watermelon mosaic virus
Mosquito VEM Anellovirus
Mosquito VEM virus
Mosquito densovirus
Mosquito flavivirus
Mossman virus
Mouse astrovirus
Mouse hepatitis virus
Mouse kobuvirus
Mouse parvovirus
Mouse polyomavirus
Moussa virus
MuLV
Mud crab dicistrovirus
Mulard duck circovirus
Mumps virus
Mungbean yellow mosaic India virus
Mungbean yellow mosaic virus
Munia coronavirus
Murid herpesvirus
Murine adenovirus
Murine astrovirus
Murine coronavirus
Murine cytomegalovirus
Murine hepatitis virus
Murine herpesvirus
Murine leukemia virus
Murine norovirus
Murine osteosarcoma virus
Murine pneumotropic virus
Murine polyomavirus
Muromegalovirus
Murray Valley encephalitis virus
Mus dunni endogenous virus
Mus musculus papillomavirus
Musca domestica salivary gland hypertrophy virus
Muscovy duck circovirus
Muscovy duck parvovirus
Mutant Porcine reproductive and respiratory syndrome virus
Mutant Rabies virus
Mycoplasma virus
Myotis myotis bocavirus
Myotis polyomavirus
Myotis ricketti papillomavirus
Mythimna loreyi densovirus
Mythimna separata entomopoxvirus
Myxoma virus
Nam Dinh virus
Nandina mosaic virus
Nanovirus
Narcissus common latent virus
Narcissus degeneration virus
Narcissus late season yellows virus
Narcissus mosaic virus
Narcissus symptomless virus
Nariva virus
Ndumu virus
Nebovirus
Neodiprion abietis nucleopolyhedrovirus
Neodiprion lecontei NPV
Neodiprion sertifer nucleopolyhdrovirus
Nepavirus
Nerine latent virus
Nerine virus
New World begomovirus
Newbury agent 1
Newcastle Disease virus
Newcastle disease virus
Ngaingan virus
Ngewotan virus
Night-heron coronavirus
Nilaparvata lugens honeydew virus
Nile crocodilepox virus
Niminivirus
Nipah virus
Nootka lupine vein-clearing virus
Nora virus
Norovirus
Northern cereal mosaic virus
Norwalk virus
Norwalk-like virus
Nse virus
Ntaya virus
Nudaurelia capensis beta virus
Nyamanini virus
O'Nyong-nyong virus
O'nyong-nyong virus
Oak-Vale virus
Oat blue dwarf virus
Oat dwarf virus
Oat golden stripe virus
Oat necrotic mottle virus
Obodhiang virus
Ockelbo virus
Odontoglossum ringspot virus
Okra leaf curl Mali virus
Okra leaf curl virus
Okra mosaic virus
Okra yellow crinkle Cameroon alphasatellite
Okra yellow crinkle virus
Old World harvest mouse papillomavirus
Olive latent virus
Olive mild mosaic virus
Omsk hemorrhagic fever virus
Onion yellow dwarf virus
Ononis yellow mosaic virus
Orange-spotted grouper iridovirus
Orangutan hepadnavirus
Orangutan polyomavirus
Orf virus
Orgyia leucostigma NPV
Orgyia pseudotsugata MNPV
Ornithogalum mosaic virus
Oryctes rhinoceros virus
Oryza rufipogon endornavirus
Oryza sativa endornavirus
Ostreid herpesvirus
Ostreococcus lucimarinus virus
Ostreococcus tauri virus
Ostreococcus virus
Otomops polyomavirus
Ovine adenovirus
Ovine enterovirus
Ovine enzootic nasal tumor virus
Ovine herpesvirus
Ovine hungarovirus
Ovine lentivirus
Ovine papillomavirus
Ovine pulmonary adenocarcinoma virus
Oyster mushroom spherical virus
PRCV ISU-1
PRRSV HB-1(sh)/2002
PRRSV HB-2(sh)/2002
PRRSV LV4.2.1
Pan troglodytes schweinfurthii polyomavirus
Pan troglodytes verus polyomavirus
Panax virus
Panicum streak virus
Panine herpesvirus
Panthera leo persica papillomavirus
Papaya leaf crumple virus
Papaya leaf curl China virus
Papaya leaf curl Guangdong virus
Papaya leaf curl virus
Papaya leaf distortion mosaic virus
Papaya mosaic virus
Papaya ringspot virus
Papilio polyxenes densovirus
Papillomavirus
Papio hamadryas papillomavirus
Paprika mild mottle virus
Parainfluenza virus
Paralichthys olivaceus rhabdovirus
Paramecium bursaria Chlorella virus
Parechovirus
Parrot hepatitis B virus
Parvovirus
Paspalum dilatatum striate mosaic virus
Paspalum striate mosaic virus
Passiflora latent carlavirus
Passion fruit mosaic virus
Passion fruit woodiness virus
Pea seed-borne mosaic virus
Pea stem necrosis virus
Peace lily mosaic virus
Peach chlorotic mottle virus
Peanut chlorotic streak caulimovirus
Peanut mottle virus
Peanut stripe virus
Peanut stunt virus
Pedilanthus leaf curl virus
Pedilathus leaf curl virus
Pelargonium chlorotic ring pattern virus
Pelargonium flower break carmovirus
Pelargonium flower break virus
Pelargonium line pattern virus
Pelargonium necrotic spot virus
Pelargonium vein banding virus
Penaeid shrimp infectious myonecrosis virus
Penaeus merguiensis densovirus
Penaeus monodon hepatopancreatic parvovirus
Pennisetum mosaic virus
Pepino mosaic virus
Pepper curly top virus
Pepper leaf curl Lahore virus
Pepper leaf curl Yunnan virus
Pepper leaf curl virus
Pepper mild mottle virus
Pepper mottle virus
Pepper severe mosaic virus
Pepper vein yellows virus
Pepper veinal mottle virus
Pepper yellow dwarf virus
Pepper yellow leaf curl China virus
Pepper yellow leaf curl Indonesia virus
Pepper yellow leaf curl virus
Pepper yellow mosaic virus
Pepper yellow vein Mali virus
Perina nuda picorna-like virus
Perinet virus
Periplaneta fuliginosa densovirus
Peromyscus papillomavirus
Persea americana endornavirus
Persimmon cryptic virus
Peru tomato mosaic virus
Peste des petits ruminants virus
Peste-des-petits-ruminants virus
Pestivirus
Petunia vein clearing virus
Phaeocystis globosa virus
Phaius virus
Philosamia cynthia ricini nucleopolyhedrovirus
Phlox Virus B
Phlox virus
Phocine distemper virus
Phocoena phocoena papillomavirus
Phocoena spinipinnis papillomavirus
Phthorimaea operculella granulovirus
Phytophthora infestans RNA virus
Picalivirus
Picobiliphyte sp. MS584-5 nanovirus
Pieris rapae granulovirus
Pig stool associated circular ssDNA virus
Pigeon paramyxovirus
Pigeon picornavirus
Pike fry rhabdovirus
Piliocolobus rufomitratus polyomavirus
Pine marten torque teno virus
Pineapple bacilliform comosus virus
Pineapple mealybug wilt-associated virus
Piscine myocarditis virus
Plantago asiatica mosaic virus
Plum bark necrosis and stem pitting-associated virus
Plum pox virus
Plutella xylostella multiple nucleopolyhedrovirus
Pneumonia virus
Po-Circo-like virus
Poinsettia mosaic virus
Pokeweed mosaic virus
Poliovirus
Polyomavirus
Poplar mosaic virus
Porcine TTV 2 from China
Porcine adenovirus
Porcine associated stool circular virus
Porcine astrovirus
Porcine bocavirus
Porcine circovirus
Porcine circovius type 2
Porcine coronavirus
Porcine endogenous retrovirus
Porcine endogenous type C retrovirus
Porcine enteric calicivirus
Porcine enteric sapovirus
Porcine enterovirus
Porcine epidemic diarrhea virus
Porcine hemagglutinating encephalomyelitis virus
Porcine kobuvirus
Porcine parvovirus
Porcine reproductive and respiratory syndrome virus
Porcine respiratory and reproductive syndrome virus
Porcine sapelovirus
Porcine teschovirus
Posavirus
Possum enterovirus
Potato Virus P from Brazil
Potato apical leaf curl disease-associated satellite DNA beta
Potato latent virus
Potato leafroll virus
Potato mop-top virus
Potato rough dwarf virus
Potato virus
Potato yellow dwarf virus
Potato yellow mosaic virus
Pothos latent virus
Powassan virus
Procyon lotor papillomavirus
Providence virus
Pseudaletia unipuncta granulovirus
Pseudocowpox virus
Pseudoplusia includens densovirus
Psittacid herpesvirus
Psittacus erithacus timneh papillomavirus
Pteronotus polyomavirus
Puma concolor papillomavirus
Pyrobaculum spherical virus
Pyrococcus abyssi virus
Quail picornavirus
Quang Binh virus
RD114 retrovirus
RHDV-BS89
RHDV-SD
Rabbit astrovirus
Rabbit calicivirus
Rabbit coronavirus
Rabbit fibroma virus
Rabbit hemorrhagic disease virus
Rabbit oral papillomavirus
Rabbitpox virus
Rabies virus
Raccoon polyomavirus
Rachiplusia ou multiple nucleopolyhedrovirus
Radish leaf curl virus
Rana grylio iridovirus
Ranid herpesvirus
Raptor adenovirus
Raspberry leaf blotch virus
Raspberry mottle virus
Rat coronavirus
Rat cytomegalovirus
Rat parvovirus
Rat theilovirus
Rattail cactus necrosis associated virus
Rattus norvegicus papillomavirus
Rauscher murine leukemia virus
Raven circovirus
Recombinant Hepatitis C Virus SA13/JFH1
Recombinant Hepatitis C virus
Recombinant chimeric Hepatitis C virus
Recombinant vesicular stomatitis Indiana virus
Red clover vein mosaic virus
Rehmannia mosaic virus
Reindeer papillomavirus
Reptile vesivirus
Respiratory syncytial virus
Reston Ebola virus
Reston ebolavirus
Reticuloendotheliosis virus
Retroviridae
Rhesus cytomegalovirus
Rhesus papillomavirus
Rhinolophus ferrumequinum circovirus
Rhododendron virus
Rhopalosiphum padi virus
Rhynchosia yellow mosaic virus
Ribgrass mosaic virus
Rice tungro bacilliform virus
Rice tungro spherical virus
Rice yellow mottle virus
Rice yellow stunt virus
Rinderpest virus
Rio Bravo virus
Rocio virus
Rock bream iridovirus
Rodent hepacivirus
Rodent herpesvirus
Rodent pegivirus
Rodent stool-associated circular genome virus
Rosa rugosa leaf distortion virus
Rose leaf curl virus
Rose spring dwarf-associated virus
Rose yellow vein virus
Rosellinia necatrix partitivirus
Ross River virus
Ross' goose hepatitis B virus
Rosy apple aphid virus
Rous sarcoma virus
Rousettus aegyptiacus papillomavirus
Rousettus bat coronavirus
Rubella virus
Rubus canadensis virus
Rudbeckia flower distortion virus
Rupestris stem pitting associated virus
Rupestris stem pitting-associated virus
Ryegrass mosaic virus
SARS Coronavirus
SARS coronavirus
SIVcpz proviral
STL polyomavirus
Sable antelope coronavirus
Sacbrood virus
Saccharomyces cerevisiae killer virus
Saccharum streak virus
Saffold virus
Sagiyama virus
Saguaro cactus virus
Saimiri sciureus polyomavirus
Saimiriine herpesvirus
Salem virus
Salivirus
Salmon pancreas disease virus
Salmonid alphavirus
Sambar deer coronavirus
San Miguel sea lion virus
Sapovirus
Scallion mosaic virus
Scallion virus
Scheffersomyces segobiensis virus
Schlumbergera virus
Sclerotinia sclerotiorum debilitation-associated RNA virus
Sclerotinia sclerotiorum dsRNA mycovirus
Sclerotinia sclerotiorum hypovirus
Sclerotinia sclerotiorum mitovirus
Scophthalmus maximus rhabdovirus
Sea Turtle Tornovirus
Seal picornavirus
Semliki forest virus
Sendai virus
Seneca valley virus
Sepik virus
Sesbania mosaic virus
Shallot latent virus
Shallot virus
Shallot yellow stripe virus
Sheep astrovirus
Sheeppox virus
Sheldgoose hepatitis B virus
Shimoni bat virus
Shrimp white spot syndrome virus
Sibine fusca densovirus
Sida golden mosaic Buckup virus
Sida golden mosaic Florida virus
Sida golden mosaic virus
Sida golden yellow vein virus
Sida leaf curl virus
Sida micrantha mosaic virus
Sida yellow vein Madurai virus
Siegesbeckia yellow vein virus
Silurus glanis circovirus
Simian (African green monkey) immunodeficiency virus
Simian (macaque) immunodeficiency virus
Simian (stump-tailed macaque) immunodeficiency virus
Simian Agent 10
Simian Mason-Pfizer D-type retrovirus
Simian SRV-1 type D retrovirus
Simian T-cell lymphotropic virus
Simian T-lymphotropic virus
Simian adenovirus
Simian agent 12
Simian agent 5
Simian endogenous retrovirus
Simian enterovirus
Simian foamy virus
Simian hemorrhagic fever virus
Simian hepatitis A virus
Simian immunodeficiency PBJ virus
Simian immunodeficiency virus
Simian retrovirus
Simian sapelovirus
Simian virus
Simian-Human immunodeficiency virus
Sindbis virus
Sindbis-like virus
Singapore grouper iridovirus
Siniperca chuatsi rhabdovirus
Sitiawan virus
Sleeping disease virus
Small anellovirus
Small ruminant lentivirus
Snake adenovirus
Snakehead retrovirus
Snakehead rhabdovirus
Snow Mountain virus
Snow goose hepatitis B virus
Soft-shelled turtle iridovirus
Soil-borne cereal mosaic virus
Soil-borne wheat mosaic virus
Solenopsis invicta virus
Sonchus yellow net virus
Sorghum mosaic virus
Sour cherry green ring mottle virus
South African cassava mosaic virus
South polar skua adenovirus
Southern bean mosaic virus
Southern cowpea mosaic virus
Southern elephant seal virus
Southern tomato virus
Sowbane mosaic virus
Soybean chlorotic blotch virus
Soybean crinkle leaf virus
Soybean dwarf virus
Soybean mild mottle pararetrovirus
Soybean mild mottle virus
Soybean mosaic virus
Soybean yellow common mosaic virus
Soybean yellow mottle mosaic virus
Sparrow coronavirus
Sphaeropsis sapinea RNA virus
Spider monkey foamy virus
Spinach curly top Arizona virus
Spinach curly top virus
Spinach severe curly top virus
Spiroplasma kunkelii virus
Spissistilus festinus virus
Spodoptera exigua Iflavirus
Spodoptera exigua iflavirus
Spodoptera exigua nucleopolyhedrovirus
Spodoptera frugiperda MNPV
Spodoptera frugiperda MNPV genotype SfMNPV-G defective
Spodoptera frugiperda ascovirus
Spodoptera littoralis NPV
Spodoptera litura granulovirus
Spodoptera litura nucleopolyhedrovirus
Sporobolus striate mosaic virus
Spring Viremia of Carp
Spring viraemia of carp virus
Spring viremia of carp virus
Squash leaf curl China virus
Squash leaf curl Philippines virus
Squash leaf curl Yunnan virus
Squash vein yellowing virus
Squirrel monkey foamy virus
Squirrel monkey polyomavirus
Squirrel monkey retrovirus
Sri Lankan cassava mosaic virus
St. Louis encephalitis virus
Stachytarpheta leaf curl virus
Starling circovirus
Steller sea lion vesivirus
Stork hepatitis B virus
Strawberry chlorotic fleck associated virus
Strawberry vein banding virus
Streptocarpus flower break virus
Suakwa aphid-borne yellows virus
Subterranean clover mottle virus
Sudan ebolavirus
Sugarcane bacilliform IM virus
Sugarcane bacilliform virus
Sugarcane mosaic virus
Sugarcane streak Egypt virus
Sugarcane streak Reunion virus
Sugarcane streak mosaic virus
Sugarcane streak virus
Sugarcane yellow leaf virus
Suid herpesvirus
Sulfolobales Mexican fusellovirus
Sulfolobales Mexican rudivirus
Sulfolobus islandicus rudivirus
Sulfolobus spindle-shaped virus
Sulfolobus tengchongensis spindle-shaped virus
Sulfolobus turreted icosahedral virus
Sulfolobus virus
Sunflower chlorotic mottle virus
Sunflower mild mosaic virus
Sunshine virus
Sus scrofa papillomavirus
Sweet potato begomovirus
Sweet potato caulimo-like virus
Sweet potato chlorotic fleck virus
Sweet potato feathery mottle virus
Sweet potato geminivirus
Sweet potato golden vein associated virus
Sweet potato latent virus
Sweet potato leaf curl Canary Island virus
Sweet potato leaf curl Canary virus
Sweet potato leaf curl China Sichuan virus
Sweet potato leaf curl China virus
Sweet potato leaf curl Georgia virus
Sweet potato leaf curl Korean virus
Sweet potato leaf curl Lanzarote virus
Sweet potato leaf curl Sao Paulo virus
Sweet potato leaf curl South Carolina virus
Sweet potato leaf curl Spain virus
Sweet potato leaf curl Uganda virus
Sweet potato leaf curl virus
Sweet potato mosaic associated virus
Sweet potato vein clearing virus
Sweet potato virus
Sweetpotato badnavirus
Swine hepatitis E virus
Swine parainfluenza virus
Swine pasivirus
Swine vesicular disease virus
Swinepox virus
Switchgrass mosaic virus
TGEV Miller M6
TGEV Miller M60
TGEV Purdue P115
TGEV virulent Purdue
TPA_exp: Aeropyrum pernix ovoid virus
TPA_exp: Aeropyrum pernix spindle-shaped virus
TPA_exp: Suid herpesvirus
TPA_inf: Human herpesvirus
TPA_inf: Porcine rubulavirus
TT virus
TTV-like mini virus
TYLCAxV-Sic1-[IT:Sic2/2:04]
TYLCAxV-Sic2-[IT:Sic2/5:04]
TYLCCNV-[Y322] satellite DNA beta sequence
Tailam virus
Tamana bat virus
Tamus red mosaic virus
Tanapox virus
Taro bacilliform virus
Taro vein chlorosis virus
Taterapox virus
Taura syndrome virus
Telosma mosaic virus
Tembusu virus
Tench rhabdovirus
Theiler murine encephalomyelitis
Theiler murine encephalomyelitis virus
Theiler's disease-associated virus
Theiler's encephalomyelitis virus
Theiler's murine encephalomyelitis virus
Theiler's-like virus
Theilers murine encephalomyelitis virus
Thermococcus prieurii virus
Thermoproteus tenax spherical virus
Thrush coronavirus
Thunberg fritillary virus
Thysanoplusia orichalcea NPV
Tianjin totivirus
Tibrogargan virus
Tick-borne encephalitis virus
Tiger frog virus
Tioman virus
Titi monkey adenovirus
Tobacco bushy top virus
Tobacco curly shoot virus
Tobacco etch virus
Tobacco leaf curl Japan virus
Tobacco leaf curl Kochi virus
Tobacco leaf curl Thailand virus
Tobacco leaf curl Yunnan virus
Tobacco leaf curl Zimbabwe virus
Tobacco leaf curl virus
Tobacco mild green mosaic virus
Tobacco mosaic virus
Tobacco necrosis virus
Tobacco rattle virus
Tobacco vein banding mosaic virus
Tobacco vein distorting virus
Tobacco vein-clearing virus
Tomato Chino La Paz virus
Tomato Yellow Leaf Curl Virus
Tomato begomovirus
Tomato bushy stunt virus
Tomato golden mosaic virus
Tomato leaf curl Bangalore virus
Tomato leaf curl Bangladesh virus
Tomato leaf curl China virus
Tomato leaf curl Comoros virus
Tomato leaf curl Cotabato virus
Tomato leaf curl Guangxi virus
Tomato leaf curl Gujarat virus
Tomato leaf curl Hainan virus
Tomato leaf curl Iran virus
Tomato leaf curl Java virus
Tomato leaf curl Karnataka alphasatellite
Tomato leaf curl Karnataka virus
Tomato leaf curl Laos virus
Tomato leaf curl Madagascar virus
Tomato leaf curl Mayotte virus
Tomato leaf curl Mindanao virus
Tomato leaf curl Namakely virus
Tomato leaf curl New Delhi virus
Tomato leaf curl Oman virus
Tomato leaf curl Pakistan virus
Tomato leaf curl Palampur virus
Tomato leaf curl Philippine virus
Tomato leaf curl Philippines virus
Tomato leaf curl Pune virus
Tomato leaf curl Ranchi betasatellite
Tomato leaf curl Ranchi virus
Tomato leaf curl Seychelles virus
Tomato leaf curl Sudan virus
Tomato leaf curl Taiwan virus
Tomato leaf curl Vietnam virus
Tomato leaf curl geminivirus
Tomato leaf curl virus
Tomato mosaic virus
Tomato necrotic stunt virus
Tomato yellow blotch virus
Tomato yellow dwarf disease associated satellite DNA beta-[Kochi] DNA
Tomato yellow leaf curl Axarquia virus
Tomato yellow leaf curl China virus
Tomato yellow leaf curl Malaga virus
Tomato yellow leaf curl Mali virus
Tomato yellow leaf curl Sardinia virus
Tomato yellow leaf curl Thailand betasatellite
Tomato yellow leaf curl Thailand virus
Tomato yellow leaf curl Vietnam virus
Tomato yellow leaf curl virus
Torque teno canis virus
Torque teno douroucouli virus
Torque teno felis virus
Torque teno midi virus
Torque teno mini virus
Torque teno sus virus
Torque teno tamarin virus
Torque teno virus
Transmissible gastroenteritis virus
Tree shrew adenovirus
Trichechus manatus latirostris papillomavirus
Trichodysplasia spinulosa-associated polyomavirus
Trichomonas vaginalis virus
Trichoplusia ni ascovirus
Trichoplusia ni single nucleopolyhedrovirus
Triticum mosaic virus
Tuber aestivum endornavirus
Tuber aestivum mitovirus
Tuhoko virus
Tulip virus
Tupaia herpesvirus
Tupaia paramyxovirus
Tupaia rhabdovirus
Turbot reddish body iridovirus
Turdivirus
Turkey adenovirus
Turkey astrovirus
Turkey avisivirus
Turkey coronavirus
Turkey gallivirus
Turkey parvovirus
Turnip crinkle virus
Turnip curly top virus
Turnip mosaic virus
Turnip rosette virus
Turnip vein-clearing virus
Turnip yellow mosaic Blue Lake
Turnip yellow mosaic virus
Turnip yellows virus
Tursiops truncatus papillomavirus
UR2 sarcoma virus
Ugandan cassava brown streak virus
Uncia uncia papillomavirus
Uncultured Microviridae clone SARssphi1
Uncultured Microviridae clone SARssphi2
Uncultured virus
Urochloa streak virus
Ursus maritimus papillomavirus
Ustilaginoidea virens RNA virus
Usutu virus
VESV-like calicivirus
Vaccinia virus
Vallota speciosa virus
Valsa ceratosperma hypovirus
Variola major virus
Variola minor virus
Variola virus
Varroa destructor virus
Velvet bean severe mosaic virus
Velvet tobacco mottle virus
Venezuelan equine encephalitis virus
Verbena virus
Vervet monkey polyomavirus
Vesicular exanthema of swine virus
Vesicular stomatitis Alagoas virus
Vesicular stomatitis Indiana virus
Vesicular stomatitis New Jersey virus
Viral haemorrhagic septicaemia virus
Viral hemorrhagic septicemia virus
Virus PhiCh1
Visna virus
Visna/Maedi virus
Visna/maedi virus
WU Polyomavirus
Walleye dermal sarcoma virus
Wasabi mottle virus
Waterbuck coronavirus
Watermelon bud necrosis virus
Watermelon mosaic virus
Wesselsbron virus
West Caucasian bat virus
West Nile virus
Western equine encephalomyelitis virus
Western roedeer papillomavirus
Wets NIle virus
Whataroa virus
Wheat dwarf India virus
Wheat dwarf virus
Wheat eqlid mosaic virus
Wheat streak mosaic virus
Wheat yellow dwarf virus
White bream virus
White spot syndrome virus
White-eye coronavirus
White-tailed deer coronavirus
Whitefly VEM 1 begomovirus
Whitefly VEM 2 begomovirus
Whitefly VEM satellite
Wigeon coronavirus
Wild potato mosaic virus
Wild tomato mosaic virus
Wiseana iridescent virus
Wisteria vein mosaic virus
Wongabel virus
Wood mouse herpesvirus
Woodchuck hepatitis B virus
Woodchuck hepatitis virus
Woolly monkey hepatitis B Virus
Woolly monkey hepatitis B virus
Xenotropic MuLV-related virus
Xenotropic murine leukemia virus
Y73 sarcoma virus
Yaba monkey tumor virus
Yaba-like disease virus
Yam bean mosaic virus
Yam mild mosaic virus
Yellow baboon polyomavirus
Yellow fever virus
Yellow head virus
Yoka poxvirus
Yokose virus
Youcai mosaic virus
Yug Bogdanovac virus
Zaire Ebola virus
Zaire ebolavirus
Zalophus californianus papillomavirus
Zantedeschia mild mosaic virus
Zika virus
Zucchini green mottle mosaic virus
Zucchini yellow mosaic virus
bat SARS coronavirus
coxsackievirus
ovine papillomavirus
pea seed-borne mosaic virus
sugarcane yellow leaf virus
variola minor virus
yellow vein China virus

jQuery-when2 – a more flexible way to work with jQuery deferreds

Saturday, July 27th, 2013

I’ve often been frustrated by the limited functionality of jQuery.when. You give it some deferred objects and it fires when all the deferreds are finished. The trouble is, if any of the deferreds is rejected the deferred returned by jQuery.when fires immediately. So you can’t use it to collect the results of all deferreds including any errors. You also can’t use it to fire when the first of the passed deferreds fires.

So last night I wrote a new version of when, called jQuery-when2 that offers the three behaviors that I commonly want:

  1. resolve on the first success,
  2. fail on the first error (the jQuery.when behavior), or
  3. resolve when all results (successes or errors) have been collected.

The API differences from jQuery.when:

  • when2 must be called with a list as its first argument.
  • An options Javascript object may be passed as a second argument.
  • If options.resolveOnFirstSuccess is true, the deferred returned by when2 will resolve as soon as any of the passed deferreds resolves. In this case, .done callbacks will be passed index and value args, where index is the index of the deferred that fired. If non-deferreds are in the arguments to when2, the first one seen will trigger the resolve (not very useful, but consistent).
  • If options.failOnFirstError is false, the deferred returned by when2 will never fail. It will collect the results from all the deferreds and pass them all back. The caller gets to figure out which values (if any) are errors.
  • If no options are given (or options.failOnFirstError is true), fail will be called on the deferred returned by when2 on the first error (this is the behavior of jQuery.when). The args passed to fail will be index and value, indicating which deferred was rejected.
  • Any .progress callbacks added to the returned deferred are also called with index and value arguments so you can tell which deferred made progress.

You can grab the source code, see examples, etc., on Github.

BTW, I’m writing a short (about 75pp) O’Reilly book, Learning jQuery Deferreds, with Nicholas Tollervey. If you’re interested in reviewing early Rough Cuts drafts, please let me know! The book will be out late this year.