Valid HIVQuery query fields and match data

Fields are organized below according to their Los Alamos HIV database tables. Use aliases in place of full field names in queries; for example:
(CCR5 CXCR4)[coreceptor]
rather than
(CCR5 CXCR4)[seq_sample.ssam_second_receptor]
(which does work, however). Click hyperlinks to see valid search options within the field. The token Any is the wildcard for all fields.

COMMAND fields aliases
genomic_region gene
author fields aliases
authornumber au_authornumber
location2 fields aliases
description loc_description
entryfeaturetype loc_entryfeaturetype
mapimage fields aliases
mi_start
mi_stop
patient fields aliases
code pat_code
pat_comment
ethnicity pat_ethnicity
hla_type pat_hla_type
infection_city pat_infection_city
infection_country pat_infection_country
infection_year pat_infection_year
num_seq pat_num_seq
num_timepoints pat_num_timepoints
progression pat_progression
project pat_project
risk_factor pat_risk_factor
sex pat_sex
species pat_species
person fields aliases
lname per_lname
publication fields aliases
articletitle pub_articletitle
consortium pub_consortium
pubmedentry pub_pubmedentry
sourcetitle pub_sourcetitle
se_pub_link fields aliases
pubnumber spl_pubnumber
seq_sample fields aliases
amplification_strategy ssam_amplification_strategy
annotated ssam_annotated
badseq ssam_badseq
cd4count ssam_cd4count
cd8count ssam_cd8count
clone_name_number ssam_clone_name_number
common_name ssam_common_name
culture_method ssam_culture_method
drug_naive ssam_drug_naive
fiebig ssam_fiebig
health_status ssam_health_status
isolate_name_number ssam_isolate_name_number
locus_name ssam_locus_name
molecule_type ssam_molecule_type
organism ssam_organism
patient_age ssam_patient_age
phenotype ssam_phenotype
postendtreatment_days ssam_postendtreatment_days
postfirstsample_days ssam_postfirstsample_days
postinfect_days ssam_postinfect_days
postseroconv_days ssam_postseroconv_days
poststarttreatment_days ssam_poststarttreatment_days
sample_city ssam_sample_city
country sample_country,ssam_sample_country
sample_georegion ssam_sample_georegion
sample_tissue ssam_sample_tissue
year sample_year,ssam_sample_year
sample_year_upper ssam_sample_year_upper
second_receptor ssam_second_receptor,coreceptor
sequencing_method ssam_sequencing_method
subtype ssam_subtype
viralload ssam_viralload
seqentryfeature fields aliases
sef_description
sef_entryfeaturetype
sequenceaccessions fields aliases
accession genbankaccession,sa_genbankaccession
gi sa_gi
version sa_version
sequenceentry fields aliases
comment db_comment,se_db_comment
gb_comment se_gb_comment
gb_create se_gb_create
gb_update se_gb_update
sequence se_sequence
sequencelength se_sequencelength
sequencefeature2 fields aliases
featuretype sf_featuretype
featurevalue sf_featurevalue
sequencemap fields aliases
start sm_start
stop sm_stop
Valid options for COMMAND.genomic_region:
Any, 5ltr, 5ltrr, 5ltru3, 5ltru5, Env, Gag, Gag_Pol, NEF, Pol, RNase, RRE, Rev, Rev1, Rev2, Tar, Tat, Tat1, Tat2, V1, V2, V3, V4, V5, Vif, Vpr, Vpu, complete, gp120, gp41, p17, p24, p31, p51, p6, p7, protease
Other aliases:
gene
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Valid options for author.au_authornumber:
Any, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 24, 32, 33, 34, 35, 36, 37
Other aliases:
au_authornumber
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Valid options for location2.loc_description:
free text
Other aliases:
loc_description
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Valid options for location2.loc_entryfeaturetype:
Any, 3'UTR, 5'UTR, CDS, GC_signal, LTR, RBS, TATA_signal, V_region, conflict, enhancer, exon, gap, gene, intron, mRNA, mat_peptide, misc_RNA, misc_binding, misc_difference, misc_feature, misc_recomb, misc_signal, misc_structure, modified_base, old_sequence, polyA_signal, polyA_site, prim_transcript, primer_bind, promoter, protein_bind, rep_origin, repeat_region, sig_peptide, source, stem_loop, tRNA, unsure, variation
Other aliases:
loc_entryfeaturetype
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Valid options for mapimage.mi_start:
free text
Other aliases:
none
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Valid options for mapimage.mi_stop:
free text
Other aliases:
none
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Valid options for patient.pat_code:
free text
Other aliases:
pat_code
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Valid options for patient.pat_comment:
free text
Other aliases:
none
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Valid options for patient.pat_ethnicity:
Any, B, Lahu, NULL, Tiriyo, W, Zulu/Xhosa, black, white
Other aliases:
pat_ethnicity
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Valid options for patient.pat_hla_type:
free text
Other aliases:
pat_hla_type
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Valid options for patient.pat_infection_city:
free text
Other aliases:
pat_infection_city
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Valid options for patient.pat_infection_country:
Any, AO, AR, AU, BE, BF, BG, BI, BJ, BR, BW, BY, CA, CD, CF, CG, CH, CI, CL, CM, CN, CO, CU, CV, CY, DE, DJ, DK, DO, DZ, EC, ER, ES, ET, FI, FR, GA, GB, GE, GH, GM, GN, GQ, GR, GW, HN, HT, IN, IR, IT, JM, JP, KE, KH, KR, LR, LV, LY, MA, ML, MM, MR, MW, MY, MZ, NA, NG, NL, NO, NP, NULL, PE, PF, PH, PK, PL, PR, PT, RO, RU, RW, SA, SE, SG, SL, SN, SO, SV, TD, TG, TH, TN, TT, TZ, UA, UG, US, UY, VE, VN, ZA, ZM, ZW
Other aliases:
pat_infection_country
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Valid options for patient.pat_infection_year:
Any, 1967, 1974, 1978, 1979, 1980, 1981, 1982, 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2003, 2004, 2006, 1983, 1997, 1998, 2005
Other aliases:
pat_infection_year
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Valid options for patient.pat_num_seq:
free text
Other aliases:
pat_num_seq
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Valid options for patient.pat_num_timepoints:
free text
Other aliases:
pat_num_timepoints
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Valid options for patient.pat_progression:
Any, EC, LTNP, NULL, P, RP, SP
Other aliases:
pat_progression
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Valid options for patient.pat_project:
Any, 1182_12, 1182_48, ACTG 229, ACTG 5211, AIIMS cohort, ALT ANRS, Amsterdam Cohort Studies, Ariel, Australian LTNP Study, Bonn Cohort, Boston Acute Infection Cohort, CDC, CHAVI, CNAB2006, Cato Manor, Copenhagen cohort, DMP266, Dakar FSW cohort, EXPLORE Study, FCHC, French ALT Study Group, HIVNET 012, HIVNET 023, HIVNET 028, Italian Seroconversion Study, MACS, MGH cohort, NULL, NVAZ, Nairobi cohort, New England Hemophilia Cohort, New York City Perinatal HIV Tr, OPTIONS cohort, Opiate Users Research Study, PACTG trial 1030, Primo-CI, Pumwani Sex Worker Cohort, Quattro, RV121, RV126, SFMHS, STI, San Francisco Men's Health St, Seattle primary infection coho, Sinikithemba, Swiss HIV Cohort Study, Sydney Blood Bank Cohort, UCLA Perinatal Transmission St, VAX004, Wadsworth Center, Western Australian HIV Cohort, Women's Interagency HIV Study, Zambia-UAB
Other aliases:
pat_project
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Valid options for patient.pat_risk_factor:
Any, EX, MB, NO, NR, NULL, OT, PB, PH, PI, SB, SG, SH, SM, SW
Other aliases:
pat_risk_factor
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Valid options for patient.pat_sex:
Any, F, M, NULL
Other aliases:
pat_sex
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Valid options for patient.pat_species:
free text
Other aliases:
pat_species
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Valid options for person.per_lname:
free text
Other aliases:
per_lname
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Valid options for publication.pub_articletitle:
free text
Other aliases:
pub_articletitle
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Valid options for publication.pub_consortium:
free text
Other aliases:
pub_consortium
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Valid options for publication.pub_pubmedentry:
free text
Other aliases:
pub_pubmedentry
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Valid options for publication.pub_sourcetitle:
free text
Other aliases:
pub_sourcetitle
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Valid options for se_pub_link.spl_pubnumber:
Any, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 24, 32, 33, 34, 35, 36, 37, 38
Other aliases:
spl_pubnumber
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Valid options for seq_sample.ssam_amplification_strategy:
Any, NULL, SGA, bulk, bulk RT-PCR
Other aliases:
ssam_amplification_strategy
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Valid options for seq_sample.ssam_annotated:
Any, 1
Other aliases:
ssam_annotated
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Valid options for seq_sample.ssam_badseq:
Any, 1, 2, 3, 4, 5, 6
Other aliases:
ssam_badseq
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Valid options for seq_sample.ssam_cd4count:
free text
Other aliases:
ssam_cd4count
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Valid options for seq_sample.ssam_cd8count:
free text
Other aliases:
ssam_cd8count
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Valid options for seq_sample.ssam_clone_name_number:
free text
Other aliases:
ssam_clone_name_number
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Valid options for seq_sample.ssam_common_name:
free text
Other aliases:
ssam_common_name
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Valid options for seq_sample.ssam_culture_method:
Any, NULL, UNK, expanded, primary, uncultured
Other aliases:
ssam_culture_method
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Valid options for seq_sample.ssam_drug_naive:
Any, NULL, no, yes
Other aliases:
ssam_drug_naive
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Valid options for seq_sample.ssam_fiebig:
Any, 2, 5, 3, NULL, 1, 4, 6
Other aliases:
ssam_fiebig
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Valid options for seq_sample.ssam_health_status:
Any, AIDS, NULL, acute infection, asymptomatic, deceased, symptomatic
Other aliases:
ssam_health_status
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Valid options for seq_sample.ssam_isolate_name_number:
free text
Other aliases:
ssam_isolate_name_number
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Valid options for seq_sample.ssam_locus_name:
free text
Other aliases:
ssam_locus_name
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Valid options for seq_sample.ssam_molecule_type:
Any, DNA, RNA, UNK, mRNA
Other aliases:
ssam_molecule_type
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Valid options for seq_sample.ssam_organism:
Any, HIV-1, HIV-2, NULL, SHIV, SIV, synthetic DNA
Other aliases:
ssam_organism
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Valid options for seq_sample.ssam_patient_age:
free text
Other aliases:
ssam_patient_age
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Valid options for seq_sample.ssam_phenotype:
Any, NSI, NULL, SI, UNK
Other aliases:
ssam_phenotype
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Valid options for seq_sample.ssam_postendtreatment_days:
free text
Other aliases:
ssam_postendtreatment_days
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Valid options for seq_sample.ssam_postfirstsample_days:
free text
Other aliases:
ssam_postfirstsample_days
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Valid options for seq_sample.ssam_postinfect_days:
free text
Other aliases:
ssam_postinfect_days
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Valid options for seq_sample.ssam_postseroconv_days:
free text
Other aliases:
ssam_postseroconv_days
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Valid options for seq_sample.ssam_poststarttreatment_days:
free text
Other aliases:
ssam_poststarttreatment_days
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Valid options for seq_sample.ssam_sample_city:
free text
Other aliases:
ssam_sample_city
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Valid options for seq_sample.ssam_sample_country:
Any, AF, AG, AL, AN, AO, AR, AT, AU, AZ, BB, BD, BE, BF, BG, BI, BJ, BO, BR, BS, BW, BY, CA, CD, CF, CG, CH, CI, CL, CM, CN, CO, CR, CS, CU, CV, CY, CZ, DE, DJ, DK, DM, DO, DZ, EC, EE, EG, ER, ES, ET, FI, FJ, FR, GA, GB, GD, GE, GF, GH, GL, GM, GP, GQ, GR, GW, GY, HK, HN, HT, HU, ID, IE, IL, IN, IR, IT, JM, JP, KE, KH, KR, KW, KZ, LB, LC, LI, LR, LT, LU, LV, LY, MA, MD, MG, ML, MM, MQ, MS, MW, MX, MY, MZ, NE, NG, NL, NO, NP, NULL, NZ, PA, PE, PG, PH, PL, PR, PT, PY, RE, RO, RU, RW, SA, SC, SD, SE, SG, SI, SK, SL, SN, SO, SR, SZ, TD, TG, TH, TN, TR, TT, TW, TZ, UA, UG, US, UY, UZ, VC, VE, VI, VN, YE, YU, ZA, ZM, ZW
Other aliases:
sample_country,ssam_sample_country
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Valid options for seq_sample.ssam_sample_georegion:
Any, AFR, AFR SSA, ASI, CAM, CRB, EUR, FUS, MEA, NAM, NULL, OCE, SAM
Other aliases:
ssam_sample_georegion
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Valid options for seq_sample.ssam_sample_tissue:
Any, Brain, CD14+ monocytes, CD4+ T cell supernatant, CD4+ T cells, CSF, Epidermis, NULL, PBMC, T-cell, activated CD4+ T cells, blood, blood plasma, blood plasma; whole saliva, bone marrow, brain, breast milk, caudate region of brain, cerebrospinal fluid, cerebrospinal fluid (CSF), cervicovaginal secretions, cervix, choroid plexus, colon, deep white matter of brain, dendrites, duodenum, epididymis, esophagus, feces, gastric aspirate, jejunum, kidney, liver, lung, lymph node, lymphocyte, lymphoma, meninges, monocyte, peripheral blood, plasma, prostate, prostatic secretion, rectum, resting CD4+ T cells, saliva, semen, seminal cells, seminal fluid, seminal plasma, seminal vesicle, serum, sigmoidum, spinal cord, spleen, stomach, stored Stump-tailed macaque tissues (SIVSTM), subclavicular lymph node, supernatant, testis, thymus, urethra, urine, vagina, vaginal cells, vaginal fluid, vaginal secretion, vas deferens, whole blood, whole saliva
Other aliases:
ssam_sample_tissue
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Valid options for seq_sample.ssam_sample_year:
Any, 1959, 1960, 1975, 1976, 1978, 1979, 1980, 1981, 1982, 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1999, 2000, 2002, 2003, 2004, 2006, 1977, 1983, 1997, 1998, 2001, 2005, 2007, 2008
Other aliases:
sample_year,ssam_sample_year
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Valid options for seq_sample.ssam_sample_year_upper:
Any, 1959, 1960, 1975, 1976, 1978, 1979, 1980, 1981, 1982, 1984, 1985, 1986, 1987, 1988, 1989, 1990, 1991, 1992, 1993, 1994, 1995, 1996, 1999, 2000, 2002, 2003, 2004, 2006, 1977, 1983, 1997, 1998, 2001, 2005, 2007, 2008
Other aliases:
ssam_sample_year_upper
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Valid options for seq_sample.ssam_second_receptor:
Any, CCR2B, CCR2b CCR3 GPR15, CCR3 CCR5, CCR3 CCR5 CXCR4, CCR3 CXCR4, CCR3 CXCR4 CCR5, CCR5, CCR5 CCR1 CCR2b CCR3 CCR4 CXCR4, CCR5 CCR2b CCR3 CXCR4, CCR5 CCR3, CCR5 CCR3 CCR8, CCR5 CCR3 GPR15, CCR5 CCR3 GPR15 STRL33 CCR8, CCR5 CCR3 STRL33, CCR5 CCR8, CCR5 CSCR4, CCR5 CXCR4, CCR5 CXCR4 CCR1 CCR2B CCR3, CCR5 CXCR4 CCR1 CCR2b CCR3, CCR5 CXCR4 CCR1 CCR2b CCR3 CCR4, CCR5 CXCR4 CCR3, CCR5 CXCR4 CCR3 CCR1, CCR5 CXCR4 CCR3 CCR2b CCR8 V28, CCR5 CXCR4 CCR3 US28 V28, CCR5 CXCR4 CCR4, CCR5 CXCR4 CCR8 V28, CCR5 CXCR4 STRL33 GPR15, CCR5 GPR15, CCR5 GPR15 STRL33, CCR5 STRL33, CCR5 STRL33 GPR1 GPR15, CCR5 STRL33 GPR15 GPR1 ChemR23, CSCR4, CXCR4, CXCR4 CCR3, CXCR4 CCR3 STRL33, CXCR4 CCR8 V28 CCR3 GPR15 STRL33, CXCR4 GPR15, CXCR4 V28, NULL, UNK
Other aliases:
ssam_second_receptor,coreceptor
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Valid options for seq_sample.ssam_sequencing_method:
Any, NULL, clone, direct
Other aliases:
ssam_sequencing_method
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Valid options for seq_sample.ssam_subtype:
Any, 0102A, 0102AG, 0102D, 0102DF, 01A1, 01A1G, 01ADF2, 01AF2U, 01B, 01BC, 01C, 01DU, 01G, 01GHJKU, 01U, 01_AE, 0206A1, 02A, 02A1, 02A1A2, 02A1C, 02A1U, 02B, 02C, 02DO, 02F, 02F2, 02G, 02GK, 02H, 02HU, 02K, 02O, 02U, 02_AG, 03_AB, 04A1, 04_cpx, 05_DF, 06G, 06U, 06_cpx, 07B, 07_BC, 08_BC, 09A, 09A1, 09A1KU, 09D, 09G, 09U, 09_cpx, 10A1, 10_CD, 11A1, 11AG, 11_cpx, 12_BF, 13U, 13_cpx, 14_BG, 17_BF, 1819B, 18B, 18D, 18G, 18U, 18_cpx, 19A1, 19B, 19U, 19_cpx, 20_BG, 21_A2D, 22_01A1, 23A1, 23_BG, 24_BG, 25_cpx, 27_cpx, 28_BF, 29_BF, 32_06A1, 33_01B, 34_01B, 35_AD, 36_cpx, 39_BF, 40_BF, 42_BF, A, A1, A1A2, A1A2D, A1B, A1BC, A1BD, A1CD, A1CDG, A1CDGKU, A1CG, A1D, A1DG, A1DHK, A1DK, A1DU, A1F1, A1F2, A1G, A1GHU, A1GJ, A1GU, A1H, A1U, A2, A2B, A2C, A2CD, A2F1, A2U, A3, AB, ABD, ABDU, AC, ACD, ACFG, ACH, ADG, ADGU, ADK, ADU, AE, AF, AF1, AF2G, AFG, AG, AGH, AGHU, AGJ, AGJU, AGK, AGKU, AGU, AH, AHJU, AJ, AJK, AKU, AO, ASC, B, BAB, BCG, BD, BDU, BG, BK, BKM, BU, CF1, CHU, CJU, CPZ, CU, DF, DF1, DH, DU, F1, F1F2, F1G, F1U, F1UB, F2, 0102, AU, F2K, FKU, 0219, 03A, 15_01B, A2G, AF2, CF1U, CGU, DK, F1GU, FU, GOR, 0708, G, GH, GHJ, GKU, HC, HJ, K, MND-1, MNE, MUS-1, NULL, O, OLC, PAT, SAB, SMM, 0103, BCF1, BH, BLU, C, CD, CGJ, COL, D, DEB, DEN, DG, DGC, DGH, DGU, FK, GHK, GJ, GJO, GRV, GU, J, LST, MUS-2, N, RCM, SUN, 0206, 0225, 06A1, AD, SYK, TAL, TAN, 0109, 02D, MND-2, 0609, A1HU, A2D, ACDJ, 0108, 1113, 16_A2D, BC, BCU, BF, CK, DRL, ERY, F, F2KU, FGHJU, GK, 0209, 31_BC, A1C, GSN, HU, JKU, JU, KU, M, 0218, 0602, 37_cpx, BCD, BF1, 0107, DHU, MAC, STM, 0211, H, MON, 1819, U, VER, WCM, WRC
Other aliases:
ssam_subtype
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Valid options for seq_sample.ssam_viralload:
free text
Other aliases:
ssam_viralload
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Valid options for seqentryfeature.sef_description:
free text
Other aliases:
none
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Valid options for seqentryfeature.sef_entryfeaturetype:
Any, BASE COUNT, DEFINITION, KEYWORDS, ORGANISM, REFERENCE, SOURCE, VERSION
Other aliases:
none
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Valid options for sequenceaccessions.sa_genbankaccession:
free text
Other aliases:
genbankaccession,sa_genbankaccession
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Valid options for sequenceaccessions.sa_gi:
free text
Other aliases:
sa_gi
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Valid options for sequenceaccessions.sa_version:
free text
Other aliases:
sa_version
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Valid options for sequenceentry.se_db_comment:
free text
Other aliases:
db_comment,se_db_comment
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Valid options for sequenceentry.se_gb_comment:
free text
Other aliases:
se_gb_comment
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Valid options for sequenceentry.se_gb_create:
free text
Other aliases:
se_gb_create
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Valid options for sequenceentry.se_gb_update:
free text
Other aliases:
se_gb_update
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Valid options for sequenceentry.se_sequence:
free text
Other aliases:
se_sequence
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Valid options for sequenceentry.se_sequencelength:
free text
Other aliases:
se_sequencelength
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Valid options for sequencefeature2.sf_featuretype:
Any, EC_number, PCR_primers, allele, bound_moiety, cell_line, cell_type, chromosome, citation, clone, clone_lib, codon_start, collected_by, collection_date, country, db_xref, dev_stage, estimated_length, exception, experiment, focus, frequency, function, gene, gene_synonym, germline, haplotype, host, inference, isolate, isolation_source, lab_host, label, locus_tag, map, mod_base, mol_type, note, number, organism, phenotype, pop_variant, product, protein_id, proviral, pseudo, rearranged, replace, ribosomal_slippage, rpt_family, rpt_type, rpt_unit_range, serotype, sex, specimen_voucher, standard_name, strain, sub_species, sub_strain, tissue_lib, tissue_type, transl_except, transl_table, translation, variety
Other aliases:
sf_featuretype
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Valid options for sequencefeature2.sf_featurevalue:
free text
Other aliases:
sf_featurevalue
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Valid options for sequencemap.sm_start:
free text
Other aliases:
sm_start
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Valid options for sequencemap.sm_stop:
free text
Other aliases:
sm_stop
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