To search for a range of accession numbers, use the format X12345..X23456. Note that some sequence names (for example, HXB2) have more than one associated accession number. To retrieve them all, use the Sequence Name field.
You can also enter a list of space separated accessions like etc.
In this field, you can search on multiple subtypes by clicking the ones you want. Also select the 'include recombinants' check box if you want recombinants of the chosen subtype(s). While most browser/operating system combinations will let you select non-adjacent fields, in some you need to use 'ctrl-click' instead of 'shift-click' to do that. Note that if your search is limited to a specific genomic region, you may bring up some recombinant sequences that are not of the selected subtype in that region.
For more information on the subtype and CRF classifications, see:
Overview of HIV-1, HIV-2, and SIV subtype nomenclature
How the HIV database classifies sequence subtypes
Overview of primate immunodeficiency viruses lists SIV subtypes
Circulating Recombinant Forms lists currently recognized CRFs
HIV-1 M group nomenclature publication 1999
This is usually a name based on the patient ID, isolate, or clone name for a sequence, and may be the way a sequence is referred to in publications. This field also searches the GenBank Locus Name field.
The country in which the sample was taken or from which the sequence was obtained. We use 2-letter Country Codes.
The city/province/state/region in which the sample was obtained.
The year in which the sample was obtained.
The length of the nucleotide sequence, in base pairs.
This field marks sequences that users usually want to exclude from a retrieval.
Please note: Our default excludes these sequences from searches, but users may select to include them if desired. Our criteria are very conservative, to have few false positives, but that leaves us with some unlabled sequences that are still problematic. You still need to check for problem sequences prior to publication!
The patient code is displayed in searches as a two-part number, for example "P1(10139520)". The first part is usually the name or number by which the patient is identified in publication(s). The second part is an internal number assigned by our database, the patient ID. A patient code such as "P1" can (and does) refer to more than one patient. However, the sequence records associated with "10139520" are specific to one patient.
To search this field, use the code (for example, "P1"). To search for a patient by ID (for example, "10139520"), a search box for this exists in the Other fields menu (below). Not all sequences in the database have an assigned patient code/id; if your search for a patient code fails, try entering the search in the "Sequence Name" field (sequence names often contain a patient code).
The search algorithm used for this field is different from the other fields, in that a space (for example, "Patient G") is not interpreted as an AND, as it is in the other fields. Instead, the entire string, including spaces, is used as the search term. You can use the words 'and' and 'or' to join several criteria.
This field is used when the infection country is distinct from the sampling country. This field is only filled in if it is actually known with high certainty where a patient was infected. For example, the database contains many sequences for which sampling country is Sweden that are actually most likely from African countries. In these cases, if a patient has indicated that his/her only chance of infection was in an African country, the infection country is set to that; but if the infection country is not expicitly named, it will be blank.
The risk factor describes the risk activity by which the patient most likely was infected. Dual risk factors are not recorded. Again, the risk factor has to be positively established to be recorded in this field.
This is the year in which the patient was infected. The year is only recorded when it is known with some certainty.
The plasma viral load in units of copies/ml of plasma. A viral load of "1" is entered for data that are below the limit of detection (usually <50 copies/ml).
When the checkbox is selected, this field will limit the output to sequences from patients with any known HLA data, and this information will be displayed.
The HLA field can be searched on the Advanced Search. To search the field, enter exactly what the author provides into a space separated list. Wildcard searches using * do not work well because HLA data often contain the * character.
The CD4+ T-cell count at the time of sampling, in absolute counts of cells/ul.
The CD8+ T-cell count at the time of sampling, in absolute counts of cells/ul.
These fields are annotated based on biological data only, not based on presumed usage inferred from sequences.
For information about these fields, see articles:
Biological and Molecular Aspects of HIV-1 Coreceptor Usage
Coreceptor Use by Primate Lentiviruses
Sequences that were sampled prior to the patient receiving any type of antiretroviral treatment. Sequences are annotated by the database staff as drug naive only when there is certainty that the patient has not undergone antiretroviral drug treatment. Values are yes or no.
This search assumes an 'and', so if you search for 'smith jones' you will retrieve all sequences for which both Smith and Jones are in the author list. Please do not include initials. Please note that our database does contain some errors in author names; we are unable to correct mistakes made in the original sequence submissions.
The number in this field indicates the estimated number of days between the patient's seroconversion and the date the sample was taken for sequencing. For samples taken before seroconversion, negative numbers are used.
Please note: Days from infection or seroconversion are almost always estimates, and different studies use different methods and definitions. In many studies these estimates are very rough. We have attempted to translate these values into a single system for study cross-comparisons, but please use these fields with caution; go back to the original papers to confirm the study-specific timing definitions.
For studies giving data in the form of days, the data are directly provided as days. When data are given in weeks, weeks are converted by multiplying by 7. For studies where the data are given in months, the number is converted to days by multiplying months by 30.42 and rounding to the nearest whole number.
Prior to December 2005, these data were available at this database only as “Months from seroconversion”. The decision to convert to days for this field was based on the assumption that the majority of new data being reported will be in days, and because this level of precision can be very valuable for longitudinal data, even if there is some uncertainty about how far into the infection the first sample was taken.
In cases where studies give data that is vague, but possibly useful, a text entry may appear in this field. The following text entries may appear:
“Pre-seroconversion”: sample was taken before seroconversion, but the exact number of days is unknown.
“Early”: <1 year after seroconversion
“Late”: ≥2 years after seroconversion
“No data”: the same meaning as a blank field
The number in this field indicates an estimate of the number of days from the time the patient was infected until the sample was taken for sequencing. Post-infection dates are relatively rare. Most often they are known when a patient seeks medical treatment for acute illness shortly after having a sexual encounter with a stranger. We use this field when the primary author presents the data as post infection in the original citation.
Please note: Days from infection or seroconversion are always estimates, and different studies use different methods and definitions. Please see notes regarding days from seroconversion for more detail.
If a user is interested in sequences from a particular timepoint relative to infection or seroconversion, it may be wise to perform 2 separate searches of both the ‘days from seroconversion’ and ‘days from infection’ fields, as most data are recorded in one field or the other, not both. For example, if the user wants sequences that are either <90 days post-infection or <30 days post-seroconversion, two separate searches are needed.
This field restricts your search to sequences from a publication specified by its PubMed ID. To find the PubMed ID for a published paper, use the NCBI PubMed search interface.
This is a way to retrieve all sequences from (for example) the African continent without having to search for each country separately.
For a list of countries included in each region, see:
Definitions of the HIV Database geographic regions
This is a shortcut to allow searches on several other fields in the database without cluttering the interface. More fields may be added in the future. If you need to limit your search by 2 or more fields listed here, use the Advanced Search Interface. As elsewhere, entering an asterisk (*) will display any available data without limiting the search.
Infection city
If the infection city is known to be different than the city where the sample was collected, that is noted here. This field rarely contains data.
Title
Any keywords from the title of the journal article.
Comment
When you search on "Comment", the comment fields in both the sequence entries and the patient records will be searched. This search can be very time-consuming. In some cases, epidemiological linkage can be found by searching on comment keywords such as "link", "partner", etc.
Patient id
The unique number that links sequences from a single patient. Numbers range from 1 to 8 digits. See explanation above for Patient Code.
Patient sex
Categories are: M and F.
Project
If the patient was enrolled in a named project or cohort, it is recorded in this field. For a list of valid entries, see
Project Field Entries.Progression
This field records the rate of progression of the patient, if recorded by the study. Categories are: EC, LTNP, SP, RP, P (elite controller, long-term non-progressor, slow progressor, rapid progressor, progressor).
# patient sequences
This option allows searches of intrapatient sequence sets. When a number is entered in this search field, the results will include only sequences from patients that have more than that number of sequences in the database. Listing the days from seroconversion or infection in the search output (by putting an asterisk in these search fields) is an easy way to label longitudinal seroconversion and early infection studies.
Patient age
The age of the patient in integer days when the sample was taken. Ages previously entered in years were converted by multiplying by 365.25. You can use y for year and m for month. For example, to select for sequences from patients under 18 years, enter either "<6575" or "<18y".
Patient health
The health status of the patient at the time of sampling. Categories are: acute infection, asymptomatic, symptomatic, AIDS, and deceased.
Isolate name
This field is usually the same as the "sequence name".
Clone name
The clone number of the sequence. This field is only used for sets of cloned samples.
Sample tissue
The tissue from which the the sample was derived. Categories include: plasma, PBMC, blood, brain, CSF, semen, cervix, feces, etc. For a list of valid entries, see
Sample Tissue Field Entries.Culture method
For samples derived from PBMC. Categories are: uncultured, primary, expanded, co-cultured.
SE id
A unique identifying number assigned sequentially to each sequence as it is imported into the LANL HIV Database.
Fiebig stage
Fiebig stage Duration in days (range) Cumulative duration (range) Eclipse 10 (7,21) 10 (7,21) 1 (vRNA+) 7 (5,10) 17 (13,28) 2 (p24Ag+) 5 (4,8) 22 (18,34) 3 (ELISA+) 3 (2,5) 25 (22,37) 4 (Western Blot +/-) 6 (4,8) 31 (27,43) 5 (Western Blot +, p31-) 70 (40,122) 101 (71,154) 6 (Western Blot +, p31+) open-ended See:
Fiebig EW, Wright DJ, Rawal BD, Garrett PE, Schumacher RT, et al. 2003. Dynamics of HIV viremia and antibody seroconversion in plasma donors: implications for diagnosis and staging of primary HIV infection. AIDS 17(13): 1871-1879.
and
Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, Wei X, Jiang C, Kirchherr JL, Gao F, Anderson JA, Ping LH, Swanstrom R, Tomaras GD, Blattner WA, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Cohen MS, Montefiori DC, Haynes BF, Gaschen B, Athreya GS, Lee HY, Wood N, Seoighe C, Perelson AS, Bhattacharya T, Korber BT, Hahn BH, Shaw GM. 2008. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A. 105(21):7552-7.
To search for HIV-1 sequences that span a given region, select the region from the list. The exact coordinates (relative to reference strain HXB2) for each fragment are listed below. Note that to be included, a given sequence must span the entire length of the region selected. The exception to this is the "complete genome" category, which yields all sequences over 7000 base pairs. You can also choose any other region of interest based on HXB2 coordinates. For a diagram of HIV-1 showing the HXB2 breakpoints, see HIV-1 Genomic Map.
If you want all sequences that partly cover a selected region, check the "Include fragments" box and enter a minimum length for the included fragments. As another example, if you want to search for fragments over 500 base pairs from any region of the genome, check the "Include fragments" box, enter "500" in the box for minimum length, and enter "complete genome" as the region; this search will not work using the "Any" selection. Do not use symbols such as < in the fragment length box.
This search feature is the incorporation of the program that used to be called HIV-MAP, which allows you to obtain all sequences (or a subset of sequences) that contain a selected region. A full description of the HIV-MAP tools has been published by Gaschen et al. 2001. Briefly, the sequences are internally aligned, and the location of their starting and ending positions are determined; then these positions are compared to the region of interest. This option is only available for HIV-1.
The following are the specific HXB2 coordinates of each of the fragments that can be downloaded from the search interface. The 3' LTR fragments in this list are not options on the search interface, but can be obtained by entering the coordinates. For additional information about HXB2 coordinates, see HIV-1 Genomic Map.
Fragment | HXB2 coordinates | ||
complete genome | any >7000 bp | ||
5' LTR | 1 - 633 | ||
5' LTR R | 456 - 551 | ||
5' LTR U3 | 1 - 455 | ||
5' LTR U5 | 552 - 633 | ||
TAR | 453 - 513 | ||
Gag-Pol | 790 - 5096 | ||
Gag | 790 - 2292 | ||
p17 (matrix) | 790 - 1185 | ||
p24 (capsid) | 1186 - 1881 | ||
p7 (nucleocapsid) | 1921 - 2085 | ||
p6 | 2134 - 2292 | ||
Pol CDS | 2085 - 5096 | ||
p51 (RT) | 2550 - 3870 | ||
p15 (RNAse H) | 3870 - 4229 | ||
p31 (integrase) | 4230 - 5096 | ||
protease | 2253 - 2550 | ||
Vif CDS | 5041 - 5619 | ||
Vpr CDS | 5559 - 5850 | ||
Tat CDS (plus intron) | 5831 - 8469 | ||
Tat exon 1 | 5831 - 6045 | ||
Tat exon 2 | 8379 - 8469 | ||
Rev CDS (plus intron) | 5970 - 8653 | ||
Rev exon 1 | 5970 - 6045 | ||
Rev exon 2 | 8379 - 8653 | ||
Vpu CDS | 6062 - 6310 | ||
Env CDS | 6225 - 8795 | ||
V1 | 6615 - 6691 | ||
V2 | 6696 - 6811 | ||
V3 | 7110 - 7216 | ||
V4 | 7377 - 7477 | ||
V5 | 7602 - 7636 | ||
RRE | 7710 - 8061 | ||
gp41 | 7758 - 8795 | ||
gp120 | 6225 - 7758 | ||
Nef CDS | 8797 - 9417 | ||
3' LTR | 9086 - 9719 | ||
3' LTR R | 9541 - 9636 | ||
3' LTR U3 | 9086 - 9540 | ||
3' LTR U5 | 9637 - 9719 |