HIV molecular immunology database

 

HIV Immunology Patient Search Help

Description

The patient tables contain information about individual subjects from whom biological samples have been acquired for immunological study related to HIV infection. Patients primarily tested for immunological response are included. Patients also may be included if they are listed in the paper as part of a cohort under study, even if their immunological response has not been annotated. Generally, each patient record is attached to one or more epitope records and each epitope record has zero, one, or more records associated with it.

Depending on the publication, patients may also be called participants, subjects, volunteers, individuals or donors.

Patient Search and Results Fields

This is a brief description of the database fields in the patient search form and results pages.

Patient code
The name or label by which the subject under study is referred. Spaces are allowed and the code name used is according to what the author published. Alias names from other publications can also be searched here. An option for the search is to query for an exact match by checking the box.
Patient record number
This is the patient record number, which is distinct from the associated CTL epitope, Helper/HTL epitope, or Ab record number. Each individual patient record is assigned a unique patient record number and can be searched for using the patient record number.
Patient MHC/HLA
The patient’s known HLAs as given in the paper, whether determined by serotype or genotype and including MHC Class I and MHC Class II molecules. The HLA Informatics Group’s current nomenclature is followed and obsolete nomenclature has been updated to current within all fields except for “Note”. Users may still search for obsolete HLA nomenclature within the note section of the patient search. The annotated note in the patient tables use the author’s terminology for HLA from the paper.
Patient sex
‘Male’ / ‘Female’ / ‘Other’: the patient’s biological sex. ‘Other’ may be more clearly explained in the notes section for an individual patient.
Risk factor
This is the primary route by which the patient acquired infection. If there is more than one route of infection acquisition, it will be mentioned in the note section.
Infection country
The country where the patient became infected with HIV, if known (not necessarily their country of origin, domicile, or sampling).
Infection city
The city or town in which the patient acquired HIV infection (not necessarily the city in which they were sampled).
Infection year
This is the year in which the patient acquired HIV infection, if known (not the year in which they were diagnosed).
Species
Usually this is homo sapien/human, but other experimental animals may also be annotated.
Ethnicity
This is the patient’s race, nationality or sometimes their ethnic background or both. It is stated as given by authors in the paper.
Progression
This is the author-defined rate of disease progression in the patient sampled at the time of the study. Possible options are listed below, along with sample definitions from literature.
Progression (Code) Definition
Controller or HIV Controller (HIC)

HIC are a subset of LTNP who additionally have undetectable viraemia. Viral load (VL) undetectable. Mandalia et al. (2012) https://doi.org/10.1371/journal.pone.0029844

Typical controllers had an average recent CD4 cell count more than 450 cells/μl, whereas discord controllers had an average recent CD4 cell count less than 450 cells/μl. Sabin and Lundgren (2013). https://journals.lww.com/co-hivandaids/fulltext/2013/07000/the_natural_history_of_hiv_infection.10.aspx

Elite Controller (EC) or Natural Controller or Viral Controller

Viral load < 200 RNA copies/ml. An EC may not reach LTNP status for years.  This group, sometimes showing plasma HIV-RNA values persistently below 50 copies/ml, is termed “elite” or “natural controllers”. Kumar, P.(2013) https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3818590/

ECs were defined as ART-naive patients infected with HIV for more than 12 months with at least three longitudinal undetectable HIV RNA determinations. Sabin and Lundgren (2013) https://journals.lww.com/co-hivandaids/fulltext/2013/07000/the_natural_history_of_hiv_infection.10.aspx

Elite Neutralizer (EN) A patient with Abs that neutralize their autologous HIV. These highest levels of bNAbs are found in the sera of rare individuals termed elite neutralizers (ENs). ENs are defined as HIV-1 infected individuals who possess antibodies capable of neutralizing tier 2 and 3 viruses from at least four different clades of virus at serum dilution titers of 1:300 or more. Mesa et al. (2019). https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0213409
Long Term Non-Progressor (LTNP) or Long-term Slow-Progressor (LTSP)

LTNP are HIV-1+ patients who maintain stable CD4+ T-cell counts, with no history of opportunistic infection or antiretroviral therapy (ART). Mandalia et al. (2012) https://doi.org/10.1371/journal.pone.0029844.

The group of HIV positive long term non-progressors comprises less than 5% of the total HIV population. They also maintain low detectable plasma viraemia (<5000 HIV-RNA copies/ml). Kumar, P. (2013). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3818590/

Viral load does not change for >12 years.

Because CD4 counts gradually fall in LTNPs, just very slowly, a more accurate term is long-term slow-progressors (LTSPs).

https://i-base.info/long-term-non-progressor-ltnp/

Progressor (P) HIV positive patient who needs to take ART in order to control infection. Sabin and Lundgren (2013), https://journals.lww.com/co-hivandaids/fulltext/2013/07000/the_natural_history_of_hiv_infection.10.aspx
Rapid Progressor (RP) Rapid progression is when AIDS develops within 3 years of infection. Kumar, P. (2013). https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3818590/
Slow Progressor (SP) People who stay stable for a long time after infection are referred to as ‘slow progressors’. The definition of a slow progressor varies in different settings. A general definition though includes still having a CD4 count about 500 after five years and without using treatment. https://i-base.info/qa/7831
Note
Any patient-specific information that is not included in the search fields above and that is mentioned in the paper being annotated. Information that changes with time for example age, CD4 count, days post-infection, plasma viral load (pVL) etc. are tied to either a specific epitope or antibody, publication, or sampling year.
Antibody records
Antibody record is a unique record number for a specific antibody in the LANL HIV Immunology Database. The antibody(ies) linked to the patient were derived from this patient’s blood, or were synthesized from antibody sequences derived from this patient. Some synthetic antibodies may be derived from protein sequences originating from more than one patient, and thus may be linked to two or more patients. Please note that antibody record numbers and patient record numbers are distinct and from separate database tables.
CTL/CD8+ records
CTL/CD8+ record refers to a unique record number for a specific cytotoxic T-lymphocyte epitope in the LANL HIV Immunology Database. The CTL records associated with a specific patient are those epitopes to which this patient had an immunological response. More than one patient may be linked to a single epitope and one patient may be linked to several epitopes if they had a response to all those epitopes. Please note that CTL/CD8+ record numbers and patient record numbers are distinct and from separate database tables.
T-Helper/CD4+ records
T-helper (HTL)/CD4+ record refers to a unique record number for a specific helper T-lymphocyte epitope in the LANL HIV Immunology Database. The T-helper (HTL) records associated with specific patient are those epitopes to which this patient had an immunological response. More than one patient may be linked to a single HTL epitope and one patient may be linked to several HTL epitopes if they had a response to all those epitopes. Please note that T-helper (HTL)/CD4+ record numbers and patient record numbers are distinct and from separate database tables.
Sequence database patient record
Some patients are annotated in both the LANL HIV Immunology database and the LANL HIV Sequence database. The two databases are independent and assign different record numbers. The sequence database patient ID provided here is a link to the same unique patient in the other database. From there, you can obtain all the HIV sequences associated with this patient.
Download

The search results may be downloaded in JSON or CSV (comma separated value) format. Individual records may be downloaded in JSON format. Note that the CSV files are encoded in UTF-8; please set Excel and other programs to UTF-8 when importing. Refer to the API Guide for details of the JSON format.

Questions or comments? Contact us at immuno@lanl.gov
 
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