HIV Immunology Patient Search Help
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
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
- 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).
Usually this is homo sapien/human, but other experimental
animals may also be annotated.
This is the patient’s race, nationality or sometimes their ethnic
background or both. It is stated as given by authors in the
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.
Controller or HIV Controller (HIC)
HIC are a subset of LTNP who additionally have
undetectable viraemia. Viral load (VL)
undetectable. Mandalia et al. (2012)
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).
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”.
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)
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).
Long Term Non-Progressor (LTNP) or Long-term Slow-Progressor
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)
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
Kumar, P. (2013).
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
HIV positive patient who needs to take ART in order to
control infection. Sabin and Lundgren (2013),
Rapid Progressor (RP)
Rapid progression is when AIDS develops within 3 years of
infection. Kumar, P. (2013).
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
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
- 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
- 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
- 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.
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.