HCV Database
HCV sequence database
 



To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.


Data Fields

The following fields may be used to add HCV-specific data to sequences for GenBank deposit. If you have questions, please contact hcv-info@lanl.gov.


Required field

Sequence name:
Must match EXACTLY the name of the sequence in the Fasta file!
Valid Values: Text string. Valid characters A-Z, a-z, 0-9, _, -
Example: 05UG102.124d would be an example of an informative name describing a Ugandan sample taken in 2005 from subject 102 at 124 days post-seroconversion.


Strongly recommended fields

Sampling country:
Country where the sequence was sampled. This may be different than the country of infection.
Valid Values: 2-letter ISO codes.
Examples: UG for Uganda, ZA for South Africa, etc.

Sampling date:
Date the sample was taken.
Valid format: MM/DD/YYYY
Note that this is the American standard format, i.e., month-day-year. If you want to enter only a year, enter 01 for the month and day.
Examples: 06/01/1999 is June 1999 (no day given). 01/01/1999 is 1999 (no month or day given).


Optional fields

Coreceptor:
The experimentally-determined coreceptor for the viral isolate. Do not enter inferred usage based on sequence analysis.
Common values: CCR5, CXCR4, CCR3, or a list such as "CCR2b CCR3 CCR5".

Drug naive:
Sequences that were sampled prior to the patient receiving any type of antiretroviral treatment.
Valid Values: yes or no

HLA type:
HLA data for the individual sampled.
Valid Values: Text string, 2 or 4 digit entries are accepted. Incomplete HLA types are accepted.
Example: A02 A34 B*4403 B*4403 Cw*0401 Cw*0701

Host:
The animal species from which the viral isolate was derived.

Infection city:
The city, province, region, or state where the sample was taken.
Valid Values: text field

Infection country:
The country where the individual was infected. This may be different than the sampling country.
Valid Values: 2-letter ISO codes only
Examples: UG for Uganda, BR for Brazil, ZA for South Africa, etc.

Infection date:
The year the patient was infected. If the infection year is uncertain, it should not be entered.
Valid format: MM/DD/YYYY
Note that this is the American standard format, i.e., month-day-year. If you want to enter only a year, enter 01 for the month and day.
Examples: 06/01/1999 is June 1999 (no day) or 01/01/1999 is 1999 (no month or day).

Isolate name:
A name that describes the sample. If no isolate name is provided, the Sequence Name will appear as the isolate in the GenBank record.
Valid Values: Text string.
Valid characters A-Z, a-z, 0-9 , -

Molecule type:
The nucleic acid source from which the sequence was obtained. For example, plasma-derived viral sequences are derived from viral RNA.
Valid Values: DNA, RNA

Note:
Text field describing any information related to the sample or the sequence, but not included in other data fields.
Values: Text string.

Organism:
Valid Values: HCV

Patient age:
Age of patient at time of sampling.
Values: Integer. Be sure to include units (days, months, years).

Patient code:
Unique identifier of the patient from which the sample was taken. Do not use patient names or initials.
Valid Values: Text string. Valid characters A-Z, a-z, 0-9, _ , -

Patient comment:
Text field describing information relating to patient.
Values: Text string.
Valid characters: A-Z, a-z, 0-9, - , .
Example: Patient infected between 1998 and 2000. Linked transmission with patient 569.

Patient ethnicity:
Description: Study appropriate description of Ethnicity, usually self-described by patient.
Valid Values: Text string. Valid characters A-Z, a-z

Patient health status:
Description: HCV related health status of the individual when the sample was taken.
Valid Values: acute infection, asymptomatic, symptomatic, AIDS, deceased.

Patient sex:
Sex of the patient.
Valid values: M or F

Risk factor:
Valid Values: any below. If patient has >1 risk factor, leave blank.

EX - Experimental
NO - Nosocomial
PB - Blood transfusion
PH - hemophiliac
PI - IV drug use
SH - heterosexual
TR - Organ transplant
VE - Vertical (mother to child)

Sampling city:
The city/province/region in which the sample was taken
Valid Values: Text string. Valid characters A-Z, a-z

Sample tissue:
The tissue from which the sample was derived.
Valid Values: Text string. Use noun, not adjective (i.e., vagina, not vaginal)
Examples: plasma, PBMC, semen, CSF, brain, etc.

Strain:
The viral strain from which the sequence was derived. In some cases, this is the same as the isolate. In some cases, one isolate may be used to produce multiple strains in vitro.

Viral load:
The patient's viral load when the sample was taken.
Valid Values: Integer.




Questions or comments? Contact us at hcv-info@lanl.gov