= SUBTYPE field =

[[PageOutline]]

 containing table::
  [[..|tblLAB_RES]]
 explanation of variable::
  Subtype of HIV- or HCV-RNA 
 format of data::
  character
 exists since HICDEP version::
  [[wiki:Hicdep_1.30|1.30]]

== Recommended codes for HIV-1 subtypes ==

The nomenclature for CRFs is taken from the http://www.hiv.lanl.gov/content/sequence/HelpDocs/classification.html

It is recommended that cohorts check the coding of subtypes according to the list below prior to submission of the data.

{{{#!CSV filename="CRF_CODES.csv"
subtype;Reference strain;Constituent subtypes
A;;A
A1;;A1
A2;;A2
A3;;A3
B;;B
C;;C
D;;D
F;;F
F1;;F1
F2;;F2
G;;G
H;;H
J;;J
K;;K
CRF01_AE;CM240;A, E
CRF02_AG;IbNG;A, G
CRF03_AB;Kal153;A, B
CRF04_cpx;94CY032;A, G, H, K, U
CRF05_DF;VI1310;D, F
CRF06_cpx;BFP90;A, G, J, K
CRF07_BC;97CN54;B', C
CRF08_BC;97CNGX-6F;B', C
CRF09_cpx;96GH2911;A, G, U
CRF10_CD;TZBF061;C, D
CRF11_cpx;GR17;A, E, G, J, U
CRF12_BF;ARMA159;B, F1
CRF13_cpx;96CM-1849;CRF01, A, G, J, U
CRF14_BG;X397;B, G
CRF15_01B;99TH.MU2079;CRF01, B
CRF16_A2D;97KR004;A2, D
CRF17_BF;ARMA038;B, F1
CRF18_cpx;CU76;A1, F, G, H, K, U
CRF19_cpx;CU7;A1, D, G
CRF20_BG;Cu103;B, G
CRF21_A2D;99KE_KER2003;A2, D
CRF22_01A1;CM001BBY;CRF01, A1
CRF23_BG;CB118;B, G
CRF24_BG;CB378;B, G
CRF25_cpx;02CM_1918LE;A, G, U
CRF26_AU;02CD_MBTB047;A, U
CRF27_cpx;04FR-KZS;A, E, G, H, J, K, U
CRF28_BF;BREPM12609;B, F1
CRF29_BF;BREPM16704;B, F1
CRF30_0206;00NE36;CRF02, CRF06
CRF31_BC;04BR142;B, C
CRF32_06A1;EE0369;CRF06, A1
CRF33_01B;05MYKL007;CRF01, B
CRF34_01B;OUR2275P;CRF01, B
CRF35_AD;AF095;A, D
CRF36_cpx;NYU830;CRF01, CRF02, A, G
CRF37_cpx;NYU926;CRF01, CRF02, A, G, U
CRF38_BF;UY03_3389;B, F1
CRF39_BF;03BRRJ103;B, F1
CRF40_BF;05BRRJ055;B, F1
CRF41_CD;CO6650V1;C, D
CRF42_BF;luBF_13_05;B, F1
CRF43_02G;J11223;CRF02, G
CRF44_BF;CH80;B, F1
CRF45_cpx;04FR.AKU;A, K, U
CRF46_BF;01BR087;B, F1
CRF47_BF;P1942;B, F1
CRF48_01B;07MYKT014;CRF01, B
CRF49_cpx;N28353;A1, C, J, K, U
CRF50;;
CRF51_01B;HM021;CRF01, B
}}}

== Recommended codes for HCV geno- and subtypes ==

From http://www.hepatitis-central.com/hcv/genotype/explained.html


=== Classifications ===

The most commonly used classification of Hepatitis C virus has HCV divided into the following genotypes (main types): 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 and 11. As we've highlighted, HCV genotypes can be broken down into sub-types, some of which include:

* 1a, 1b, 1c
* 2a, 2b, 2c
* 3a, 3b
* 4a, 4b, 4c, 4d, 4e
* 5a
* 6a
* 7a, 7b
* 8a, 8b
* 9a
* 10a
* 11a

=== Genotype patterns ===

It is believed that the hepatitis C virus has evolved over a period of several thousand years. This would explain the current general global patterns of genotypes and subtypes:

* 1a - mostly found in North & South America; also common in Australia 1b - mostly found in Europe and Asia.
* 2a - is the most common genotype 2 in Japan and China.
* 2b - is the most common genotype 2 in the U.S. and Northern Europe.
* 2c - the most common genotype 2 in Western and Southern Europe.
* 3a - highly prevalent here in Australia (40% of cases) and South Asia.
* 4a - highly prevalent in Egypt
* 4c - highly prevalent in Central Africa
* 5a - highly prevalent only in South Africa
* 6a - restricted to Hong Kong, Macau and Vietnam
* 7a and 7b - common in Thailand
* 8a, 8b & 9a - prevalent in Vietnam
* 10a & 11a - found in Indonesia

=== HICDEP Conventions ===

Indicate only the genotype (numbers from 1-11) if the subtype is unknown.

Combinations of geno- and subtypes: Use the "/" to separate (e.g. "4c/4d" or
"1a/1b")
Combinations