wiki:Hicdep_1.80/TableLabRes/FieldSubtype

Version 1 (modified by admin, 4 years ago) (diff)

Copy from Hicdep 1.70

SUBTYPE field

containing table
tblLAB_RES
explanation of variable
Subtype of HIV- or HCV-RNA
format of data
character
exists since HICDEP version
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.

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subtypeReference strainConstituent subtypes
AA
A1A1
A2A2
A3A3
BB
CC
DD
FF
F1F1
F2F2
GG
HH
JJ
KK
CRF01_AECM240A, E
CRF02_AGIbNGA, G
CRF03_ABKal153A, B
CRF04_cpx94CY032A, G, H, K, U
CRF05_DFVI1310D, F
CRF06_cpxBFP90A, G, J, K
CRF07_BC97CN54B', C
CRF08_BC97CNGX-6FB', C
CRF09_cpx96GH2911A, G, U
CRF10_CDTZBF061C, D
CRF11_cpxGR17A, E, G, J, U
CRF12_BFARMA159B, F1
CRF13_cpx96CM-1849CRF01, A, G, J, U
CRF14_BGX397B, G
CRF15_01B99TH.MU2079CRF01, B
CRF16_A2D97KR004A2, D
CRF17_BFARMA038B, F1
CRF18_cpxCU76A1, F, G, H, K, U
CRF19_cpxCU7A1, D, G
CRF20_BGCu103B, G
CRF21_A2D99KE_KER2003A2, D
CRF22_01A1CM001BBYCRF01, A1
CRF23_BGCB118B, G
CRF24_BGCB378B, G
CRF25_cpx02CM_1918LEA, G, U
CRF26_AU02CD_MBTB047A, U
CRF27_cpx04FR-KZSA, E, G, H, J, K, U
CRF28_BFBREPM12609B, F1
CRF29_BFBREPM16704B, F1
CRF30_020600NE36CRF02, CRF06
CRF31_BC04BR142B, C
CRF32_06A1EE0369CRF06, A1
CRF33_01B05MYKL007CRF01, B
CRF34_01BOUR2275PCRF01, B
CRF35_ADAF095A, D
CRF36_cpxNYU830CRF01, CRF02, A, G
CRF37_cpxNYU926CRF01, CRF02, A, G, U
CRF38_BFUY03_3389B, F1
CRF39_BF03BRRJ103B, F1
CRF40_BF05BRRJ055B, F1
CRF41_CDCO6650V1C, D
CRF42_BFluBF_13_05B, F1
CRF43_02GJ11223CRF02, G
CRF44_BFCH80B, F1
CRF45_cpx04FR.AKUA, K, U
CRF46_BF01BR087B, F1
CRF47_BFP1942B, F1
CRF48_01B07MYKT014CRF01, B
CRF49_cpxN28353A1, C, J, K, U
CRF50
CRF51_01BHM021CRF01, 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