HIV-1 subtype kindergarden Hauke Walter Arevir 2015 HIV-1 subtype - PowerPoint PPT Presentation

HIV-1 subtype kindergarden Hauke Walter Arevir 2015

HIV-1 subtype distribution Source: Is HIV-1 evolving to a less virulent form in humans? Kevin K. Ariën, Guido Vanham and Eric J. Arts Nature Reviews Microbiology 5, 141-151 (February 2007)

Relevance of HIV subtyping • Low level of relevance – Diagnosis and therapy monitoring – Laboratory: done by the way (resistance test) • High level of relevance – Epidemiological observations – Vaccine research

Personal Impression: increasing problems while subtyping by the way to identify subtype Check …

Subtyping tools – how are you? • Stanford hivDB subtyping tool last update? – Hard to find: 2002 • NCBI last update 2009, no more funding • HIV-GRADE subtyping is a copy of hivDB subtyping – Last update 2009 (minimal changes) • Geno2pheno - … ? (many different variants....) • Rega ( Belgian system, but samples often without result) • Comet (maybe best today, but no resistence testing, last update 2014)

Feeling to facts - methods • 651 samples for resistance analysis – 02/2014 – 01/2015 • Fasta analysed by HIV-GRADE subtyping tool – discrepant subtyping result for PR and RT  re-analyzed by  NCBI subtyping tool (each 300bp analyzed in 100bp steps; (http://www.ncbi.nlm.nih.gov/projects/genotyping/genotype.cgi)  COMET tool (http://www.hiv.lanl.gov/content/sequence/HIV/CRFs/CRFs.html)  Manual comparison in CRF list (http://www.hiv.lanl.gov/content/sequence/HIV/CRFs/CRFs.html)

Feeling to facts - results 651 Total – Distribution typically 59 ( 9.1%) MIST for Germany 11 A 478 B 23 CRF01_AE – MIST = discrepant 29 CRF02_AG subtype in PR and RT 34 C by HIV-GRADE 5 D 4 F 8 G

Subytping discrepancies in HIV GRADE - overview RT CRF01 CRF02 PR A B _AE _AG C D F G H K A 25 2 1 B 1 CRF01_AE 3 1 1 CRF02_AG 1 1 2 C D 12 1 1 F 1 G 3 1 J 1 K 1

Examples HIV-GRADE: CRF01_AE or B HIV-GRADE and NCBI NCBI: CRF03_AB (10390017) clearly B (10387515) • COMET: B CRF03_AB

Examples NCBI salad HIV-GRADE: B or CRF01_AE NCBI CRF list: NCBI: CRF33_01B or CRF15_01B  COMET: CRF33_01B (ID: 30195430)

Examples NCBI salad HIV GRADE: A oder CRF01_AE NCBI: CRF03_AB/CRF01_AE/ CRF15_01B/A  COMET: A1 (10386227)

Examples NCBI salad HIV GRADE: D oder B NCBI:  COMET: unassigned; D, 29_BF  Patient from Brasilia: CRF29_BF (10383311)

Examples NCBI salad HIV GRADE: F or B NCBI: many BF`s  COMET: unassigned_1;29_BF, F1, B  Clade BF ? (10369869)

Examples NCBI salad HIV-GRADE: NCBI: D/A/CRF15-01B/CRF_35_AD A mit niedriger Homologie (< 92%) D A1  COMET: unassigned_1;10_CD, A1 ??? (10379034)

Subtyping discrepancies in NCBI - overview

Summary • 59 of 651 (9,1%) fastas discrepant subtypes for PR/RT by GRADE • 46 of 59 are A/CRF02 and D/B mixtures and some more A/A1/CRF01_AG/CRF02_AG.... – Easy to solve • Remaining 13 (2.3% of all) of all GRADE subtyping discrepancies were harder to identify – 5 strains were unassigned by all tools

Discussion • Couldn ‘ t it be better? • Somebody interested (maybe MPI?) • Implications for – vaccination strategies (has to be up to date, identification of new variants possible, old stuctures are confusing  need for a new classification system e.g. like clade BF_brasil and clade BG_cuba? – Transferable for other viruses???  HCV problem: need to know genotype before resistence testing can be done (variability !; generate methods: Alignment and genotyping) – …?

Thank You

Comet results name virus subtype 15StN_30195430_HIV2835B30195430.0.3 HIV-1 33_01B 30StN_10386227_HIV2715B10386227.0.2 HIV-1 A1 21StN_10383311_HIV2715B10383311.0.1 HIV-1 unassigned_2;D, 29_BF 27StN_10379034_HIV2835B10379034.0.2 HIV-1 unassigned_1;10_CD, A1 03StN_10369869_HIV2835B10369869.0.3 HIV-1 unassigned_1;29_BF, F1, B