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Special Interest Data:
Belgian Transmission Chain

Description

Data from two studies of Belgian patients with a known transmission chain and treatment histories.

Data (2005)

Data provided from Lemey et al. 2005

Alignment - env 12 env gp41 sequences from 9 patients (Fasta format)
Alignment - pol 16 pol sequences from 9 patients (Fasta format)

  • Alignments provided by authors.
  • Sequences correspond to accession numbers:
    AF338984, AF338990, AF338992, AF338997, AF339013, AF339017 (pol local control sequences)
    AY749169 to AY749181 (pol transmission chain sequences)
    AY749182 to AY749196 (env local control sequences)
    AY749197 to AY749208 (env gp41 transmission chain sequences)
  • Transmission chain and treatment histories are presented in the primary reference.
Data (2014)

Data provided from Vrancken et al. 2014

Alignment - env 212 env gp41 sequences from 11 patients (Fasta format)
Alignment - pol 237 pol sequences from 11 patients (Fasta format)
Sample dates (.csv)
Transmission dates (.csv)

  • Alignments provided by authors.
  • Sequences correspond to accession numbers: KF773157 - KF773625
Primary references

Lemey, P., Derdelinckx, I., Rambaut, A., Van Laethem, K., Dumont, S., Vermeulen, S., Van Wijngaerden, E., Vandamme, A.M.
Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain.
J Virol 2005 79(18): 11981-11989.
PMID 16140774

Vrancken B, Rambaut A, Suchard MA, Drummond A, Baele G, Derdelinckx I, Van Wijngaerden E, Vandamme AM, Van Laethem K, Lemey P.
The genealogical population dynamics of HIV-1 in a large transmission chain: bridging within and among host evolutionary rates.
PLoS Comput Biol. 2014 Apr 3;10(4):e1003505.
PMID 24699231

Additional studies that used these data

O'Brien JD, Minin VN, Suchard MA.
Learning to count: robust estimates for labeled distances between molecular sequences.
Mol Biol Evol. 2009 Apr;26(4):801-14.
PMID 19131426

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last modified: Wed May 21 13:34 2014


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