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1.  Whole-genome sequencing to establish relapse or re-infection with Mycobacterium tuberculosis: a retrospective observational study 
The Lancet. Respiratory Medicine  2013;1(10):786-792.
Recurrence of tuberculosis after treatment makes management difficult and is a key factor for determining treatment efficacy. Two processes can cause recurrence: relapse of the primary infection or re-infection with an exogenous strain. Although re-infection can and does occur, its importance to tuberculosis epidemiology and its biological basis is still debated. We used whole-genome sequencing—which is more accurate than conventional typing used to date—to assess the frequency of recurrence and to gain insight into the biological basis of re-infection.
We assessed patients from the REMoxTB trial—a randomised controlled trial of tuberculosis treatment that enrolled previously untreated participants with Mycobacterium tuberculosis infection from Malaysia, South Africa, and Thailand. We did whole-genome sequencing and mycobacterial interspersed repetitive unit-variable number of tandem repeat (MIRU-VNTR) typing of pairs of isolates taken by sputum sampling: one from before treatment and another from either the end of failed treatment at 17 weeks or later or from a recurrent infection. We compared the number and location of SNPs between isolates collected at baseline and recurrence.
We assessed 47 pairs of isolates. Whole-genome sequencing identified 33 cases with little genetic distance (0–6 SNPs) between strains, deemed relapses, and three cases for which the genetic distance ranged from 1306 to 1419 SNPs, deemed re-infections. Six cases of relapse and six cases of mixed infection were classified differently by whole-genome sequencing and MIRU-VNTR. We detected five single positive isolates (positive culture followed by at least two negative cultures) without clinical evidence of disease.
Whole-genome sequencing enables the differentiation of relapse and re-infection cases with greater resolution than do genotyping methods used at present, such as MIRU-VNTR, and provides insights into the biology of recurrence. The additional clarity provided by whole-genome sequencing might have a role in defining endpoints for clinical trials.
Wellcome Trust, European Union, Medical Research Council, Global Alliance for TB Drug Development, European and Developing Country Clinical Trials Partnership.
PMCID: PMC3861685  PMID: 24461758
2.  Human rotavirus vaccine Rotarix™ provides protection against diverse circulating rotavirus strains in African infants: a randomized controlled trial 
BMC Infectious Diseases  2012;12:213.
Rotaviruses are the most important cause of severe acute gastroenteritis worldwide in children <5 years of age. The human, G1P[8] rotavirus vaccine Rotarix™ significantly reduced severe rotavirus gastroenteritis episodes in a Phase III clinical trial conducted in infants in South Africa and Malawi. This paper examines rotavirus vaccine efficacy in preventing severe rotavirus gastroenteritis, during infancy, caused by the various G and P rotavirus types encountered during the first rotavirus-season.
Healthy infants aged 5–10 weeks were enrolled and randomized into three groups to receive either two (10 and 14 weeks) or three doses of Rotarix™ (together forming the pooled Rotarix™ group) or three doses of placebo at a 6,10,14-week schedule. Weekly home visits were conducted to identify gastroenteritis episodes. Rotaviruses were detected by ELISA and genotyped by RT-PCR and nucleotide sequencing. The percentage of infants with severe rotavirus gastroenteritis caused by the circulating G and P types from 2 weeks post-last dose until one year of age and the corresponding vaccine efficacy was calculated with 95% CI.
Overall, 4939 infants were vaccinated and 4417 (pooled Rotarix™ = 2974; placebo = 1443) were included in the per protocol efficacy cohort. G1 wild-type was detected in 23 (1.6%) severe rotavirus gastroenteritis episodes from the placebo group. This was followed in order of detection by G12 (15 [1%] in placebo) and G8 types (15 [1%] in placebo). Vaccine efficacy against G1 wild-type, G12 and G8 types were 64.1% (95% CI: 29.9%; 82%), 51.5% (95% CI:-6.5%; 77.9%) and 64.4% (95% CI: 17.1%; 85.2%), respectively. Genotype P[8] was the predominant circulating P type and was detected in 38 (2.6%) severe rotavirus gastroenteritis cases in placebo group. The remaining circulating P types comprised of P[4] (20 [1.4%] in placebo) and P[6] (13 [0.9%] in placebo). Vaccine efficacy against P[8] was 59.1% (95% CI: 32.8%; 75.3%), P[4] was 70.9% (95% CI: 37.5%; 87.0%) and P[6] was 55.2% (95% CI: -6.5%; 81.3%)
Rotarix™ vaccine demonstrated efficacy against severe gastroenteritis caused by diverse circulating rotavirus types. These data add to a growing body of evidence supporting heterotypic protection provided by Rotarix™.
Trial registration number
PMCID: PMC3462149  PMID: 22974466
3.  HIV Prevalence and Incidence among Sexually Active Females in Two Districts of South Africa to Determine Microbicide Trial Feasibility 
PLoS ONE  2011;6(8):e21528.
The suitability of populations of sexually active women in Madibeng (North-West Province) and Mbekweni (Western Cape), South Africa, for a Phase III vaginal microbicide trial was evaluated.
Sexually active women 18–35 years not known to be HIV-positive or pregnant were tested cross-sectionally to determine HIV and pregnancy prevalence (798 in Madibeng and 800 in Mbekweni). Out of these, 299 non-pregnant, HIV-negative women were subsequently enrolled at each clinical research center in a 12-month cohort study with quarterly study visits.
HIV prevalence was 24% in Madibeng and 22% in Mbekweni. HIV incidence rates based on seroconversions over 12 months were 6.0/100 person-years (PY) (95% CI 3.0, 9.0) in Madibeng and 4.5/100 PY (95% CI 1.8, 7.1) in Mbekweni and those estimated by cross-sectional BED testing were 7.1/100 PY (95% CI 2.8, 11.3) in Madibeng and 5.8/100 PY (95% CI 2.0, 9.6) in Mbekweni. The 12-month pregnancy incidence rates were 4.8/100 PY (95% CI 2.2, 7.5) in Madibeng and 7.0/100 PY (95% CI 3.7, 10.3) in Mbekweni; rates decreased over time in both districts. Genital symptoms were reported very frequently, with an incidence of 46.8/100 PY (95% CI 38.5, 55.2) in Madibeng and 21.5/100 PY (95% CI 15.8, 27.3) in Mbekweni. Almost all (>99%) participants said that they would be willing to participate in a microbicide trial.
These populations might be suitable for Phase III microbicide trials provided that HIV incidence rates over time remain sufficiently high to support endpoint-driven trials.
PMCID: PMC3154187  PMID: 21853020

Results 1-3 (3)