Molecular epidemiology of hepatitis B virus in an isolated Afro-Brazilian community

This study was conducted in an Afro-Brazilian, slave-descendant community with high (42.4%) hepatitis B virus (HBV) prevalence. Twenty (8.4%) out of the 239 subjects under study were HBsAg-positive, and HBV-DNA was detected in 59 (25%) individuals. A high rate (18.3%) of occult infection was therefore observed that was associated to low HBV loads (mean, 1.8 × 10⁴ copies/ml) and to a specific amino acid substitution (C100Y) in the small surface antigen. Genotyping of 50 isolates showed that 43 (86%) were of subgenotype A1, one (2%) from subgenotype A2, and five (10%) from subgenotype D. Mixed genotypes A1 and E were observed in one (2%) sample. The genetic distance (0.8 ± 0.3%) among the HBV/A1 isolates from the community was smaller than the intragroup divergence among A1 isolates from Brazil as a whole, but it was similar to that found between A2 isolates from different countries, suggesting that HBV/A1 was introduced in the community through different sources. The substitution W501R (polymerase), previously reported only in Gambia, was observed in 46% of the HBV/A1 isolates. The precore/core promoter region of HBsAg-positive isolates showed several substitutions that could explain the anti-HBe phenotype found in 18 of 20 (90%) of the HBsAg-positive subjects. Nucleotide sequence data reported are available in the DDBJ/EMBL/GenBank databases under the accession numbers EF547828 to EF547858 and FJ174794 to FJ174800.     

Detection of cystic fibrosis transmembrane conductance regulator (CFTR) gene rearrangements enriches the mutation spectrum in congenital bilateral absence of the vas deferens and impacts on genetic counselling

BACKGROUND: Mutations in the cystic fibrosis (CF) transmembrane conductanceregulator (CFTR) gene have been widely detected in infertilemen with congenital bilateral absence of the vas deferens (CBAVD).Despite extensive analysis of the CFTR gene using varied screeningmethods, a number of cases remain unsolved and could be attributableto the presence of large gene rearrangements, as recently shownfor CF patients. METHODS: We carried out a complete CFTR gene study in a group of 222CBAVD patients with strict diagnosis criteria and without renalanomaly, and searched for rearrangements using a semi-quantitativeassay in a subgroup of 61 patients. RESULTS: The overall mutation detection rate was 87.8%, and 82% of patientscarried two mutations. Ten out of the 99 different mutationsaccounted for 74.6% of identified alleles. Four large rearrangementswere found in patients who already carried a mild mutation:two known partial deletions (exons 17a to 18 and 22 to 23),a complete deletion and a new partial duplication (exons 11to 13). The rearrangements accounted for 7% of the previouslyunknown alleles and 1% of all identified alleles. CONCLUSIONS: Screening for rearrangements should be part of comprehensiveCFTR gene studies in CBAVD patients and may have impacts ongenetic counselling for the patients and their families.     

Biofire pneumonia panel in lung donors: faster detection but limited pathogens

Background

Culture of bronchoalveolar lavage (BAL) specimens takes time to report. We tested whether a molecular diagnostic test could accelerate donor lung assessment and treatment.

Methods

We compared BioFire Film Array Pneumonia Panel (BFPP) with standard of care (SOC) tests on lung allograft samples at three time points: (1) donor BAL at organ recovery, (2) donor bronchial tissue and airway swab at implantation, and (3) first recipient BAL following lung implantation. Primary outcomes were the difference in time to result (Wilcoxon signed-ranked tests) and the agreement in results between BFPP and SOC assays (Gwet's agreement coefficient).

Results

We enrolled 50 subjects. In donor lung BAL specimens, BFPP detected 52 infections (14 out of 26 pathogens in the panel). Viral and bacterial BFPP results were reported 2.4 h (interquartile range, IQR 2.0–6.4) following BAL versus 4.6 h (IQR 1.9–6.0, p = 0.625) for OPO BAL viral SOC results and 66 h (IQR 47–87, p < .0001) for OPO BAL bacterial SOC results. Although there was high overall agreement of results between BAL–BFPP versus OPO BAL–SOC tests (Gwet's AC p < .001 for all), the level of agreement differed among 26 pathogens designed in BFPP and differed by types of specimens. BFPP could not detect many infections identified by SOC assays.

Conclusions

BFPP decreased time to detection of lung pathogens among donated lungs, but it cannot replace SOC tests due to the limited number of pathogens in the panel.