Population divergence time estimation using individual lineage label switching

Divergence time estimation from multilocus genetic data has become common in population genetics and phylogenetics. We present a new Bayesian inference method that treats the divergence time as a random variable. The divergence time is calculated from an assembly of splitting events on individual lineages in a genealogy. The time for such a splitting event is drawn from a hazard function of the truncated normal distribution. This allows easy integration into the standard coalescence framework used in programs such as Migrate. We explore the accuracy of the new inference method with simulated population splittings over a wide range of divergence time values and with a reanalysis of a dataset of 5 populations consisting of 3 present-day populations (Africans, Europeans, Asian) and 2 archaic samples (Altai and Ust’Isthim). Evaluations of simple divergence models without subsequent geneflow show high accuracy, whereas the accuracy of the results of isolation with migration models depends on the magnitude of the immigration rate. High immigration rates lead to a time of the most recent common ancestor of the sample that, looking backward in time, predates the divergence time. Even with many independent loci, accurate estimation of the divergence time with high immigration rates becomes problematic. Our comparison to other software tools reveals that our lineage-switching method, implemented in Migrate, is comparable to IMa2p. The software Migrate can run large numbers of sequence loci (>1,000) on computer clusters in parallel.

Modeling the Impact of Recommendations for Primary Care-Based Screening for Latent Tuberculosis Infection in California

OBJECTIVE

Targeted testing and treatment of persons with latent tuberculosis infection (LTBI) is a critical component of the US tuberculosis (TB) elimination strategy. In January 2016, the California Department of Public Health issued a tool and user guide for TB risk assessment (California tool) and guidance for LTBI testing, and in September 2016, the US Preventive Services Task Force (USPSTF) issued recommendations for LTBI testing in primary care settings. We estimated the epidemiologic effect of adherence to both recommendations in California.

METHODS

We used an individual-based Markov micro-simulation model to estimate the number of cases of TB disease expected through 2026 with baseline LTBI strategies compared with implementation of the USPSTF or California tool guidance. We estimated the risk of LTBI by age and country of origin, the probability of being in a targeted population, and the probability of presenting for primary care based on available data. We assumed 100% adherence to testing guidance but imperfect adherence to treatment.

RESULTS

Implementation of USPSTF and California tool guidance would result in nearly identical numbers of tests administered and cases of TB disease prevented. Perfect adherence to either recommendation would result in approximately 7000 cases of TB disease averted (40% reduction compared with baseline) by 2026. Almost all of this decline would be driven by a reduction in the number of cases among non-US-born persons.

CONCLUSIONS

By focusing on the non-US-born population, adherence to LTBI testing strategies recommended by the USPSTF and the California tool could substantially reduce the burden of TB disease in California in the next decade.

Declining trends in HIV and other sexually transmitted infections among female sex workers in Iran could be attributable to reduced drug injection: a cross-sectional study

OBJECTIVE

The HIV trend among female sex workers (FSWs) is understudied. We assessed the prevalence and trend of HIV and five other STIs among FSWs in Iran.

METHODS

We recruited FSWs (1337 in 2015, 1005 in 2010) from 21 sites in 13 cities in two cross-sectional biobehavioural surveys. Eligible FSWs were women aged ≥18 years who reported selling sex to more than one male client in the past 12 months. Consenting FSWs were interviewed using a behavioural questionnaire and tested for HIV and five other STIs. We considered study sites as clusters in the analysis and two-sided Fisher's exact test to compare the HIV prevalence between the two survey rounds.

RESULTS

HIV prevalence was 2.1% in 2015 (vs 4.0% in 2010, p=0.007). Lifetime drug injection was reported by 6.1% of participants in 2015 (vs 14.6% in 2010, p=0.003). In 2015, among FSWs with history of lifetime drug injection, HIV prevalence was 8.6% (vs 9.8% in 2010, p=0.425). The prevalence of other STIs in 2015 was 0.4% (95% CI 0.2 to 1.0) for syphilis, 1.3% (95% CI 0.8 to 2.1) for gonorrhoea, 6.0% (95% CI 4.8 to 7.4) for chlamydia, 11.9% (95% CI 8.5 to 16.5) for trichomoniasis and 41.8% (95% CI 39.2 to 44.5) for human papillomavirus.

CONCLUSIONS

HIV prevalence among FSWs in Iran decreased, but remains considerably high. The decrease in HIV prevalence compared with 2010 might be explained by a decrease in drug injection. Other STIs are also high in this population. Harm reduction programmes need to be continued and scaled up among this underserved population in Iran.