Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Improved reference genome of Aedes aegypti informs arbovirus vector control

Female Aedes aegypti mosquitoes infect more than 400 million people each year with dangerous viral pathogens including dengue, yellow fever, Zika and chikungunya. Progress in understanding the biology of mosquitoes and developing the tools to fight them has been slowed by the lack of a high-quality genome assembly. Here we combine diverse technologies to produce the markedly improved, fully re-annotated AaegL5 genome assembly, and demonstrate how it accelerates mosquito science. We anchored physical and cytogenetic maps, doubled the number of known chemosensory ionotropic receptors that guide mosquitoes to human hosts and egg-laying sites, provided further insight into the size and composition of the sex-determining M locus, and revealed copy-number variation among glutathione S-transferase genes that are important for insecticide resistance. Using high-resolution quantitative trait locus and population genomic analyses, we mapped new candidates for dengue vector competence and insecticide resistance. AaegL5 will catalyse new biological insights and intervention strategies to fight this deadly disease vector

Seroprevalence, predictors and estimated incidence of maternal and neonatal Herpes Simplex Virus Type 2 infection in semi-urban women in Kilifi, Kenya

Background: Herpes Simplex Virus type 2 (HSV-2) has public health importance as a leading cause of genital ulcers, a co-factor in HIV-1 acquisition and transmission and as a cause of neonatal herpes infections. Little is known of its epidemiology and burden in Coastal Kenya. Methods: We screened plasma samples for HSV-2 infection from 826 women aged 15-34 years who participated in an HIV-1 survey in Kilifi in 2004. The sample comprised 563 women selected randomly from a demographic surveillance system (DSS) and 263 women who presented for voluntary counseling and testing (VCT). Predictors for HSV-2 seropositivity were determined using multivariate logistic regression. The incidence of HSV-2 infection and risk of neonatal herpes were estimated by a simple catalytic model fitted to age-seroprevalence data. Results: HSV-2 prevalence was 32% in the DSS recruits vs. 44% in the VCT recruits (P < 0.001), while, HIV-1 prevalence was 8% in the DSS recruits vs. 12% in the VCT recruits (P = 0.12). Independent risk factors for HSV-2 infection in all women were: older age (30-34 years; odds ratio (OR) 10.5, 95% confidence interval (CI): 5.2 - 21.0), recruitment from VCT (OR 1.5, 95% CI: 1.1 - 2.1), history of genital ulcers (OR 1.7, 95% CI: 1.2 - 2.3) and HIV infection (OR 2.7, 95% CI: 1.6-4.6). Education beyond primary (OR 0.7, 95% CI: 0.5 - 0.9) was inversely associated with HSV-2 infection. In the DSS sample, HSV-2 incidence was estimated at 4 cases (95% CI: 3.3 - 4.4) per 100 women per year, 17 cases (95% CI: 16-18) per 1,000 pregnancies per year and 33 neonatal cases (95% CI: 31-36) per 100,000 births per year. Conclusions: HSV-2 transmission is rapid following the onset of sexual activity and likely to result in a significant burden of genital ulcer disease. Nevertheless, the burden of neonatal HSV-2 can be predicted to be low. Educating young women about HSV-2 infection may help in reducing its burden in this semi-urban population