Epidemiology

  • Article |

    The viral lineage responsible for the February 2021 outbreak of Ebola virus disease in Guinea is nested within a clade that predominantly consists of genomes sampled during the 2013–2016 epidemic, suggesting that the virus might have re-emerged after a long period of latency within a previously infected individual.

    • Alpha Kabinet Keita
    • , Fara R. Koundouno
    •  & N’. Faly Magassouba
  • Article |

    Statistical analysis of COVID-19 transmission among users of a smartphone-based digital contact-tracing app suggests that such apps can be an effective measure for reducing disease spread.

    • Chris Wymant
    • , Luca Ferretti
    •  & Christophe Fraser
  • Article |

    The 501Y.V2 variant of SARS-CoV-2 in South Africa became dominant over other variants within weeks of its emergence, suggesting that this variant is linked to increased transmissibility or immune escape.

    • Houriiyah Tegally
    • , Eduan Wilkinson
    •  & Tulio de Oliveira
  • Article |

    An epidemiological model that integrates fine-grained mobility networks illuminates mobility-related mechanisms that contribute to higher infection rates among disadvantaged socioeconomic and racial groups, and finds that restricting maximum occupancy at locations is especially effective for curbing infections.

    • Serina Chang
    • , Emma Pierson
    •  & Jure Leskovec
  • Article |

    Analysis of the full-spectrum transmission dynamics of COVID-19 in Wuhan reveals that multipronged non-pharmaceutical interventions were effective in controlling the outbreak, and highlights that covert infections may pose risks of resurgence when reopening without intervention measures.

    • Xingjie Hao
    • , Shanshan Cheng
    •  & Chaolong Wang
  • Article |

    OpenSAFELY, a new health analytics platform that includes data from over 17 million adult NHS patients in England, is used to examine factors associated with COVID-19-related death.

    • Elizabeth J. Williamson
    • , Alex J. Walker
    •  & Ben Goldacre
  • Article |

    A model of the effects of different non-pharmaceutical interventions on the spread of COVID-19 in China suggests that a strategy involving the rapid implementation of a combination of interventions is most effective.

    • Shengjie Lai
    • , Nick W. Ruktanonchai
    •  & Andrew J. Tatem
  • Article
    | Open Access

    Pneumococcal and rotavirus vaccines have reduced antibiotic consumption substantially among children under five years old in low- and middle-income countries; however, this effect could be doubled if all countries were to implement vaccination programmes and meet universal vaccine coverage targets.

    • Joseph A. Lewnard
    • , Nathan C. Lo
    •  & Ramanan Laxminarayan
  • Article |

    Detailed virological analysis of nine cases of coronavirus disease 2019 (COVID-19) provides proof of active replication of the SARS-CoV-2 virus in tissues of the upper respiratory tract.

    • Roman Wölfel
    • , Victor M. Corman
    •  & Clemens Wendtner
  • Article
    | Open Access

    Fine-scale estimates of the prevalence of HIV in adults across sub-Saharan Africa reveal substantial within-country variation and local differences in both the direction and rate of change in the prevalence of HIV between 2000 and 2017.

    • Laura Dwyer-Lindgren
    • , Michael A. Cork
    •  & Simon I. Hay
  • Letter
    | Open Access

    The prevalence of improved housing (with improved drinking water and sanitation, sufficient living area and durable construction) in urban and rural sub-Saharan Africa doubled between 2000 and 2015.

    • Lucy S. Tusting
    • , Donal Bisanzio
    •  & Samir Bhatt
  • Letter
    | Open Access

    Multiple transcriptome approaches, including single-cell sequencing, demonstrate that escape from X chromosome inactivation is widespread and occasionally variable between cells, chromosomes, and tissues, resulting in sex-biased expression of at least 60 genes and potentially contributing to sex-specific differences in health and disease.

    • Taru Tukiainen
    • , Alexandra-Chloé Villani
    •  & Daniel G. MacArthur
  • Letter |

    A huge smartphone dataset of physical activity yields global insights, revealing that activity inequality predicts obesity better than does volume of activity and that much of the inequality is a result of reduced activity in females.

    • Tim Althoff
    • , Rok Sosič
    •  & Jure Leskovec
  • Brief Communications Arising |

    • Xiao Dong
    • , Brandon Milholland
    •  & Jan Vijg
  • Brief Communications Arising |

    • Xiao Dong
    • , Brandon Milholland
    •  & Jan Vijg
  • Brief Communications Arising |

    • Xiao Dong
    • , Brandon Milholland
    •  & Jan Vijg
  • Brief Communication |

    • John Collinge
    • , Zane Jaunmuktane
    •  & Sebastian Brandner
  • Article |

    In this study, the authors present an analysis of the malaria burden in sub-Saharan Africa between 2000 and 2015, and quantify the effects of the interventions that have been implemented to combat the disease; they find that the prevalence of Plasmodium falciparum infection has been reduced by 50% since 2000 and the incidence of clinical disease by 40%, and that interventions have averted approximately 663 million clinical cases since 2000, with insecticide-treated bed nets being the largest contributor.

    • S. Bhatt
    • , D. J. Weiss
    •  & P. W. Gething
  • Letter |

    The results of a 23-year study of caloric restriction in rhesus macaques are reported; restricted caloric intake did not increase survival, but improved the metabolic profile of monkeys started at older ages and showed a trend towards delaying age-associated disease in monkeys started at a young age.

    • Julie A. Mattison
    • , George S. Roth
    •  & Rafael de Cabo
  • Article |

    Whole-genome sequencing of 78 Icelandic parent–offspring trios is used to study the de novo mutation rate at the genome-wide level; the rate is shown to increase by about two mutations a year as a function of the increasing age of the father at conception, highlighting the importance of father’s age on the risk of diseases such as autism and schizophrenia.

    • Augustine Kong
    • , Michael L. Frigge
    •  & Kari Stefansson
  • Letter |

    Analyses of strontium elemental and isotopic ratios in fossil teeth show that Australopithecus africanus—the presumed ancestor of early Homo and Paranthropus robustus—had a much more varied diet than Homo and Paranthropus; this sheds light on the diet and home ranges of fossil hominins.

    • Vincent Balter
    • , José Braga
    •  & J. Francis Thackeray
  • Article |

    The human gut microbiome from a large cohort of more than 500 indivduals living on three continents with three distinct cultures is analysed, emphasizing the effect of host age, diet and environment on the composition and functional repertoire of fecal microbiota.

    • Tanya Yatsunenko
    • , Federico E. Rey
    •  & Jeffrey I. Gordon
  • Review Article |

    Pathogenic fungi are increasingly contributing to the global emerging disease burden, threatening biodiversity and imposing increasing costs on ecosystem health, hence steps must be taken to tighten biosecurity worldwide to reduce the rate of fungal disease emergence.

    • Matthew C. Fisher
    • , Daniel. A. Henk
    •  & Sarah J. Gurr
  • Article |

    The evolutionary origin of the human malaria parasite Plasmodium falciparum has been much debated. Genetic analysis of a large number of faecal samples from wild-living African apes now shows that Plasmodium parasites from Western gorillas are most closely related to the human parasite. The data suggest that human P. falciparum evolved from a gorilla parasite after a single host transfer event.

    • Weimin Liu
    • , Yingying Li
    •  & Beatrice H. Hahn
  • Letter |

    Rising global temperatures resulting from climate change have been predicted to increase the future incidence of infectious diseases, including malaria. However, it is known that the range of malaria has contracted through a century of economic development and disease control. This contraction has now been quantified, and compared with the predicted effects of climate on malaria incidence. It is suggested that the impact of rising temperature is likely to be minor.

    • Peter W. Gething
    • , David L. Smith
    •  & Simon I. Hay