Public health

  • Article
    | Open Access

    SARS-CoV-2 was detected in mink farms in the Netherlands in the first wave of the pandemic with evidence of human-to-mink and mink-to-human transmission. Here, the authors investigate this outbreak using phylodynamic analysis and show that personnel links and spatial proximity are predictors of transmission between farms.

    • Lu Lu
    • , Reina S. Sikkema
    •  & Marion P. G. Koopmans
  • Article
    | Open Access

    Multi-strain pathogens, such as influenza, present challenges for interpretation of seroprevalence data as estimates may vary by strain. Here, the authors develop a method for estimating age-specific seroprevalence based on principal components analysis and apply it to influenza data from Vietnam.

    • Dao Nguyen Vinh
    • , Nguyen Thi Duy Nhat
    •  & Maciej F. Boni
  • Article
    | Open Access

    Post-acute sequelae of COVID-19 (PASC, or ‘Long COVID’) has caused concern but the burden and risk factors are not well understood. Here, the authors use US electronic health record data and estimate an overall burden of PASC of ~7% at six months, with variation by severity of acute infection, baseline health status and demographics.

    • Yan Xie
    • , Benjamin Bowe
    •  & Ziyad Al-Aly
  • Article
    | Open Access

    In this study, Delaune et al., isolate and characterise a SARS-CoV-2-related coronavirus from two bats sampled in Cambodia. Their findings suggest that the geographic distribution of SARS-CoV-2-related viruses is wider than previously reported.

    • Deborah Delaune
    • , Vibol Hul
    •  & Veasna Duong
  • Article
    | Open Access

    The ChAdOx1 nCoV-19 vaccine requires two doses, but under limited supply single dose regimens have also been considered. Here, the authors show using static transmission modelling that under certain conditions it is optimal to more expediently administer a single dose to a larger proportion of the population.

    • Ricardo Aguas
    • , Anouska Bharath
    •  & Rima Shretta
  • Article
    | Open Access

    Estimates of the severity of emerging infections did not consider the case ascertainment method, but secondary cases identified by contact tracing of index cases may be more reliable as they are less susceptible to ascertainment bias. Here, the authors perform a systematic review to quantify these differences and model their impacts for COVID-19.

    • Tim K. Tsang
    • , Can Wang
    •  & Benjamin J. Cowling
  • Article
    | Open Access

    The state of Victoria, Australia experienced a substantial second wave of COVID-19 but brought it under control with strict non-pharmaceutical interventions. Here, the authors model the second wave in Victoria to estimate the impacts of the different interventions.

    • James M. Trauer
    • , Michael J. Lydeamore
    •  & Romain Ragonnet
  • Article
    | Open Access

    Cost, supply and logistics present challenges to COVID-19 vaccine rollout in low and middle income countries. Here, the authors model vaccination programmes in South Africa and demonstrate the importance of the pace of vaccine rollout, with even moderately efficacious vaccines likely to be cost-effective.

    • Krishna P. Reddy
    • , Kieran P. Fitzmaurice
    •  & Mark J. Siedner
  • Article
    | Open Access

    The timely hepatitis B birth dose vaccination is recommended for all new-borns by the WHO, but coverage is inconsistent. Here, the authors model the impact of scaling-up coverage in 110 low and middle income countries and assess how it may be affected by delays for example caused by the COVID-19 pandemic.

    • Margaret J. de Villiers
    • , Shevanthi Nayagam
    •  & Timothy B. Hallett
  • Article
    | Open Access

    Forecasting models have been used extensively to inform decision making during the COVID-19 pandemic. In this preregistered and prospective study, the authors evaluated 14 short-term models for Germany and Poland, finding considerable heterogeneity in predictions and highlighting the benefits of combined forecasts.

    • J. Bracher
    • , D. Wolffram
    •  & Frost Tianjian Xu
  • Article
    | Open Access

    Mass gathering events represent a risk for transmission of SARS-CoV-2. Here, the authors describe an experimental indoor test event in which individual contacts were measured and use aerosol and epidemiological modelling to evaluate transmission risks of different types of restrictions in the arena.

    • Stefan Moritz
    • , Cornelia Gottschick
    •  & Rafael Mikolajczyk
  • Article
    | Open Access

    China operates a national surveillance program for acute respiratory infections and sampled over 200,000 patients between 2009–2019. Here, the authors present results from this program and describe patterns by age, pathogen type, presence of pneumonia, and season.

    • Zhong-Jie Li
    • , Hai-Yang Zhang
    •  & Jun Wang
  • Article
    | Open Access

    Reopening of universities to students following COVID-19 restrictions risks increased transmission due to high numbers of social contacts and the potential for asymptomatic transmission. Here, the authors use a mathematical model with social contact data to estimate the impacts of reopening a typical non-campus based university in the UK.

    • Ellen Brooks-Pollock
    • , Hannah Christensen
    •  & Leon Danon
  • Article
    | Open Access

    SARS-CoV-2 was first detected in Kenya in March 2020 and there was evidence of local transmission in the following months. Here, the authors characterise the early stages of the epidemic in coastal Kenya using phylogenetics and find evidence of multiple strain importations from international points of entry.

    • George Githinji
    • , Zaydah R. de Laurent
    •  & Charles N. Agoti
  • Article
    | Open Access

    West and colleagues develop the Variant Database software tool for examination of changing Spike mutations in SARS-CoV-2 genomes. The authors use this to detect emerging lineages of SARS-CoV-2 in New York and report the rapid spread of the B.1.526 lineage in the city.

    • Anthony P. West Jr.
    • , Joel O. Wertheim
    •  & Pamela J. Bjorkman
  • Article
    | Open Access

    Detailed information on SARS-CoV-2 infection rates in Latin America by occupation, socioeconomic group and geographic area are rarely available. Here, the authors provide these estimates for in Bogota, Colombia using data from a sentinel surveillance scheme, and find that over half the population had been infected by March 2021.

    • Rachid Laajaj
    • , Camilo De Los Rios
    •  & Duncan Webb
  • Article
    | Open Access

    Plasmodium vivax generally accounts for a low proportion of malaria cases in Africa, but population-level data on the distribution of infections is limited. Here, the authors use data from the Democratic Republic of the Congo and show that the prevalence is low (~3%) and diffusely spread.

    • Nicholas F. Brazeau
    • , Cedar L. Mitchell
    •  & Jonathan J. Juliano
  • Article
    | Open Access

    Sex and gender have been associated with differences in SARS-CoV-2 incidence and clinical outcomes and therefore warrant consideration in study designs. Here, the authors assess registered and published clinical COVID-19 studies and find that sex-disaggregated analyses are infrequently presented or planned.

    • Emer Brady
    • , Mathias Wullum Nielsen
    •  & Sabine Oertelt-Prigione
  • Article
    | Open Access

    Selection of COVID-19 mitigation measures requires balancing health outcomes with economic impacts. Here, the authors derive a system to set triggers for increasing mitigation measures to preserve healthcare capacity, and describe how it has been used to support public health decision making in Austin, Texas.

    • Haoxiang Yang
    • , Özge Sürer
    •  & Lauren Ancel Meyers
  • Article
    | Open Access

    Despite the consensus that mass vaccination against SARS-CoV-2 will ultimately end the pandemic, it is not clear when and which control measures can be relaxed during the rollout of vaccination programmes. Here, the authors investigate relaxation scenarios using an age-structured transmission model that has been fitted to data for Portugal.

    • João Viana
    • , Christiaan H. van Dorp
    •  & Ganna Rozhnova
  • Article
    | Open Access

    The concentration of SARS-CoV-2 changes during an individual’s infection, and mutations accumulate as viruses are transmitted between people. Here, the authors use data from Iceland to demonstrate how this information can be exploited at the population-level to determine the phase of the epidemic.

    • Hakon Jonsson
    • , Olafur T. Magnusson
    •  & Kari Stefansson
  • Article
    | Open Access

    The role of meteorological factors in SARS-COV-2 transmission is not well understood. Here, the authors use county-level data from the United States to the end of 2020 and find evidence of a moderate association between increased transmissibility and cold, dry weather and low ultraviolet radiation.

    • Yiqun Ma
    • , Sen Pei
    •  & Kai Chen
  • Article
    | Open Access

    Disentangling the impacts of non-pharmaceutical interventions on COVID-19 transmission is challenging as they have been used in different combinations across time and space. This study shows that, early in the epidemic, school/daycare closures and stopping nursing home visits were associated with the biggest reduction in transmission in the United States.

    • Bingyi Yang
    • , Angkana T. Huang
    •  & Derek A. T. Cummings
  • Article
    | Open Access

    Longitudinal multi-omics measurements are highly valuable in studying heterogeneity in health and disease phenotypes. Here, the authors apply Pareto Task Inference to analyze the clinical lab tests of 3094 individuals and find three wellness states, and one aberrant health state defining this cohort.

    • Anat Zimmer
    • , Yael Korem
    •  & Nathan D. Price
  • Article
    | Open Access

    Non-pharmaceutical interventions (NPIs) implemented to interrupt COVID-19 transmission may also impact the spread of other infectious diseases. Here, the authors estimate that influenza activity in China and the United States reduced by up to 80% when NPIs were in place in the 2019–2020 season.

    • Luzhao Feng
    • , Ting Zhang
    •  & George F. Gao
  • Article
    | Open Access

    In response to COVID-19, many states have implemented social distancing orders, but the effect of these orders on population mobility has not been fully quantified. Here, the authors use data from the US to show that state-level social distancing orders substantially reduced mobility and limited the spread of disease.

    • Gregory A. Wellenius
    • , Swapnil Vispute
    •  & Evgeniy Gabrilovich
  • Article
    | Open Access

    Generics contribute to increased availability of antibiotics, benefiting healthcare systems but potentially leading to increased consumption with implications for antibiotic stewardship and resistance. Here, the authors found no consistent changes in prescribing patterns of the 13 antibiotics that entered the US market as generics from 2000–2012.

    • Cecilia Kållberg
    • , Jemma Hudson
    •  & Ramanan Laxminarayan
  • Article
    | Open Access

    Whole genome sequencing data are increasingly becoming routinely available but generating actionable insights is challenging. Here, the authors describe Pathogenwatch, a web tool for genomic surveillance of S. Typhi, and demonstrate its use for antimicrobial resistance assignment and strain risk assessment.

    • Silvia Argimón
    • , Corin A. Yeats
    •  & David M. Aanensen
  • Article
    | Open Access

    Estimates of COVID-19-related mortality are limited by incomplete testing. Here, the authors perform counterfactual analyses and estimate that there were 59,000–62,000 deaths from COVID-19 in Italy until 9th September 2020, approximately 1.5 times higher than official statistics.

    • Chirag Modi
    • , Vanessa Böhm
    •  & Uroš Seljak
  • Article
    | Open Access

    Indoor residual spraying (IRS) of insecticide is one of the primary malaria vector control initiatives, but implementation is limited. Here, the authors show that discontinuation of IRS in Uganda was associated with increased malaria incidence, and introduction of IRS was associated with decreased incidence.

    • Jane F. Namuganga
    • , Adrienne Epstein
    •  & Isabel Rodriguez-Barraquer
  • Article
    | Open Access

    Diarrhoea is a major cause of morbidity and mortality in China. Here, the authors present results from a large sentinel surveillance scheme from 217 hospitals in all 31 provinces in mainland China, including ~150,000 patients with acute diarrhoea and covering years 2009-2018.

    • Li-Ping Wang
    • , Shi-Xia Zhou
    •  & Jun Wang
  • Article
    | Open Access

    Sleep dysregulation has been linked to dementia, but it is unknown whether sleep duration earlier in life is associated with dementia risk. Here, the authors show higher dementia risk associated with short sleep duration (six hours or less) in a longitudinal study of middle and older age adults.

    • Séverine Sabia
    • , Aurore Fayosse
    •  & Archana Singh-Manoux
  • Article
    | Open Access

    Estimating the effects of non-pharmaceutical interventions for COVID-19 is challenging, partly due to variations in testing. Here, the authors use viral sequence data as an alternative means of inferring intervention effects, and show that delays in implementation resulted in more severe epidemics.

    • Manon Ragonnet-Cronin
    • , Olivia Boyd
    •  & Erik Volz
  • Article
    | Open Access

    Large fissure eruptions can cause air pollution events when the volcanic plume returns to the same area after the initial advisory has been lifted. Here, the authors show that these events had a significant impact on health care usage in Iceland, and the impact was exacerbated when advisories were not issued successfully.

    • Hanne Krage Carlsen
    • , Evgenia Ilyinskaya
    •  & Thorolfur Gudnason
  • Article
    | Open Access

    Population-based studies of SARS-CoV-2 seroprevalence are needed to understand levels of immunity and antibody dynamics. Here, the authors show that the seroprevalence in Bonn, Germany was low (<1%) following the first epidemic wave, and that neutralising antibodies waned within a few months.

    • N. Ahmad Aziz
    • , Victor M. Corman
    •  & Monique M. B. Breteler