Epidemiology

  • Article
    | Open Access

    In this study, Tran Kiem et al. examine the contribution of different age groups to COVID-19 transmission. Using data from the French epidemic in summer 2020, they report that while individuals aged 80 years and older are more at risk, pandemic control in the absence of vaccines required measures targeted at all age groups.

    • Cécile Tran Kiem
    • , Paolo Bosetti
    •  & Simon Cauchemez
  • 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

    O’nyong nyong and Chikungunya virus are arboviruses present in Africa but their prevalence is unknown, partly due to high antibody cross-reactivity with one another. Here, the authors develop a statistical model that accounts for cross-reactivity to characterise circulation of both viruses from seroprevalence surveys.

    • Nathanaël Hozé
    • , Issa Diarra
    •  & Simon Cauchemez
  • Article
    | Open Access

    Schizophrenia is a complex disorder where individuals experience different symptoms and outcomes that can be captured by patterns in other diagnoses. Here the authors use computational approaches to summarize these patterns and suggest they are associated with genetic and environmental exposure.

    • Morten Dybdahl Krebs
    • , Gonçalo Espregueira Themudo
    •  & Wesley K. Thompson
  • 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

    Estimating disease prevalence in biobanks is prone to error, especially for self-reported traits. Here, the authors propose a method to estimate the prevalence of a disease within a cohort based on genetic risk scores.

    • Benjamin D. Evans
    • , Piotr Słowiński
    •  & Nicholas J. Thomas
  • Article
    | Open Access

    Vitamin A, of which retinol is the major form in the circulation, is a determinant of human health but whether vitamin A status is associated with mortality is not well understood. Here the authors report that in a prospective observational analysis of 29 104 men, higher serum retinol associates with lower risk of overall and cause-specific mortality.

    • Jiaqi Huang
    • , Stephanie J. Weinstein
    •  & Demetrius Albanes
  • Article
    | Open Access

    The duration of effectiveness of SARS-CoV-2 vaccination is not yet known. Here, the authors present preliminary evidence of BNT162b2 vaccine waning across all age groups above 16, with a higher incidence of infection in people who received their second dose early in 2021 compared to later in the year.

    • Barak Mizrahi
    • , Roni Lotan
    •  & Tal Patalon
  • Article
    | Open Access

    Higher intake of dietary fiber and whole grains are associated with reduced risk of various diseases including some cancers. Here, the authors estimate reductions in liver cancer of 22% and 31% and chronic liver disease mortality of 56% and 63% associated with increased whole grain and dietary fiber intake, respectively.

    • Xing Liu
    • , Wanshui Yang
    •  & Xuehong Zhang
  • 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

    Most people who are infected with SARS-CoV-2 seroconvert within a few weeks, but the determinants and duration of the antibody response are not known. Here, the authors characterise these features of the immune response using data from a large representative community sample of the UK population.

    • Jia Wei
    • , Philippa C. Matthews
    •  & Chris Cunningham
  • 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

    The proportion of a population that has previously been infected by a pathogen is typically estimated using antibody thresholds adjusted for sensitivity and specificity. Here, the authors present a model-based alternative to threshold methods which accounts for antibody waning and other sources of spectrum bias.

    • C. Bottomley
    • , M. Otiende
    •  & J. A. G. Scott
  • Article
    | Open Access

    The true number of infections from SARS-Cov-2 is unknown and believed to exceed the reported numbers by several fold. National testing policies, in particular, can strongly affect the proportion of undetected cases. Here, the authors propose a method that reconstructs incidence profiles within minutes, solely from publicly available, time-stamped viral genomes.

    • Maureen Rebecca Smith
    • , Maria Trofimova
    •  & Max von Kleist
  • Article
    | Open Access

    The effectiveness of digital contact tracing for COVID-19 control remains uncertain. Here, the authors use data from the Smittestopp app, used in Norway in spring 2020, and estimate that 80% of nearby devices were detected by the app, and at least 11% of close contacts were not visible to manual contact tracing.

    • Ahmed Elmokashfi
    • , Joakim Sundnes
    •  & Olav Lysne
  • Article
    | Open Access

    Many African countries have reported relatively low numbers of COVID-19 cases but the true scale of the epidemic is unclear. Here, the authors conduct a population-based survey in a province of Cameroon and estimate 29% seroprevlance, >300 fold higher than the nationwide attack rate implied by case counts.

    • Kene Nwosu
    • , Joseph Fokam
    •  & Laura Ciaffi
  • Article
    | Open Access

    Lassa Fever is a rodent-borne viral haemorrhagic fever that is a public health problem in West Africa. Here, the authors develop a spatiotemporal model of the socioecological drivers of disease using surveillance data from Nigeria, and find evidence of climate sensitivity.

    • David W. Redding
    • , Rory Gibb
    •  & Chikwe Ihekweazu
  • Article
    | Open Access

    Understanding the potential impacts of new variants of SARS-CoV-2 is important for pandemic planning. Here, the authors develop a model incorporating hypothetical new variants with varying transmissibility and immune evasion properties, and use it to project possible future epidemic waves in the UK.

    • Louise Dyson
    • , Edward M. Hill
    •  & Matt J. Keeling
  • Article
    | Open Access

    Huang and colleagues used machine-learning estimators to analyse a broad range of parameters in a prospective cohort consisting ART and spontaneously conceived children. Small differences in stature and growth could not be explained by parental or perinatal environment factors, nor differences in fetal DNA methylation. No strong differences in metabolic parameters were seen.

    • Jonathan Yinhao Huang
    • , Shirong Cai
    •  & Shiao-Yng Chan
  • Article
    | Open Access

    There has been limited research on the role of the mucosal immune response to SARS-CoV-2 infection. Here, the authors perform a prospective observational household study and find that mucosal antibody responses are associated with decreased viral load and faster resolution of systemic symptoms.

    • Janeri Fröberg
    • , Joshua Gillard
    •  & Dimitri A. Diavatopoulos
  • Article
    | Open Access

    Rift Valley fever is a zoonotic haemorrhagic fever with complex transmission dynamics influenced by environmental variables and animal movements. Here, the authors develop a metapopulation model incorporating these factors and use it to identify the main drivers of transmission in the Comoros archipelago.

    • Warren S. D. Tennant
    • , Eric Cardinale
    •  & Raphaëlle Métras
  • 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

    In the context of limited supply, strategies for optimising allocation of COVID-19 vaccines are needed. Here, the authors explore time-varying strategies that adapt to the epidemiological situation and simultaneously optimise for multiple objectives including reducing numbers of infections, hospitalisations, and deaths.

    • Shasha Han
    • , Jun Cai
    •  & Hongjie Yu
  • Article
    | Open Access

    Diet and food intake have been associated with a risk of developing different types of cancer but individual nutritional epidemiology studies are prone to inherent bias. Here, the authors perform an umbrella review of meta-analyses of observational studies and show the level of evidence for associating food and nutrients to cancer risk.

    • Nikos Papadimitriou
    • , Georgios Markozannes
    •  & Konstantinos K. Tsilidis
  • Article
    | Open Access

    Vo’, Italy, is a unique setting for studying SARS-CoV-2 antibody dynamics because mass testing was conducted there early in the pandemic. Here, the authors perform two follow-up serological surveys and estimate seroprevalence, the extent of within-household transmission, and the impact of contact tracing.

    • Ilaria Dorigatti
    • , Enrico Lavezzo
    •  & Andrea Crisanti
  • 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