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  • Di Domenico and Sabbatini et al. model the impact of lockdowns of varying duration and intensity on the control of COVID-19, using data from the third wave of the epidemic in the Paris region of France. The authors introduce a measure of policy-induced fatigue, the ‘distress index’, that helps to explain why shorter, more stringent restrictions might be more effective.

    • Laura Di Domenico
    • Chiara E. Sabbatini
    • Vittoria Colizza
    Article Open Access
  • Papillon-Cavanagh et al. evaluate the impact of biopsy site on measurements of tumor mutational burden (TMB) in a large cohort of tumor samples. The authors observe cancer- and tissue-specific patterns in TMB scores, as well as differences in TMB scores between primary and metastatic samples from the same cancer type.

    • Simon Papillon-Cavanagh
    • Julia F. Hopkins
    • Alice M. Walsh
    Article Open Access
  • Kalka and Gavrieli et al. assessed the heritability of variation in the glycaemic response to metformin by leveraging electronic health records data gathered from a large cohort of patients with diabetes and combining it with pedigree information. The authors show that although the variability in this response has a heritable component, most of it is likely non-genetic.

    • Iris N. Kalka
    • Amir Gavrieli
    • Eran Segal
    Article Open Access
  • Marks and Calix et al. perform a case-control genomic epidemiology study comparing Staphylococcus aureus isolates from intravenous drug use-associated bloodstream infections with those from other bloodstream infections. The authors show there is clonal expansion of lineages in intravenous drug use-associated bloodstream infections suggesting person-to-person transmission of S. aureus.

    • Laura R. Marks
    • Juan J. Calix
    • Gautam Dantas
    Article Open Access
  • Nahkuri et al. evaluate potential prognostic factors for COVID-19 mortality in a large US database of electronic health records. They find that fluid, pH and electrolyte imbalances – diagnosed at least one month prior to COVID-19 diagnosis – are associated with mortality.

    • Satu Nahkuri
    • Tim Becker
    • Anna Bauer-Mehren
    Article Open Access
  • Coutinho et al. use genomic and epidemiological data from Manaus, Brazil, to estimate the transmissibility and potential for reinfection with the SARS-CoV-2 variant-of-concern P.1 (gamma). Using mathematical modelling, the authors estimate that P.1 is 2.6 times more transmissible than previous SARS-CoV-2 variants circulating in Manaus and underlies a large proportion of reinfections in Manaus.

    • Renato Mendes Coutinho
    • Flavia Maria Darcie Marquitti
    • Paulo Inácio Prado
    Article Open Access
  • Wurzel et al. describe the kinetics of the immune response in relation to clinical and virological features in a 5-month old infant with congenital heart disease and severe COVID-19. The immune response was characterised by an elevated inflammatory response in the acute phase of infection, followed by Th2 skewing and prolonged T cell activation.

    • Danielle Wurzel
    • Melanie R. Neeland
    • Nigel W. Crawford
    Article Open Access
  • Campos et al. study the genetic aetiology of antidepressant side effects. Using data from the Australian Genetics of Depression study, the authors show that polygenic risk scores for traits such as BMI, insomnia and headaches have a shared genetic basis with side effects to commonly used antidepressant drugs.

    • Adrian I. Campos
    • Aoibhe Mulcahy
    • Miguel E. Rentería
    Article Open Access
  • Jeong et al. report a series of COVID-19 patients with hearing- and balance-related symptoms. The authors show that human and mouse inner ear tissues, as well as human inner ear cells and organoids derived from induced pluripotent stem cells, express SARS-CoV-2 entry factors, and that these in vitro models of the human inner ear are susceptible to SARS-CoV-2 infection

    • Minjin Jeong
    • Karen E. Ocwieja
    • Konstantina M. Stankovic
    Article Open Access
  • Zhang et al. develop a natural language processing approach, based on the BERT model, to extract linguistic information from chest X-ray radiography reports. The authors establish a 25-label classification system for abnormal findings described in the reports and validate their model using data from multiple sites.

    • Yaping Zhang
    • Mingqian Liu
    • Xueqian Xie
    Article Open Access
  • Konigsberg et al. profile DNA methylation in blood samples from SARS-CoV-2 cases and controls. The authors use machine learning to classify infected vs. non-infected individuals and predict clinical outcomes related to disease severity.

    • Iain R. Konigsberg
    • Bret Barnes
    • Kathleen C. Barnes
    Article Open Access
  • Sachak-Patwa et al. estimate the risk of SARS-CoV-2 outbreaks in low prevalence settings following the removal of travel restrictions and other non-pharmaceutical interventions, with the Isle of Man and Israel as case studies. Using a branching process mathematical model, the authors show that even after a large proportion of the population is vaccinated, there remains a risk of local outbreaks from imported cases.

    • Rahil Sachak-Patwa
    • Helen M. Byrne
    • Robin N. Thompson
    Article Open Access
  • Dalle Carbonare et al. perform a serology study in participants with a prior infection of SARS-CoV-2 and those who are SARS-CoV-2-naïve, who received two doses of the Pfizer-BioNTech BNT162b2 vaccine. After a single dose they observe a quicker recall of pseudovirus neutralization titres in previously-infected participants and a potent IgA response in both groups that was not associated with serum neutralization titres.

    • Luca Dalle Carbonare
    • Maria Teresa Valenti
    • Donato Zipeto
    Article Open Access
  • Plontke et al. report data on the preservation of vestibular function in a series of patients undergoing surgical removal of intracochlear tumors. Using objective clinical tests, the authors show that in most patients the vestibular system can function normally despite major surgical trauma to the cochlea.

    • Stefan K. Plontke
    • Torsten Rahne
    • Laura Fröhlich
    Article Open Access
  • Ying et al. conduct a multi-instrument Mendelian randomization study looking at the link between aging and COVID-19 risk. They observe an association between genetic variation implicated in longevity and decreased risk of COVID-19 infection and hospitalization, with Notch signaling and immune system development loci found to be important in aging-related COVID-19 risk.

    • Kejun Ying
    • Ranran Zhai
    • Vadim N. Gladyshev
    Article Open Access
  • Wong and Ngan et al. characterize the expression and structural variation of SARS-CoV-2 subgenomic RNAs (sgRNAs) in diagnostic specimens from symptomatic and asymptomatic COVID-19 patients. In a series of genomic and transcriptomic analyses, the authors observe reduced sgRNA expression and a distinct set of structural deletions in asymptomatic infections compared with symptomatic infections.

    • Chee Hong Wong
    • Chew Yee Ngan
    • Chia-Lin Wei
    Article Open Access
  • Levi and Ubaldi et al. evaluate SARS-CoV-2 seroprevalence in a cohort of 4735 healthcare workers in northern Italy. In seropositive individuals, they show that antibodies are maintained over a period of 8 to 10 months and associate changes in antibody levels over this period with symptoms and specific subgroups of participants.

    • Riccardo Levi
    • Leonardo Ubaldi
    • Maria Rescigno
    Article Open Access
  • Nemira et al. study the genomic epidemiology and phylodynamics of SARS-CoV-2 in Belarus. They identify potential introduction routes of the virus from other countries, determine that during the first wave of the pandemic the number of infections was likely several times higher than reported case numbers, and estimate the impact of early non-pharmaceutical interventions on SARS-CoV-2 transmission.

    • Alina Nemira
    • Ayotomiwa Ezekiel Adeniyi
    • Pavel Skums
    Article Open Access
  • de Figueiredo et al. perform a global exploratory study to estimate COVID-19 vaccination acceptance and its determinants based on a survey across 32 countries. With some exceptions, they find that factors associated with increased vaccine acceptance are male sex, age over 65, being highly educated, and a belief that their government is handling the pandemic well.

    • Alexandre de Figueiredo
    • Heidi J. Larson
    Article Open Access