Covid-19. Translational and Clinical Research
Edited by
Jos WM van der Meer et al.

Infectious Diseases: A Collection of Translational and Clinical Research Articles

eLife has published articles on a wide range of infectious diseases, including COVID-19, influenza, tuberculosis, HIV/AIDS, malaria and typhoid fever.
Collection
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This collection brings together translational and clinical research articles on COVID-19, influenza, tuberculosis, HIV/AIDS, malaria, typhoid fever and a number of other neglected, tropical and emerging infectious diseases.

Readers of this collection may also be interested in other eLife articles found on COVID-19: A Collection of Articles, Malaria: A Collection of Articles and on our subject pages for Microbiology and Infectious Disease, Medicine and Epidemiology and Global Health.

For more on publishing your translational research and clinical studies on Infectious Diseases with eLife explore our author guide.

Collection

    1. Epidemiology and Global Health
    2. Medicine

    Investigating phenotypes of pulmonary COVID-19 recovery: A longitudinal observational prospective multicenter trial

    Thomas Sonnweber, Piotr Tymoszuk ... Judith Löffler-Ragg
    Protracted systemic and microvascular inflammation, as well as high anti-SARS-CoV-2 antibody levels, is associated with a high risk of persistent structural and functional lung deficits 6 months after COVID-19.
    1. Epidemiology and Global Health

    Anopheles salivary antigens as serological biomarkers of vector exposure and malaria transmission: A systematic review with multilevel modelling

    Ellen A Kearney, Paul A Agius ... Freya JI Fowkes
    A systematic review with multilevel modelling quantified the positive association between human antibodies to Anopheles salivary proteins with Anopheles-human biting rate and epidemiological measures of malaria transmission, highlighting their potential as a tool to measure vector exposure and malaria transmission.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Transcriptional correlates of malaria in RTS,S/AS01-vaccinated African children: a matched case–control study

    Gemma Moncunill, Jason Carnes ... Raphael Gottardo
    Prevaccination levels of transcriptional modules related to monocytes, dendritic cells, and other immune categories correlate with clinical malaria risk in RTS,S/AS01E-vaccinated African children, suggesting that certain monocyte subsets may inhibit RTS,S/AS01E-induced protective responses.
    1. Epidemiology and Global Health
    2. Medicine

    Ten months of temporal variation in the clinical journey of hospitalised patients with COVID-19: An observational cohort

    ISARIC Clinical Characterisation Group, Matthew D Hall ... Piero L Olliaro
    Patient outcomes, and the time spent by patients during hospital admission, showed considerable variation over the first year of the COVID-19 pandemic.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Cross-reactive antibodies after SARS-CoV-2 infection and vaccination

    Marloes Grobben, Karlijn van der Straten ... Marit J van Gils
    SARS-CoV-2 infection and vaccination elicit antibodies that cross-react with other human coronavirus spike proteins, indicating the spike S2 subdomain as a potential target strategy to develop a pan-coronavirus vaccine.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Efficacy of FFP3 respirators for prevention of SARS-CoV-2 infection in healthcare workers

    Mark Ferris, Rebecca Ferris ... Michael P Weekes
    Healthcare workers working on COVID-19 wards experience a 31-fold increased risk of infection with SARS-CoV-2 compared to colleagues on non-COVID-19 wards whilst wearing fluid-resistant surgical masks, and FFP3 respirators provide up to 100% protection against infection.
    1. Microbiology and Infectious Disease

    Total parasite biomass but not peripheral parasitaemia is associated with endothelial and haematological perturbations in Plasmodium vivax patients

    João L Silva-Filho, João CK Dos-Santos ... Fabio TM Costa
    Data exploring host and parasite signatures in the peripheral blood indicate that total parasite biomass is a better predictor of P. vivax-induced host responses and pathogenesis than peripheral parasitemia.
    1. Medicine
    2. Microbiology and Infectious Disease

    An open label randomized controlled trial of tamoxifen combined with amphotericin B and fluconazole for cryptococcal meningitis

    Nguyen Thi Thuy Ngan, Nhat Thanh Hoang Le ... Jeremy N Day
    Despite evidence of significant anti-cryptococcal activity in vitro and animal models, including synergy with other antifungal agents, high-dose tamoxifen has no impact on cerebrospinal fluid sterilization in cryptococcal meningitis.
    1. Microbiology and Infectious Disease

    Monocyte-derived transcriptome signature indicates antibody-dependent cellular phagocytosis as a potential mechanism of vaccine-induced protection against HIV-1

    Shida Shangguan, Philip K Ehrenberg ... Rasmi Thomas
    Using single-cell CITE-seq to implicate monocytes as the cellular origin of a protective HIV vaccine gene signature.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Multiple introductions of multidrug-resistant typhoid associated with acute infection and asymptomatic carriage, Kenya

    Samuel Kariuki, Zoe A Dyson ... Gordon Dougan
    Carriage of MDR S. Typhi H58 sublineages that also cause acute disease provides understanding of the transmission dynamics of typhoid fever and maintenance of local pathogen populations in Kenya children.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    SARS-CoV-2 shedding dynamics across the respiratory tract, sex, and disease severity for adult and pediatric COVID-19

    Paul Z Chen, Niklas Bobrovitz ... Frank X Gu
    COVID-19 severity, rather than sex or age, predicts SARS-CoV-2 kinetics, and SARS-CoV-2 viral load from lower respiratory tract specimens may predict severe disease days before clinical deterioration for COVID-19 patients.
    1. Medicine
    2. Microbiology and Infectious Disease

    Non-nucleoside reverse transcriptase inhibitor-based combination antiretroviral therapy is associated with lower cell-associated HIV RNA and DNA levels compared to protease inhibitor-based therapy

    Alexander O Pasternak, Jelmer Vroom ... The Co-morBidity in Relation to Aids (COBRA) Collaboration
    In two independent cohorts, NNRTI-based cART regimens are associated with significantly lower cell-associated HIV RNA levels than PI-based regimens, suggesting more potent suppression of residual virus replication by NNRTI-based regimens.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Genetic surveillance in the Greater Mekong subregion and South Asia to support malaria control and elimination

    Christopher G Jacob, Nguyen Thuy-Nhien ... Olivo Miotto
    Large-scale genetic surveillance of malaria implemented by National Malaria Control Programmes informs public health decision makers about the spread of strains resistant to antimalarials.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Malaria: A genetic intervention

    Colin Sutherland, Didier Menard
    A tool that analyzes the genome of parasites found in the blood of malaria patients can help inform policy decisions on how best to tackle the rise in drug-resistant infections.
    Insight
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    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Identification of drugs associated with reduced severity of COVID-19 – a case-control study in a large population

    Ariel Israel, Alejandro A Schäffer ... Eytan Ruppin
    Large-scale retrospective analysis suggests medications and dietary supplements, such as rosuvastatin, ezetimibe, ubiquinone, risedronate, vitamin D, and magnesium, are associated with a lower rate of severe COVID-19 disease.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Impact of asymptomatic Plasmodium falciparum infection on the risk of subsequent symptomatic malaria in a longitudinal cohort in Kenya

    Kelsey M Sumner, Judith N Mangeni ... Steve M Taylor
    The increased risk for symptomatic malaria following an asymptomatic Plasmodium falciparum infection supports targeting asymptomatic infections as a tool to reduce clinical malaria in high-transmission settings.
    1. Medicine
    2. Microbiology and Infectious Disease

    Ct threshold values, a proxy for viral load in community SARS-CoV-2 cases, demonstrate wide variation across populations and over time

    A Sarah Walker, Emma Pritchard ... COVID-19 Infection Survey team
    Wide variation in cycle threshold (Ct) values from SARS-CoV-2 RT-PCR tests over calendar time offers the potential for their broader use in public testing programmes as an ‘early-warning’ system for shifts in infectious load and hence transmission.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data

    Oliver Stirrup, Joseph Hughes ... Judith Breuer
    Epidemiological and viral sequence data can be combined to provide standardised feedback on cases of hospital onset COVID-19 infection that would be useful for infection prevention and control.
    1. Medicine
    2. Microbiology and Infectious Disease

    Combination of inflammatory and vascular markers in the febrile phase of dengue is associated with more severe outcomes

    Nguyen Lam Vuong, Phung Khanh Lam ... Sophie Yacoub
    Relationships of biomarkers with clinical outcome differed between children and adults and the best combinations associated with moderate/severe dengue comprised of six/seven vascular and immune biomarkers.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Systematic screening of viral and human genetic variation identifies antiretroviral resistance and immune escape link

    Huyen Nguyen, Christian Wandell Thorball ... The Swiss HIV Cohort Study
    The presence of certain HLA alleles drives the emergence or maintenance of otherwise deleterious drug-resistant mutations in patients living with HIV, even when the patient is antiretroviral treatment naïve.
    1. Medicine

    Insights from a Pan India Sero-Epidemiological survey (Phenome-India Cohort) for SARS-CoV2

    Salwa Naushin, Viren Sardana ... Shantanu Sengupta
    Widespread asymptomatic SARS-CoV2 infection affected nearly 100 million Indians by September 2020 with a subsequent decline in new cases, which may be attributable to increased population immunity, albeit seeing reduced neutralization activity at 6 months this respite may be temporary.
    Short Report Updated
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    1. Medicine

    Sensitivity of ID NOW and RT–PCR for detection of SARS-CoV-2 in an ambulatory population

    Yuan-Po Tu, Jameel Iqbal, Timothy O'Leary
    Although the ID NOW platform is less sensitive than RT–PCR for identification of SARS-CoV-2 infection, it provides high positive and negative predictive values in low-prevalence populations.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Heterogeneity in transmissibility and shedding SARS-CoV-2 via droplets and aerosols

    Paul Z Chen, Niklas Bobrovitz ... Frank X Gu
    Broader case variation in respiratory viral load, and in shedding virus via droplets and aerosols, for SARS-CoV-2 than influenza A(H1N1)pdm09 facilitates greater transmission heterogeneity in the COVID-19 pandemic than the 2009 flu pandemic.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Single-dose BNT162b2 vaccine protects against asymptomatic SARS-CoV-2 infection

    Nick K Jones, Lucy Rivett ... Michael P Weekes
    A fourfold reduction in the rate of asymptomatic SARS-CoV-2 infection in healthcare workers ≥12 days after a single dose of BNT162b2 mRNA COVID-19 vaccine (Pfizer-BioNTech) has been found.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Early postmortem mapping of SARS-CoV-2 RNA in patients with COVID-19 and the correlation with tissue damage

    Stefanie Deinhardt-Emmer, Daniel Wittschieber ... Gita Mall
    Early postmortem autopsy of COVID-19 patients shows high viral loads and damage of the lung, although extrapulmonary cells demonstrate no injury, they contribute to inflammation, hyper-coagulation, and multiple organ dysfunction.
    1. Microbiology and Infectious Disease

    Saliva TwoStep for rapid detection of asymptomatic SARS-CoV-2 carriers

    Qing Yang, Nicholas R Meyerson ... Sara L Sawyer
    A quick and portable test makes saliva samples turn yellow when people are carrying SARS-CoV-2, the virus that causes COVID-19.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Genomic and healthcare dynamics of nosocomial SARS-CoV-2 transmission

    Jamie M Ellingford, Ryan George ... Graeme CM Black
    Characterisation of SARS-CoV-2 genomic divergence in healthcare-associated outbreaks demonstrates that the inclusion of healthcare workers in contact networks identifies additional links in SARS-CoV-2 transmission pathways.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Estimating SARS-CoV-2 seroprevalence and epidemiological parameters with uncertainty from serological surveys

    Daniel B Larremore, Bailey K Fosdick ... Yonatan H Grad
    Integrating over multiple forms of statistical uncertainty associated with serological surveys can improve serosurvey design while also enabling that uncertainty to be appropriately propagated through epidemiological models.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Viral load and contact heterogeneity predict SARS-CoV-2 transmission and super-spreading events

    Ashish Goyal, Daniel B Reeves ... Bryan T Mayer
    A mathematical model was used to establish a simple conceptual basis for why super-spreader events fundamentally drive the spread of SARS-CoV-2 but not influenza.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    In-host population dynamics of Mycobacterium tuberculosis complex during active disease

    Roger Vargas, Luca Freschi ... Maha Reda Farhat
    Bulk whole genome sequencing data can be used to study the genetic variation present in pathogenic bacterial populations over the time-course of a single infection within a host.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    A Bayesian analysis of the association between Leukotriene A4 Hydrolase genotype and survival in tuberculous meningitis

    Laura Whitworth, Jacob Coxon ... Lalita Ramakrishnan
    In this ideal example of pharmacogenomics, individuals with a common variant in a gene encoding for an inflammatory lipid mediator benefit selectively from standard-of-care anti-inflammatory treatment used for tuberculous meningitis.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Mixed cytomegalovirus genotypes in HIV-positive mothers show compartmentalization and distinct patterns of transmission to infants

    Juanita Pang, Jennifer A Slyker ... Judith Breuer
    Genomic analyses provide new insights into natural history and pathogenesis of cytomegalovirus infection and suggest new testable hypotheses that could be important for the design and implementation of new vaccines.
    1. Medicine

    A novel haemocytometric COVID-19 prognostic score developed and validated in an observational multicentre European hospital-based study

    Joachim Linssen, Anthony Ermens ... Andre J van der Ven
    Distinct haemocytometric parameters, including cell activation markers, combined in a prognostic score may support early identification of COVID-19 patients likely to deteriorate and thus may benefit from ICU admission.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Sex-based differences in clearance of chronic Plasmodium falciparum infection

    Jessica Briggs, Noam Teyssier ... Bryan Greenhouse
    Lower malaria prevalence in females does not appear to be due to lower rates of infection but rather due to faster clearance of asymptomatic infections.
    1. Medicine
    2. Microbiology and Infectious Disease

    Early prediction of level-of-care requirements in patients with COVID-19

    Boran Hao, Shahabeddin Sotudian ... Ioannis Ch Paschalidis
    Using data for 2566 COVID-19 patients from five hospitals, models are developed to predict for each patient hospitalization and critical care needs, based on demographics, comorbidities, medications, and laboratory findings.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Poultry farmer response to disease outbreaks in smallholder farming systems in southern Vietnam

    Alexis Delabouglise, Nguyen Thi Le Thanh ... Maciej F Boni
    Longitudinal monitoring of poultry farms in southern Vietnam reveals that when outbreaks occur with symptoms similar to highly pathogenic avian influenza, farmers respond by sending their chickens to market early.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    The contribution of asymptomatic SARS-CoV-2 infections to transmission on the Diamond Princess cruise ship

    Jon C Emery, Timothy W Russell ... Rein MGJ Houben
    Nearly 75% of SARS-CoV-2 infections on the Diamond Princess were asymptomatic, half were never detected, and asymptomatic infections may have contributed substantially to transmission.
    1. Medicine

    Inference from longitudinal laboratory tests characterizes temporal evolution of COVID-19-associated coagulopathy (CAC)

    Colin Pawlowski, Tyler Wagner ... Venky Soundararajan
    Longitudinal laboratory testing results tied to SARS-CoV-2 diagnostic PCR results of more than 2500 patients reveal the temporal evolution of COVID-associated coagulopathy.
    1. Medicine
    2. Microbiology and Infectious Disease

    Augmented curation of clinical notes from a massive EHR system reveals symptoms of impending COVID-19 diagnosis

    Tyler Wagner, FNU Shweta ... Venky Soundararajan
    Applying deep learning technology for the large-scale curation of symptoms from unstructured EHR clinical notes accurately predicts the differential signals of COVID-19 diagnosis over the week preceding typical PCR testing.
    Short Report Updated
    Formats available:
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    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Earliest infections predict the age distribution of seasonal influenza A cases

    Philip Arevalo, Huong Q McLean ... Sarah Cobey
    First influenza infections determine susceptibility to future seasonal influenza infection throughout life, and may impact vaccine effectiveness.
    1. Computational and Systems Biology
    2. Medicine

    A mechanistic model and therapeutic interventions for COVID-19 involving a RAS-mediated bradykinin storm

    Michael R Garvin, Christiane Alvarez ... Daniel Jacobson
    Gene expression analysis reveals a novel, integrated molecular mechanism for much of the pathogenesis of COVID-19 that provides therapeutic intervention points that can be addressed with existing approved pharmaceuticals.
    Short Report Updated
    Formats available:
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    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Targeted surveillance strategies for efficient detection of novel antibiotic resistance variants

    Allison L Hicks, Stephen M Kissler ... Yonatan H Grad
    Sampling informed by pathogen genomic data may facilitate more efficient detection of novel antibiotic resistance than random sampling.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Antibiotic Resistance: Genomics against gonorrhoea

    Nicholas Medland
    Surveillance strategies based on whole genome sequencing could help with the early identification and detection of new forms of drug-resistant gonorrhoea.
    Insight
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    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Local emergence in Amazonia of Plasmodium falciparum k13 C580Y mutants associated with in vitro artemisinin resistance

    Luana C Mathieu, Horace Cox ... Lise Musset
    The de novo selection of a mutation responsible for Plasmodium falciparum in vitro artemisinin resistance is confirmed in Guyana, making artemisinin combination therapies vulnerable to complete resistance in this region.
    1. Medicine
    2. Immunology and Inflammation

    Kallikrein-kinin blockade in patients with COVID-19 to prevent acute respiratory distress syndrome

    Frank L van de Veerdonk, Mihai G Netea ... Hans van der Hoeven
    The kinin-kallikrein system is a crucial target for the treatment of COVID-19.
    Short Report Updated
    Formats available:
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    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Systematic detection of horizontal gene transfer across genera among multidrug-resistant bacteria in a single hospital

    Daniel R Evans, Marissa P Griffith ... Daria Van Tyne
    Mobile genetic elements were identified and tracked as they exchanged between multidrug-resistant bacteria causing infections at a single hospital.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Impact of community piped water coverage on re-infection with urogenital schistosomiasis in rural South Africa

    Polycarp Mogeni, Alain Vandormael ... Frank Tanser
    Scale-up of piped water coverage in the local community strongly protects against S. haematobium re-infection intensity among primary school-going children following treatment with praziquantel.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Potential impact of outpatient stewardship interventions on antibiotic exposures of common bacterial pathogens

    Christine Tedijanto, Yonatan H Grad, Marc Lipsitch
    Antibiotic stewardship in the outpatient setting can substantially reduce exposures of potential pathogens to common antibiotics, and complementary efforts are needed to reduce remaining exposures that occur in 'necessary' contexts.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Zika seroprevalence declines and neutralizing antibodies wane in adults following outbreaks in French Polynesia and Fiji

    Alasdair D Henderson, Maite Aubry ... Adam J Kucharski
    A combination of eight serological surveys shows a decline in seroprevalence over a two-year period following the first reports of Zika transmission in Fiji and French Polynesia.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Transmission dynamics and control of multidrug-resistant Klebsiella pneumoniae in neonates in a developing country

    Thomas Crellen, Paul Turner ... Ben S Cooper
    Colonisation with resistant Klebsiella pneumoniae in a Cambodian neonatal unit is driven by person-to-person transmission, transmissibility varies by sequence type, and antibiotic consumption generally increases the risk of acquisition.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Adaptation of hepatitis C virus to interferon lambda polymorphism across multiple viral genotypes

    Nimisha Chaturvedi, Evguenia S Svarovskaia ... Jacques Fellay
    Integrated analysis of IFN-λ and HCV amino acid variation indicates the key role of host innate immunity in viral control.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    The origins and relatedness structure of mixed infections vary with local prevalence of P. falciparum malaria

    Sha Joe Zhu, Jason A Hendry ... Gil McVean
    Variation in the rate of mixed infections by malaria parasites and the relatedness structure among infecting strains reveals diversity in local epidemiological processes.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Persistent inflammation during anti-tuberculosis treatment with diabetes comorbidity

    Nathella Pavan Kumar, Kiyoshi F Fukutani ... Hardy Kornfeld
    Systemic inflammation is greater in individuals with concurrent TB and diabetes than in euglycemic individuals with TB, and this disparity persists through the full 6-month course of anti-tubercular treatment.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Potential herd protection against Plasmodium falciparum infections conferred by mass antimalarial drug administrations

    Daniel M Parker, Sai Thein Than Tun ... François Nosten
    Given sufficient population adherence, mass drug administration for falciparum malaria can provide group level benefits, also known as ‘herd effects’.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Panton–Valentine leucocidin is the key determinant of Staphylococcus aureus pyomyositis in a bacterial GWAS

    Bernadette C Young, Sarah G Earle ... Catrin E Moore
    Genome-wide association studies have established staphylococcal pyomyositis as a disease whose pathogenesis depends critically on expression of a single toxin, Panton–Valentine leukocidin.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Panproteome-wide analysis of antibody responses to whole cell pneumococcal vaccination

    Joseph J Campo, Timothy Q Le ... Nicholas J Croucher
    Panproteome array analysis of antibody responses to a pneumococcal whole cell vaccine reveals consistent induction of immune responses to multiple surface proteins, despite individuals' unique pre-existing antibody profiles.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Using paired serology and surveillance data to quantify dengue transmission and control during a large outbreak in Fiji

    Adam J Kucharski, Mike Kama ... Martin L Hibberd
    A combination of surveillance data, paired sera and mathematical modelling reveals which factors may influence dengue transmission and control in island settings.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Synergy in anti-malarial pre-erythrocytic and transmission-blocking antibodies is achieved by reducing parasite density

    Ellie Sherrard-Smith, Katarzyna A Sala ... Andrew M Blagborough
    Combining pre-erythrocytic and transmission blocking antibodies enhances the overall control and potential elimination of malaria within both mosquito and vertebrate populations.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Two complement receptor one alleles have opposing associations with cerebral malaria and interact with α+thalassaemia

    D Herbert Opi, Olivia Swann ... J Alexandra Rowe
    Analysis of a large Kenyan dataset may resolve previously conflicting studies by identifying polymorphisms which interact to modify the risk of cerebral malaria.
    1. Microbiology and Infectious Disease
    2. Medicine

    A randomised double blind placebo controlled phase 2 trial of adjunctive aspirin for tuberculous meningitis in HIV-uninfected adults

    Nguyen TH Mai, Nicholas Dobbs ... Guy E Thwaites
    Adjunctive aspirin may reduce new brain infarcts and deaths in the first 60 days of treatment for HIV-uninfected adults with tuberculous meningitis.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Impact of the scale-up of piped water on urogenital schistosomiasis infection in rural South Africa

    Frank Tanser, Daniel K Azongo ... Christopher Appleton
    Scale-up of safe water supplies decreases a child's risk of urogenital schistosomiasis infection by eight-fold in a typical rural African population.
    1. Microbiology and Infectious Disease
    2. Medicine

    A randomized feasibility trial comparing four antimalarial drug regimens to induce Plasmodium falciparum gametocytemia in the controlled human malaria infection model

    Isaie J Reuling, Lisanne A van de Schans ... Teun Bousema
    Controlled human malaria infection model allows the study of gametocyte biology and dynamics providing novel insights and tools in malaria transmission and elimination efforts.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    MERS-CoV spillover at the camel-human interface

    Gytis Dudas, Luiz Max Carvalho ... Trevor Bedford
    MERS-CoV infections in the Arabian Peninsula are the result of several hundred spillover events from viruses circulating in camels into the human population.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Assessing the danger of self-sustained HIV epidemics in heterosexuals by population based phylogenetic cluster analysis

    Teja Turk, Nadine Bachmann ... Swiss HIV Cohort Study
    A method to assess the risk of self-sustained HIV transmission in heterosexuals from phylogenetic and epidemiological data is developed and, when applied to the Swiss HIV epidemic, shows that this risk is negligibly small for Switzerland.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Epidemiological and ecological determinants of Zika virus transmission in an urban setting

    José Lourenço, Maricelia Maia de Lima ... Mario Recker
    An ento-epidemiological model reveals that what made the Zika virus a public health problem in Feira de Santana, Brazil, was a surprisingly high attack rate coupled with a low risk of Microcephaly per challenged pregnancy.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Genome-wide identification of lineage and locus specific variation associated with pneumococcal carriage duration

    John A Lees, Nicholas J Croucher ... Stephen D Bentley
    Sequence changes in the pneumococcal genome explain most of the variability in duration of asymptomatic carriage with serotype, antibiotic resistance and prophage accounting for the largest effects.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Epidemiology: Promiscuous bacteria have staying power

    Ruth C Massey, Daniel J Wilson
    Being able to take up DNA from their environment might allow pneumococcal bacteria to colonize the human nose and throat for longer periods of time.
    Insight
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    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    APOL1 renal risk variants have contrasting resistance and susceptibility associations with African trypanosomiasis

    Anneli Cooper, Hamidou Ilboudo ... Annette MacLeod
    Common kidney disease risk variants in African populations are associated with reduced susceptibility to deadly African trypanosomes.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    Gene Variation: The double-edged sword of evolution

    Etty Kruzel-Davila, Karl Skorecki
    Two gene variants provide different levels of protection against sleeping sickness, but this comes with an increased risk of developing chronic kidney disease.
    Insight
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    1. Medicine
    2. Microbiology and Infectious Disease

    Reproducible diagnostic metabolites in plasma from typhoid fever patients in Asia and Africa

    Elin Näsström, Christopher M Parry ... Stephen Baker
    Mass spectrometry on plasma from patients with typhoid fever and other febrile disease identified and validated 24 metabolites that can distinguish typhoid from other febrile diseases, providing a new approach for typhoid diagnostics.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    The skin is a significant but overlooked anatomical reservoir for vector-borne African trypanosomes

    Paul Capewell, Christelle Cren-Travaillé ... Annette MacLeod
    African trypanosomes residing within the skin of infected humans represent an important yet overlooked transmissible parasite population that may thwart efforts to eliminate African sleeping sickness.
    Short Report Updated
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    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Trypanosomiasis: Skin deep

    Aitor Casas-Sánchez, Álvaro Acosta-Serrano
    Insight
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    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Updates to the zoonotic niche map of Ebola virus disease in Africa

    David M Pigott, Anoushka I Millear ... Simon I Hay
    Building on previous work (Pigott et al. 2014), estimates of areas of potential transmission of Ebola virus are revised and updated to provide a contemporary map for use by researchers and policymakers.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    A novel ciprofloxacin-resistant subclade of H58 Salmonella Typhi is associated with fluoroquinolone treatment failure

    Duy Pham Thanh, Abhilasha Karkey ... Stephen Baker
    A fluoroquinolone resistant variant of Salmonella Typhi has emerged that is likely to be widespread in the Indian subcontinent; therefore fluoroquinolones should not be recommended for empirical typhoid fever therapy in this setting.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Mapping global environmental suitability for Zika virus

    Jane P Messina, Moritz UG Kraemer ... Simon I Hay
    A global map of environmental suitability for Zika virus and the estimated population living at potential risk can help refine public health guidelines, travel advisories and intervention strategies at a crucial time in the global emergence of this arbovirus.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Evolutionary genomics of epidemic visceral leishmaniasis in the Indian subcontinent

    Hideo Imamura, Tim Downing ... James A Cotton
    Genome sequencing reveals the evolution and epidemiology of Leishmania donovani in the Indian subcontinent, where epidemics have caused up to 30,000 deaths per year.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Eighteenth century Yersinia pestis genomes reveal the long-term persistence of an historical plague focus

    Kirsten I Bos, Alexander Herbig ... Hendrik N Poinar
    The analysis of 18th century Y. pestis genomes reveals a bacterial lineage that might be responsible for the 400-year period of European plague epidemics from the Renaissance through early modern times.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Genomic epidemiology of artemisinin resistant malaria

    MalariaGEN Plasmodium falciparum Community Project
    Plasmodium falciparum kelch13 mutations that cause artemisinin resistant malaria in Southeast Asia show markedly different patterns of evolutionary selection in Africa.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Evaluating probabilistic dengue risk forecasts from a prototype early warning system for Brazil

    Rachel Lowe, Caio AS Coelho ... Xavier Rodó
    The evaluation of a dengue early warning system demonstrates its potential to assist dengue prevention and control up to three months ahead of future epidemics.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Mapping influenza transmission in the ferret model to transmission in humans

    Michael G Buhnerkempe, Katelyn Gostic ... James O Lloyd-Smith
    Influenza transmission among ferrets correlates strongly with transmission among humans, so the ferret model for influenza transmission is a valid tool for pandemic potential in humans.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance

    Caroline Colijn, Ted Cohen
    Both within and between hosts, the key factor guiding whether increasing treatment strength will increase or decrease antibiotic resistance is whether inter-strain competition is effective, not whether it is present.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Integrating between-host transmission and within-host immunity to analyze the impact of varicella vaccination on zoster

    Benson Ogunjimi, Lander Willem ... Niel Hens
    An individual-based model estimates exogenous boosting of immunity following re-exposure to chickenpox is limited to 2 years after re-exposure, but an increase in herpes zoster incidence is still expected to occur following universal varicella vaccination.
    1. Medicine
    2. Microbiology and Infectious Disease

    Mucosal effects of tenofovir 1% gel

    Florian Hladik, Adam Burgener ... Ian McGowan
    Mucosal application of the anti-retroviral drug tenofovir, which is intended to prevent HIV transmission, has many off-target effects on the mucosa itself.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Epidemiological dynamics of Ebola outbreaks

    Thomas House
    The pattern of past Ebola outbreaks is indicative of an effective reproductive ratio of less than 1, which can lead to the generation of a range of outbreak sizes consistent with the scale of the ongoing epidemic.
    Short Report Updated
    Formats available:
    • HTML
    • PDF
    1. Medicine
    2. Microbiology and Infectious Disease

    HIV-1 DNA predicts disease progression and post-treatment virological control

    James P Williams, Jacob Hurst ... John Frater
    Measuring HIV-1 DNA levels at the time of stopping antiretroviral therapy (when initiated during primary infection) predicts clinical progression and the time taken for plasma viraemia to become detectable.
    1. Medicine
    2. Microbiology and Infectious Disease

    HIV Cure Research: Biomarker reveals HIV's hidden reservoir

    Leslie R Cockerham, Steven G Deeks
    Insight
    Formats available:
    • HTML
    • PDF
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Mapping the zoonotic niche of Ebola virus disease in Africa

    David M Pigott, Nick Golding ... Simon I Hay
    Understanding where future Ebola virus outbreaks may start and the changing nature of the populations living in these places is of critical importance in helping to prepare for future outbreaks.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Global distribution maps of the leishmaniases

    David M Pigott, Samir Bhatt ... Simon I Hay
    Maps defining environmental risk of the leishmaniases provide insights into the ecology of these diseases and identify regions to target public health measures and inform future burden estimates.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Salmonella Typhi and Salmonella Paratyphi A elaborate distinct systemic metabolite signatures during enteric fever

    Elin Näsström, Nga Tran Vu Thieu ... Henrik Antti
    Metabolite analysis of plasma from enteric fever patients define signals of organism specific host–pathogen interactions and provides opportunities for new diagnostics.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Host-pathogen Interactions: Honing in on enteric fever

    Lyle R McKinnon, Quarraisha Abdool Karim
    Insight
    Formats available:
    • HTML
    • PDF
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    A micro-epidemiological analysis of febrile malaria in Coastal Kenya showing hotspots within hotspots

    Philip Bejon, Thomas N Williams ... Steffen Borrmann
    Malaria 'hotspots' can be identified that range in size from a few homesteads to a village, and it will be necessary to eliminate hotspots at varying scales as we progress towards eliminating malaria.
    1. Genetics and Genomics
    2. Microbiology and Infectious Disease

    A genome-to-genome analysis of associations between human genetic variation, HIV-1 sequence diversity, and viral control

    István Bartha, Jonathan M Carlson ... Jacques Fellay
    An innovative strategy in genome analysis has generated a detailed description of how pathogens mutate when facing human genetic diversity.
    1. Immunology and Inflammation
    2. Microbiology and Infectious Disease

    Rapid localized spread and immunologic containment define Herpes simplex virus-2 reactivation in the human genital tract

    Joshua T Schiffer, David Swan ... Lawrence Corey
    A combination of detailed sampling and mathematical modeling suggests that the response of immune cells to reactivation of herpes simplex virus 2 is extremely rapid and effective within microscopic areas of genital skin.
    1. Epidemiology and Global Health
    2. Microbiology and Infectious Disease

    Global divergence in critical income for adult and childhood survival: analyses of mortality using Michaelis–Menten

    Ryan J Hum, Prabhat Jha ... Yu-Ling Cheng
    A mathematical model based on enzyme kinetics shows how the relationships between life expectancy, survival rates for children and adults, and national income change over time.

Contributors

  1. Jos WM van der Meer
    Senior Editor
  2. Miles P Davenport
    Senior Editor
  3. Bavesh Kana
    Senior Editor
  4. Marc J Bonten
    Reviewing Editor
  5. Christine Clayton
    Reviewing Editor
  6. Sarah E Cobey
    Reviewing Editor
  7. Caroline Colijn
    Reviewing Editor
  8. Ben Cooper
    Reviewing Editor
  9. Marcelo U Ferreira
    Reviewing Editor
  10. Jennifer Flegg
    Reviewing Editor
  11. Evangelos J Giamarellos-Bourboulis
    Reviewing Editor
  12. Frederik Graw
    Reviewing Editor
  13. Niel Hens
    Reviewing Editor
  14. Prabhat Jha
    Reviewing Editor
  15. Mark Jit
    Reviewing Editor
  16. Urszula Krzych
    Reviewing Editor
  17. Gabriel M Leung
    Reviewing Editor
  18. Joseph Lewnard
    Reviewing Editor
  19. Marc Lipsitch
    Reviewing Editor
  20. James M McCaw
    Reviewing Editor
  21. Sara Mitri
    Reviewing Editor
  22. Richard A Neher
    Reviewing Editor
  23. Isabel Rodriguez-Barraquer
    Reviewing Editor
  24. Joshua T Schiffer
    Reviewing Editor
  25. Viviana Simon
    Reviewing Editor
  26. Margaret Stanley
    Reviewing Editor
  27. Frank van de Veerdonk
    Reviewing Editor
  28. Amy Wesolowski
    Reviewing Editor