Infectious diseases

  • Article
    | Open Access

    COVID-19 is a critical public health threat, but molecular characterizations of patients’ immunity is still lacking. Here the authors collected blood from patients with various disease severity, and prefiltered to exclude selected comorbidity, to obtain genomic, transcriptomic, proteomic, metabolomic and lipidomic profiles to report a trans-omics landscape.

    • Peng Wu
    • , Dongsheng Chen
    •  & Gang Chen
  • Article
    | Open Access

    Genome-wide association studies of COVID-19 have identified genetic loci affecting disease severity, but the mechanisms remain to be fully described. Here, the authors use genetically predicted transcriptome, splicing and proteome data to identify potential genes and pathways underlying COVID- 19 severity.

    • Gita A. Pathak
    • , Kritika Singh
    •  & Nicholas Mancuso
  • Article
    | Open Access

    Human cytomegalovirus (HCMV) is the prototypical member of the β-herpesvirinae subfamily and the leading viral cause of congenital infections that can lead to birth defects and it can also cause life-threatening disease in immunocompromised individuals. Here, the authors present the in-situ cryo-EM structures of the symmetry-mismatched portal and the capsid vertex-specific components (CVSCs) of HCMV and discuss the mechanistic implications for genome package, retention and ejection.

    • Zhihai Li
    • , Jingjing Pang
    •  & Xuekui Yu
  • Article
    | Open Access

    The human pathogen Neisseria meningitidis colonizes blood vessels and causes vascular damage, despite a neutrophil-rich inflammatory infiltrate. Here, Manriquez et al. use a humanized mouse model to show that pathogen colonization of capillaries and arterioles creates an intravascular niche that precludes an effective action of neutrophils.

    • Valeria Manriquez
    • , Pierre Nivoit
    •  & Guillaume Duménil
  • Article
    | Open Access

    A longitudinal analysis of SARS-CoV-2 infection in humans is challenging. Here the authors show a single cell RNA-sequencing analysis of BAL fluid cells from ferrets and characterise the time dependent recruitment of macrophage subsets to the lungs in response to SARS-CoV-2 infection.

    • Jeong Seok Lee
    • , June-Young Koh
    •  & Su-Hyung Park
  • Article
    | Open Access

    Repeating fever is a hallmark of malaria. Here, a large-scale forward genetic screen in malaria-causing Plasmodium falciparum identifies genes associated with parasite tolerance to host fever, including apicoplast targeted isoprenoid biosynthesis—sharing features with artemisinin resistance.

    • Min Zhang
    • , Chengqi Wang
    •  & John H. Adams
  • 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

    Patients with chronic lung disease (CLD) have an increased risk for severe coronavirus disease-19 and poor outcomes. Here the authors compare the transcriptomes of single cells isolated from healthy and CLD lungs to identify molecular characteristics of lung cells that may account for worse COVID-19 outcomes in these patients.

    • Linh T. Bui
    • , Nichelle I. Winters
    •  & Laure Emmanuelle Zaragosi
  • Article
    | Open Access

    The virulence of some infectious diseases seems to depend on the sex of the host the infection came from, as well as that of the current host. Here, McLeod et al. develop an epidemiological model to investigate the evolution of virulence when pathogens can retain epigenetic memories of their previous host.

    • David V. McLeod
    • , Geoff Wild
    •  & Francisco Úbeda
  • Article
    | Open Access

    RIFINs are Plasmodium surface antigens that suppress the immune response by binding inhibitory receptors such as LAIR1. Here, Xu et al. characterize the interaction between RIFIN-variable 2 domain and a LAIR1 domain and identify LAIR1-binding RIFINs in several Plasmodium species.

    • Kai Xu
    • , Yiran Wang
    •  & Peter D. Kwong
  • 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

    Many domestic animals, among them dogs, have been infected with SARS-CoV-2 during the COVID-19 pandemic. Here, the authors present the crystal structure of the SARS-CoV-2 spike protein receptor binding domain (RBD) bound to its receptor, dog angiotensin-converting enzyme 2 (dACE2), and show that the RBD N501Y mutation increases the infectivity and host range of SARS-CoV-2, which highlights the need to monitor emerging SARS-CoV-2 mutations in domestic animals.

    • Zengyuan Zhang
    • , Yanfang Zhang
    •  & Yeping Sun
  • Article
    | Open Access

    COVID-19 pandemic is a global health risk, but our understanding on the induced durable immunity remains scarce. Here the authors assess antibody responses in 869 convalescent COVID-19 patients to find that specific antibody titers reduce with time, and the RBD-IgG positive rate exceed 70% at 12 month post diagnosis, with male and older patients showing stronger responses.

    • Cesheng Li
    • , Ding Yu
    •  & Xiaoming Yang
  • Article
    | Open Access

    T cells are instrumental to protective immune responses against SARS-CoV-2, the pathogen responsible for the COVID-19 pandemic. Here the authors show that, in convalescent COVID-19 patients, memory T cell responses are detectable up to 317 days post-symptom onset, in which the presence of stem cell-like memory T cells further hints long-lasting immunity.

    • Jae Hyung Jung
    • , Min-Seok Rha
    •  & Eui-Cheol Shin
  • Article
    | Open Access

    The CD8 T cell response to Zika virus is known to be a critical component of the host immune response to infection. Here the authors show a Zika virus isolate specific disruption of antigen processing that impacts the host response and impairs viral clearance providing evidence of isolate specific impacts on the immune response to infection

    • Ryan D. Pardy
    • , Stefanie F. Valbon
    •  & Martin J. Richer
  • Article
    | Open Access

    Current HIV cure-focused clinical trials rely on analytic treatment interruption (ATI) to evaluate post-treatment control (PTC). Here, combining untargetted metabolomics and glycomics in two HIV clinical cohorts, in vitro assays, and machine learning, the authors identify and validate metabolic and glycomic biomarkers linked to inflammatory pathways and HIV latency reactivation associated with PTC, suggesting non-invasive biomarkers as an alternative to predict HIV remission.

    • Leila B. Giron
    • , Clovis S. Palmer
    •  & Mohamed Abdel-Mohsen
  • Article
    | Open Access

    Type II alveolar cells play central roles in multiple aspects of lung biology. Here the authors show that type II alveolar cells also constitutively express MHCII, exhibit limited MHCII antigen presentation capacity, and are a component of the host response to respiratory viral infection.

    • Sushila A. Toulmin
    • , Chaitali Bhadiadra
    •  & Laurence C. Eisenlohr
  • Article
    | Open Access

    Release of freshwater into the oceans as a result of ice sheet melting could impact the distribution of climate-sensitive diseases. Here, the authors show that a rapid ice sheet melting in Greenland could cause an emergence of malaria in Southern Africa whilst transmission risks in West Africa may decline.

    • Alizée Chemison
    • , Gilles Ramstein
    •  & Cyril Caminade
  • Article
    | Open Access

    Applying complexome profiling, Evers et al. unravel the composition of mitochondrial oxidative phosphorylation complexes in P. falciparum asexual and sexual blood stages. Abundance of these complexes differs between both stages, supporting the hypothesis that a mitochondrial metabolic switch is central to gametocyte development and functioning.

    • Felix Evers
    • , Alfredo Cabrera-Orefice
    •  & Taco W. A. Kooij
  • 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

    Estimating the effectiveness of COVID-19 control measures requires large prospective data including symptoms and personal risk factors. Here, the authors used data from smartphone-based application and found that individual face mask use was associated with a 64% reduced risk of COVID-19 symptoms.

    • Sohee Kwon
    • , Amit D. Joshi
    •  & Andrew T. Chan
  • Article
    | Open Access

    In addition to SARS-CoV-2, other coronaviruses also infect human, but whether consecutive infections cross-modulate the induced immune response is still unclear. Here the authors show that SARS-CoV-2 infection boosts pre-existing responses to other coronaviruses, yet such back-boosting hampers the induction of specific antibodies against SARS-CoV-2.

    • Teresa Aydillo
    • , Alexander Rombauts
    •  & Adolfo García-Sastre
  • Article
    | Open Access

    Rapid, accurate and specific point-of-care diagnostics can help manage and contain fast-spreading infections. Here, the authors present a nanopore-based system that uses artificial intelligence to discriminate between four coronaviruses in saliva, with little need for sample pre-processing.

    • Masateru Taniguchi
    • , Shohei Minami
    •  & Kazunori Tomono
  • Article
    | Open Access

    To provide in depth characterization of HIV reservoir cells, the authors here develop a single-cell approach to simultaneously sequence TCR, integration sites and proviral genomes, called STIP-Seq, and show that the translation-competent reservoir mainly consists of proviruses with short deletions at the 5’-end of the genome.

    • Basiel Cole
    • , Laurens Lambrechts
    •  & Linos Vandekerckhove
  • Article
    | Open Access

    A central problem in the COVID-19 pandemic is that there is not enough testing to prevent infectious spread of SARS-CoV-2, causing surges and lockdowns with human and economic toll. Here, the authors evaluate an alternative strategy based on the monitoring of olfactory dysfunction with a mathematical model.

    • Daniel B. Larremore
    • , Derek Toomre
    •  & Roy Parker
  • Article
    | Open Access

    SARS-CoV-2 3CL protease (3CLpro) is essential for coronavirus replication and of great interest as an antiviral drug target. Here, the authors show that the naturally occurring flavonoid myricetin is a non-peptidomimetic and covalent inhibitor of 3CLpro, and they solve crystal structures of 3CLpro with myricetin and derivatives, which reveal that the pyrogallol group covalently modifies the catalytic cysteine.

    • Haixia Su
    • , Sheng Yao
    •  & Yechun Xu
  • Article
    | Open Access

    Yellow fever virus (YFV) is an arbovirus affecting humans and non-human primates (NHPs) with seasonal transmission. Here Hamlet et al. model the monthly occurrence of YF in humans and NHPs across Brazil and show that seasonality of agriculture is an important predictor of seasonal YF transmission.

    • Arran Hamlet
    • , Daniel Garkauskas Ramos
    •  & Neil M. Ferguson
  • Article
    | Open Access

    Yeast form part of the host microbiome with known impact on host immunity. Here the authors identify and investigate the impact of commensal yeast-derived polysaccharides in modulating host inflammation, and show its potential for inhibiting inflammation in a number of models of inflammatory diseases.

    • Changhon Lee
    • , Ravi Verma
    •  & Sin-Hyeog Im
  • 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

    Population-based surveys are the gold standard for estimating seroprevalence but are expensive and often only capture a small geographic area or window of time. This study describes a new platform, SCALE-IT, for serosurveillance based on algorithmic sampling of electronic health records, and uses it to estimate the seroprevalence of SARS-CoV-2 in San Francisco.

    • Isobel Routledge
    • , Adrienne Epstein
    •  & Isabel Rodriguez-Barraquer
  • Article
    | Open Access

    New-onset hyperglycemia and complications of preexisting diabetes have been observed in COVID-19 patients, however, the underlying mechanisms are not fully understood. Here, the authors show that SARS-CoV-2 is detectable in both endocrine and exocrine cells of the pancreata of patients with COVID-19.

    • Charlotte Steenblock
    • , Stefanie Richter
    •  & Stefan R. Bornstein
  • Article
    | Open Access

    Some patients with COVID-19 fail to clear the viral infection quickly, yet our understanding for the underlying immune characteristics is still lacking. Here the authors use single-cell RNA sequencing and other data form such patients to show that persistent infection is associated with immune suppression and reduced expression of ribosomal protein genes.

    • Bin Yang
    • , Junpeng Fan
    •  & Chaoyang Sun
  • Article
    | Open Access

    Many job sectors classified as ‘essential’ have continued operating with limited restrictions during the COVID-19 pandemic, potentially placing workers at higher risk of infection. Here, the authors show that seropositivity rates in workers vary widely across and between job sectors in Geneva, Switzerland.

    • Silvia Stringhini
    • , María-Eugenia Zaballa
    •  & Idris Guessous
  • Article
    | Open Access

    CCR5 is a co-receptor for many transmitted HIV strains. Here, the authors show that biweekly injection of the CCR5-specific antibody Leronlimab protects rhesus macaques against infection following repeated intrarectal challenges of a CCR5-tropic SHIV.

    • Xiao L. Chang
    • , Gabriela M. Webb
    •  & Jonah B. Sacha