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Article
| Open Access
Digital measurement of SARS-CoV-2 transmission risk from 7 million contacts
Digital measurements of proximity and duration of exposure by the NHS COVID-19 app show a strong relation to actual infections among 7 million contacts notified in England and Wales, with longer durations translating to increased risk of transmission.
- Luca Ferretti
- , Chris Wymant
- & Christophe Fraser
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Article |
Prevention of respiratory virus transmission by resident memory CD8+ T cells
Experiments in a mouse model of natural parainfluenza virus transmission show that tissue-resident memory T cells in the respiratory tract have important interferon-γ-dependent roles in protection against and limiting the transmission of viral disease.
- Ida Uddbäck
- , Sarah E. Michalets
- & Jacob E. Kohlmeier
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Article
| Open Access
Repeated Omicron exposures override ancestral SARS-CoV-2 immune imprinting
Exposure to early variants of SARS-CoV-2 results in immune imprinting in mouse models and in humans, reducing neutralizing antibody titres against Omicron variants, which could be mitigated with multiple updated boosters.
- Ayijiang Yisimayi
- , Weiliang Song
- & Yunlong Cao
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Antigenicity and receptor affinity of SARS-CoV-2 BA.2.86 spike
A severe acute respiratory syndrome coronavirus 2 Omicron subvariant, BA.2.86, was found to be no more resistant to human sera than the currently dominant XBB.1.5 and EG.5.1, but it had a remarkably higher receptor affinity.
- Qian Wang
- , Yicheng Guo
- & David D. Ho
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Article
| Open Access
The burden and dynamics of hospital-acquired SARS-CoV-2 in England
Data from acute hospitals in England are used to quantify hospital-acquired SARS-CoV-2 infections, evaluate likely pathways of spread and factors associated with heightened transmission risk, and explore the impact on community transmission.
- Ben S. Cooper
- , Stephanie Evans
- & Gwenan M. Knight
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Article
| Open Access
Distinguishing features of long COVID identified through immune profiling
Individuals with long COVID show marked biological changes in cortisol and immune factors relative to convalescent populations.
- Jon Klein
- , Jamie Wood
- & Akiko Iwasaki
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The β1-adrenergic receptor links sympathetic nerves to T cell exhaustion
Stress-associated catecholamines promote CD8+ T cell exhaustion through the β1-adrenergic receptor, and blocking β-adrenergic signalling may help restore anti-tumour functions.
- Anna-Maria Globig
- , Steven Zhao
- & Susan M. Kaech
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Article
| Open Access
Neutralization, effector function and immune imprinting of Omicron variants
Convergent mutations in hot spots of the spike proteins of currently circulating SARS-CoV-2 Omicron variants increase the binding affinity for the host receptor and promote more efficient fusion with host cell membranes.
- Amin Addetia
- , Luca Piccoli
- & David Veesler
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Article |
Endothelial AHR activity prevents lung barrier disruption in viral infection
The environmental sensor aryl hydrocarbon receptor (AHR) and diet-derived AHR ligands play an important part in protecting against tissue damage following viral pathogen infection in the lung.
- Jack Major
- , Stefania Crotta
- & Andreas Wack
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Article
| Open Access
Dissecting human population variation in single-cell responses to SARS-CoV-2
Population differences in immune responses to SARS-CoV-2 can be explained by environmental exposures, but also by local adaptation acting through genetic variants acquired after admixture with archaic hominin forms.
- Yann Aquino
- , Aurélie Bisiaux
- & Lluis Quintana-Murci
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Article
| Open Access
A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection
The human leukocyte antigen allele HLA-B*15:01 is associated with asymptomatic SARS-CoV-2 infection due to pre-existing T cell immunity.
- Danillo G. Augusto
- , Lawton D. Murdolo
- & Jill A. Hollenbach
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Article
| Open Access
PLSCR1 is a cell-autonomous defence factor against SARS-CoV-2 infection
Phospholipid scramblase 1 (PLSCR1), a protein induced by IFNγ, acts as a defence factor against SARS-CoV-2 and other coronaviruses by inhibiting the fusion of the virus with host-cell membranes.
- Dijin Xu
- , Weiqian Jiang
- & John D. MacMicking
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Article
| Open Access
GWAS and meta-analysis identifies 49 genetic variants underlying critical COVID-19
An analysis of 24,202 critical cases of COVID-19 identifies potentially druggable targets in inflammatory signalling (JAK1), monocyte–macrophage activation and endothelial permeability (PDE4A), immunometabolism (SLC2A5 and AK5), and host factors required for viral entry and replication (TMPRSS2 and RAB2A).
- Erola Pairo-Castineira
- , Konrad Rawlik
- & J. Kenneth Baillie
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Molecular fate-mapping of serum antibody responses to repeat immunization
Serum antibody responses to sequential homologous booster vaccines derive overwhelmingly from primary cohort B cells at the expense of de novo responses; this ‘primary addiction’ can be overcome by boosting with variant antigens.
- Ariën Schiepers
- , Marije F. L. van ’t Wout
- & Gabriel D. Victora
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Influenza vaccination reveals sex dimorphic imprints of prior mild COVID-19
Immune responses to influenza vaccination are affected by previous mild COVID-19 in a sex-dimorphic manner.
- Rachel Sparks
- , William W. Lau
- & John S. Tsang
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Article
| Open Access
Neonatal imprinting of alveolar macrophages via neutrophil-derived 12-HETE
The production of eicosanoids by neutrophils during the neonatal period is necessary for the self-renewal and maintenance of alveolar macrophages during lung development.
- Erwan Pernet
- , Sarah Sun
- & Maziar Divangahi
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Article
| Open Access
Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution
Convergent mutations in hotspots of the SARS-CoV-2 Omicron receptor-binding domain can cause immune evasion and maintain sufficient ACE2-binding capability.
- Yunlong Cao
- , Fanchong Jian
- & Xiaoliang Sunney Xie
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SARS-CoV-2 infection and persistence in the human body and brain at autopsy
A study reports the distribution, replication and persistence of SARS-CoV-2 throughout the human body including in the brain at autopsy from acute infection to more than seven months following symptom onset.
- Sydney R. Stein
- , Sabrina C. Ramelli
- & Daniel S. Chertow
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Article
| Open Access
FXR inhibition may protect from SARS-CoV-2 infection by reducing ACE2
FXR regulates the levels of ACE2 in tissues of the respiratory and gastrointestinal systems that are affected by COVID-19, and inhibiting FXR with ursodeoxycholic acid downregulates ACE2 and reduces susceptibility to SARS-CoV-2 infection.
- Teresa Brevini
- , Mailis Maes
- & Fotios Sampaziotis
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Article |
PD-1 combination therapy with IL-2 modifies CD8+ T cell exhaustion program
PD-1+TCF1+ stem-like CD8+ T cells—precursors of exhausted CD8+ T cells—are not fate-locked into the exhaustion program; their differentiation trajectory can be changed by IL-2 signals.
- Masao Hashimoto
- , Koichi Araki
- & Rafi Ahmed
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Article
| Open Access
Dysregulated naive B cells and de novo autoreactivity in severe COVID-19
Single-cell B cell repertoire analysis identifies the expansion of a naive-derived population of antibody-secreting cells contributing to de novo autoreactivity in patients with severe COVID-19 and those with post-COVID symptoms.
- Matthew C. Woodruff
- , Richard P. Ramonell
- & Ignacio Sanz
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Article
| Open Access
Context-specific emergence and growth of the SARS-CoV-2 Delta variant
Analysis of SARS-CoV-2 genomes from around the world show that following initial importation largely from India, Delta spread in England was driven first by inter-regional travel and then by local population mixing.
- John T. McCrone
- , Verity Hill
- & Moritz U. G. Kraemer
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Article
| Open Access
DOCK2 is involved in the host genetics and biology of severe COVID-19
A genome-wide association study highlights a variant in DOCK2, which is common in East Asian populations but rare in Europeans, as a host genetic risk factor for severe COVID-19.
- Ho Namkoong
- , Ryuya Edahiro
- & Yukinori Okada
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Article
| Open Access
Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission
Emerging SARS-CoV-2 variants of concern were detected early and multiple cases of virus spread not captured by clinical genomic surveillance were identified using high-resolution wastewater and clinical sequencing.
- Smruthi Karthikeyan
- , Joshua I. Levy
- & Rob Knight
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Article
| Open Access
Limited cross-variant immunity from SARS-CoV-2 Omicron without vaccination
Infection with Omicron after vaccination produces cross-neutralizing antibodies to other variants of concern, whereas this induces a limited response to non-Omicron variants in unvaccinated individuals.
- Rahul K. Suryawanshi
- , Irene P. Chen
- & Melanie Ott
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Article
| Open Access
Omicron infection enhances Delta antibody immunity in vaccinated persons
A study quantifying the neutralization of severe acute respiratory syndrome coronavirus 2 variants in individuals infected with Omicron/BA.1 shows that vaccinated individuals previously infected with Omicron have enhanced protection against reinfection with current variants, \including Omicron/BA.2, while Omicron/BA.1 infected unvaccinated individuals have limited protection.
- Khadija Khan
- , Farina Karim
- & Alex Sigal
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Inflammasome activation in infected macrophages drives COVID-19 pathology
A new humanized mouse model for COVID-19 demonstrates SARS-CoV-2 infection and subsequent activation of inflammasomes in human macrophages as a critical driver of disease.
- Esen Sefik
- , Rihao Qu
- & Richard A. Flavell
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Perspective |
Defining the risk of SARS-CoV-2 variants on immune protection
The SARS-CoV-2 Assessment of Viral Evolution (SAVE) programme provides a real-time risk assessment of SARS-CoV-2 variants with the potential to affect transmission, virulence and resistance to infection- and vaccine-induced immunity.
- Marciela M. DeGrace
- , Elodie Ghedin
- & Mehul S. Suthar
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Article
| Open Access
T cell responses to SARS-CoV-2 spike cross-recognize Omicron
T cell responses to spike protein from the SARS-CoV-2 Omicron variant (B.1.1.529) are broadly similar to the responses to ancestral, Beta (B.1.351) and Delta (B.1.617.2) spike protein in vaccinated, infected and unvaccinated individuals.
- Roanne Keeton
- , Marius B. Tincho
- & Catherine Riou
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Review Article |
Human genetic and immunological determinants of critical COVID-19 pneumonia
The COVID Human Genetic Effort examines the molecular, cellular and immunological determinants of the various SARS-CoV-2-related disease manifestations by searching for causal errors of immunity.
- Qian Zhang
- , Paul Bastard
- & Jean-Laurent Casanova
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Broadly neutralizing antibodies overcome SARS-CoV-2 Omicron antigenic shift
Pseudovirus assays and surface plasmon resonance show that the Omicron receptor-binding domain binds to human ACE2 with increased affinity relative to the ancestral virus, and that most neutralizing antibodies are considerably less potent against Omicron.
- Elisabetta Cameroni
- , John E. Bowen
- & Davide Corti
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SARS-CoV-2 infection in free-ranging white-tailed deer
More than one-third of wild deer tested in northeast Ohio showed evidence of SARS-CoV-2 infection of human origin.
- Vanessa L. Hale
- , Patricia M. Dennis
- & Andrew S. Bowman
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Considerable escape of SARS-CoV-2 Omicron to antibody neutralization
An isolate of the Omicron variant of SARS-COV-2 was completely or partially resistant to neutralization by all nine clinically approved monoclonal antibodies tested.
- Delphine Planas
- , Nell Saunders
- & Olivier Schwartz
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Article
| Open Access
Enhanced fitness of SARS-CoV-2 variant of concern Alpha but not Beta
The Alpha variant of SARS-CoV-2 outcompetes progenitor SARS-CoV-2 in upper respiratory tract replication competition in vivo.
- Lorenz Ulrich
- , Nico Joel Halwe
- & Charaf Benarafa
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Review Article |
The emergence, genomic diversity and global spread of SARS-CoV-2
The potential origins and global spread of SARS-CoV-2, the emergence of SARS-CoV-2 variants of concern and the importance of genomic surveillance for the control of the COVID-19 pandemic are discussed.
- Juan Li
- , Shengjie Lai
- & Weifeng Shi
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Article
| Open Access
A COVID-19 peptide vaccine for the induction of SARS-CoV-2 T cell immunity
A phase I open-label trial evaluating the immunogencity, reactogenicity and safety of a peptide-based SARS-CoV-2 vaccine candidate to induce SARS-CoV-2-specific T cell responses.
- Jonas S. Heitmann
- , Tatjana Bilich
- & Juliane S. Walz
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Immunogenicity and efficacy of heterologous ChAdOx1–BNT162b2 vaccination
An observational study of more than 13,000 healthcare workers shows that a prime–boost vaccine regimen of AstraZeneca ChAdOx1-S-nCoV-19 with Pfizer BNT162b2 provides enhanced protection against SARS-CoV-2 infection compared with two doses of BNT162b2.
- Bruno Pozzetto
- , Vincent Legros
- & Sophie Trouillet-Assant
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Article
| Open Access
Genomic reconstruction of the SARS-CoV-2 epidemic in England
A study of the evolution of the SARS-CoV-2 virus in England between September 2020 and June 2021 finds that interventions capable of containing previous variants were insufficient to stop the more transmissible Alpha and Delta variants.
- Harald S. Vöhringer
- , Theo Sanderson
- & Moritz Gerstung
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Matters Arising |
Reply to: A finding of sex similarities rather than differences in COVID-19 outcomes
- Takehiro Takahashi
- , Mallory K. Ellingson
- & Akiko Iwasaki
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Fc-engineered antibody therapeutics with improved anti-SARS-CoV-2 efficacy
Optimization of monoclonal antibodies against SARS-CoV-2 for enhanced Fc-effector function increase their effectiveness for prevention and treatment of COVID-19 in multiple animal models of SARS-CoV-2 infection.
- Rachel Yamin
- , Andrew T. Jones
- & Stylianos Bournazos
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Lectins enhance SARS-CoV-2 infection and influence neutralizing antibodies
C-type lectins and SIGLEC1 function as attachment receptors for SARS-CoV-2 and enhance ACE2-mediated infection.
- Florian A. Lempp
- , Leah B. Soriaga
- & Davide Corti
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Burden and characteristics of COVID-19 in the United States during 2020
Data-driven modelling including numbers of cases and population movements is used to simulate the COVID-19 pandemic in the United States in 2020, providing insights into the transmission of the disease.
- Sen Pei
- , Teresa K. Yamana
- & Jeffrey Shaman
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Article
| Open Access
Rapid and stable mobilization of CD8+ T cells by SARS-CoV-2 mRNA vaccine
Longitudinal analyses of SARS-CoV-2 mRNA vaccine-elicited epitope-specific CD8+ T cell responses shows that CD8+ T cells are rapidly induced after prime vaccination and stably maintained after boost vaccination.
- Valerie Oberhardt
- , Hendrik Luxenburger
- & Maike Hofmann
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Broad sarbecovirus neutralization by a human monoclonal antibody
The human monoclonal antibody S2X259 cross-reacts with spike proteins from all clades of sarbecovirus, and provides prophylactic and therapeutic protection in vivo against parental SARS-CoV-2 and emerging variants of concern.
- M. Alejandra Tortorici
- , Nadine Czudnochowski
- & Matteo Samuele Pizzuto
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SARS-CoV-2 RBD antibodies that maximize breadth and resistance to escape
A survey of SARS-CoV-2 RBD antibodies identifies those with activity against diverse SARS-CoV-2 variants and SARS-related coronaviruses, highlighting epitopes and features to prioritize in antibody and vaccine development.
- Tyler N. Starr
- , Nadine Czudnochowski
- & Gyorgy Snell
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Perspective |
After the pandemic: perspectives on the future trajectory of COVID-19
This Perspective discusses possible future patterns of SARS-CoV-2 infection, the development of variants, potential changes in the patterns of spread and the implications for vaccine deployment and the potential consequences of these issues for the development of policy.
- Amalio Telenti
- , Ann Arvin
- & Herbert W. Virgin
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Article
| Open Access
Mapping the human genetic architecture of COVID-19
A global network of researchers was formed to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity; this paper reports 13 genome-wide significant loci and potentially actionable mechanisms in response to infection.
- Mari E. K. Niemi
- , Juha Karjalainen
- & Chloe Donohue
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Spread of a SARS-CoV-2 variant through Europe in the summer of 2020
Analysis of the spread of the 20E (EU1) variant of SARS-CoV-2 through Europe suggests that international travel and insufficient containment, rather than increased transmissibility, led to a resurgence of infections.
- Emma B. Hodcroft
- , Moira Zuber
- & Richard A. Neher
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Article |
BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells in humans
In a phase-I/II trial in healthy adults, the BNT162b2 vaccine induces neutralizing antibodies and poly-specific T cells against SARS-CoV-2 epitopes that are conserved in a wide range of currently circulating variants.
- Ugur Sahin
- , Alexander Muik
- & Özlem Türeci
Role of IL-27 in Epstein–Barr virus infection revealed by IL-27RA deficiency