The Amy papers

Amy Rosenfeld regularly sends me papers and preprints, mostly on viruses but not always. Here they are for your enjoyment and education.

Effectiveness of Nirmatrelvir–Ritonavir Against the Development of Post–COVID-19 Conditions Among U.S. Veterans (Ann Int Med)

T cell receptor sequences are the dominant factor contributing to the phenotype of CD8⁺ T cells with specificities against immunogenic viral antigens (Cell Rep)

SARS-CoV-2 infection triggers pro-atherogenic inflammatory responses in human coronary vessels (Nat Cardio Res)

Viral kinetics of sequential SARS-CoV-2 infections (Nat Comm)

History of primary-series and booster vaccination and protection against Omicron reinfection (Sci Adv)

Rapid, high throughput, automated detection of SARS-CoV-2 neutralizing antibodies against Wuhan-WT, Delta and Omicron BA1, BA2 spike trimers (iScience)

Vaccine-mediated protection against Merbecovirus and Sarbecovirus challenge in mice (Cell Rep)

Distinguishing features of Long COVID identified through immune profiling (Nature)

Host range, transmissibility and antigenicity of a pangolin coronavirus (Nat Micro)

Blockade of interferon signaling decreases gut barrier integrity and promotes severe West Nile virus disease (Nat Comm)

Does Everyone Need a Yearly Covid Booster? (Beyond the Noise)

Closing in on Zero: Adapting to Complexity and risk on the path to end polio (Polio Eradication pdf)

Wastewater-based epidemiology predicts COVID-19-induced weekly new hospital admissions in over 150 USA counties (Nat Comm)

SARS-CoV-2 Omicron BA.1 breakthrough infection drives late remodeling of the memory B cell repertoire in vaccinated individuals (Immunity)

Postacute sequelae of COVID-19 at 2 years (Nat Med)

Baseline innate and T cell populations are correlates of protection against symptomatic influenza virus infection independent of serology (Nat Immunol)

Airborne transmission of human-isolated avian H3N8 influenza virus between ferrets (Cell)

Mpox infection protects against re-challenge in rhesus macaques (Cell)

Omicron infection following vaccination enhances a broad spectrum of immune responses dependent on infection history (Nat Comm)

Mpox cases rise in China, but response is affected by anti-LGBTQ bias and ‘technology nationalism’ (South China Morning Post)

Genetic stabilization of attenuated oral vaccines against poliovirus types 1 and 3 (Nature)

IFN-λ derived from nonsusceptible enterocytes acts on tuft cells to limit persistent norovirus (Sci Adv)

Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic (bioRxiv)

The Case for Studying New Viruses of New Hosts (Ann Rev Virol)

Immunogenicity and efficacy of vaccine boosters against SARS-CoV-2 Omicron subvariant BA.5 in male Syrian hamsters (Nat Comm)

FDA Approves New Drug to Prevent RSV in Babies and Toddlers (FDA)

WHO reports dozens of babies sickened by deadly viral infections (NBC News)

Memory B cells (Nat Rev Immunol)

An immunostimulatory glycolipid that blocks SARS-CoV-2, RSV, and influenza infections in vivo (Nat Commun)

Rare link between coronavirus vaccines and Long Covid–like illness starts to gain acceptance (Science)

Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential (Nat Commun)

Intrinsic and Effective Severity of Coronavirus Disease 2019 Cases Infected With the Ancestral Strain and Omicron BA.2 Variant in Hong Kong (J Inf Dis)

Incidence of myopericarditis after mRNA COVID-19 vaccination: A meta-analysis with focus on adolescents aged 12–17 years (Vaccine)

Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection (Nat Comm)

Vaccine-induced protection against SARS-CoV-2 requires IFN-γ-driven cellular immune response (Nat Comm)

Targets and cross-reactivity of human T cell recognition of common cold coronaviruses (Cell Rep Med)

Dichotomy of neutralizing antibody, B cell and T cell responses to SARS-CoV-2 vaccination and protection in healthy adults (bioRxiv)

Understanding the Risk of Bat Coronavirus Emergence (EcoHealth Alliance)

Broadly neutralizing antibodies against sarbecoviruses generated by immunization of macaques with an AS03-adjuvanted COVID-19 vaccine (Sci Transl Med)

A novel bat coronavirus with a polybasic furin-like cleavage site (Virologica Sinica)

Single-cell analyses and host genetics highlight the role of innate immune cells in COVID-19 severity (Nat Genetics)

Protective effectiveness of previous SARS-CoV-2 infection and hybrid immunity against the omicron variant and severe disease: a systematic review and meta-regression (Lancet Inf Dis)

Real-world COVID-19 vaccine effectiveness against the Omicron BA.2 variant in a SARS-CoV-2 infection-naive population (Nat Med)

Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape (Nat Comm)

Functional T cells are capable of supernumerary cell division and longevity (Nature)

SARS-CoV-2 breakthrough infection induces rapid memory and de novo T cell responses (Immunity)

Maternal SARS-CoV-2 vaccination and infant protection against SARS-CoV-2 during the first six months of life (Nat Comm)

Notes from the Field: Epidemiologic Characteristics of SARS-CoV-2 Recombinant Variant XBB.1.5 — New York City, November 1, 2022–January 4, 2023 (MMWR)

Long-term gastrointestinal outcomes of COVID-19 (Nat Comm)

Sarbecoviruses of British Horseshoe Bats; Sequence Variation and Epidemiology (bioRxiv)

Archival wild-type poliovirus 1 infected central nervous system tissues of the pre-vaccination era in Switzerland reveal a distinct virus genotype (Acta Neuropath)

SARS-CoV-2 Spike protein induces TLR4-mediated long-term cognitive dysfunction recapitulating post-COVID-19 syndrome in mice (Cell Rep)

Evidence for an aquatic origin of influenza virus and the order Articulavirales (bioRxiv)

Isolation of ACE2-dependent and -independent sarbecoviruses from Chinese horseshoe bats (bioRxiv)

The crystal structure of a simian Foamy Virus receptor binding domain provides clues about entry into host cells (Nature Comm)

Influenza at the human-animal interface: Summary and risk assessment, from 6 to 26 January 2023 (WHO)

A systems immunology study comparing innate and adaptive immune responses in adults to COVID-19 mRNA and adenovirus vectored vaccines (Cell Rep Med)

Pre-existing immunity modulates responses to mRNA boosters (Cell Rep)

SARS-CoV-2 Neutralizing Antibodies After Bivalent vs. Monovalent Booster (bioRxiv)

Equatorial Guinea confirms first-ever Marburg virus disease outbreak (WHO)

Cross-protective antibodies against common endemic respiratory viruses (Nat Comm)

Coronavirus (COVID-19) Infection Survey technical article: Cumulative incidence of the percentage of people who have been infected with COVID-19 by variant and age, England: 9 February 2023 (UK Office for National Statistics)

The impacts of SARS-CoV-2 vaccine dose separation and targeting on the COVID-19 epidemic in England (Nat Comm)

Highly pathogenic avian influenza A(H5N1) virus infection in farmed minks, Spain, October 2022 (Eurosurveillance)

Prior vaccination enhances immune responses during SARS-CoV-2 breakthrough infection with early activation of memory T cells followed by production of potent neutralizing antibodies (bioRxiv)

ACE2 binding and antibody evasion in enhanced transmissibility of XBB.1.5 (Lancet Inf Dis)

How quickly does COVID immunity fade? What scientists know (Nature)

White-tailed deer (Odocoileus virginianus) may serve as a wildlife reservoir for nearly extinct SARS-CoV-2 variants of concern (PNAS)

Effectiveness of Bivalent Boosters against Severe Omicron Infection (NEJM)

Tracking the clonal dynamics of SARS-CoV-2-specific T cells in children and adults with mild/asymptomatic COVID-19 (Clin Immunol)

Facing the New Covid-19 Reality (NEJM)

U.S. scientists brace for tighter scrutiny of potentially risky research (Science)

Real-world effectiveness of a single dose of mpox vaccine in males (Nature Med)

COVID-19 vaccines versus pediatric hospitalization (Cell Rep Med)

Waning Immunity Against XBB.1.5 Following Bivalent mRNA Boosters (bioRxiv)

Extremely potent pan-sarbecovirus neutralizing antibodies generated by immunization of macaques with an AS03-adjuvanted monovalent subunit vaccine against SARS-CoV-2 (bioRxiv)

Protective effectiveness of previous SARS-CoV-2 infection and hybrid immunity against the omicron variant and severe disease: a systematic review and meta-regression (Lancet Inf Dis)

Real-world COVID-19 vaccine effectiveness against the Omicron BA.2 variant in a SARS-CoV-2 infection-naive population (Nat Med)

Epistasis lowers the genetic barrier to SARS-CoV-2 neutralizing antibody escape (Nat Comm)

Functional T cells are capable of supernumerary cell division and longevity (Nature)

Rapid transmission and tight bottlenecks constrain the evolution of highly transmissible SARS-CoV-2 variants (Nat Comm)

Therapeutic and vaccine-induced cross-reactive antibodies with effector function against emerging Omicron variants (bioRxiv)

Estimating the transmission dynamics of SARS-CoV-2 Omicron BF.7 in Beijing after the adjustment of zero-COVID policy in November – December 2022 (Nature Med)

7-month duration of SARS-CoV-2 mucosal immunoglobulin-A responses and protection (Lancet Inf Dis)

Bivalent Covid-19 Vaccines — A Cautionary Tale (NEJM)

B cell analyses after SARS-CoV-2 mRNA third vaccination reveals a hybrid immunity like antibody response (Nat Comm).

Stability of hybrid versus vaccine immunity against BA.5 infection over 8 months (Lancet Inf Dis)

Wastewater surveillance for public health (Science).

SARS-CoV-2 Omicron subvariants Spike recognition and neutralization elicited after the third dose of mRNA vaccine (Cell Rep).

Bivalent mRNA vaccine improves antibody-mediated neutralization of many SARS-CoV-2 Omicron lineage variants (bioRxiv).

Human iPS cell-derived sensory neurons can be infected by SARS-CoV-2 strain WA1/2020 as well as variants delta and omicron (bioRxiv)

Antibody-dependent cellular cytotoxicity against SARS-CoV-2 Omicron sub-lineages is reduced in convalescent sera regardless of infecting variant (Cell Rep Med)

Continuous germinal center invasion contributes to the diversity of the immune response (Cell)

The SARS-CoV-2 Delta (B.1.617.2) variant with spike N501Y mutation in the shadow of Omicron emergence (Heliyon)

Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 Omicron sub-lineages (bioRxiv)

Massive measles outbreak threatens India’s goal to eliminate disease by 2023 (Nature)

SARS-CoV-2 infection and persistence in the human body and brain at autopsy (Nature)

The Fc-effector function of COVID-19 convalescent plasma contributes to SARS-CoV-2 treatment efficacy in mice (Cell Rep Med)

Infectiousness of SARS-CoV-2 breakthrough infections and reinfections during the Omicron wave (Nature Med)

Comparative effectiveness of third doses of mRNA-based COVID-19 vaccines in US veterans (Nature Micro)

Virological characteristics of the SARS-CoV-2 XBB variant derived from recombination of two Omicron subvariants (bioRxiv)

Alarming antibody evasion properties of rising SARS-CoV-2 BQ and XBB subvariants (Cell)

The WHO estimates of excess mortality associated with the COVID-19 pandemic (Nature)

COVID drug Paxlovid was hailed as a game-changer. What happened? (Nature)

Neutralization against BA.2.75.2, BQ.1.1, and XBB from mRNA Bivalent Booster (NEJM)

Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution (Nature)

Impact of SARS-CoV-2 exposure history on the T cell and IgG response (Cell Rep Med)

COVID-19 Convalescent Plasma Outpatient Therapy to Prevent Outpatient Hospitalization: A Meta-analysis of Individual Participant Data From Five Randomized Trials (medRxiv)

Immunological dysfunction persists for 8 months following initial mild-to-moderate SARS-CoV-2 infection (Nat Immunol)

AZD1222-induced mucosal immune responses are influenced by prior SARS-CoV-2 infection and correlate with virologic outcomes in breakthrough infection (Cell Rep Med)

Fcγ receptor-dependent antibody effector functions are required for vaccine protection against infection by antigenic variants of SARS-CoV-2 (bioRxiv).

Antibody effector functions are associated with protection from respiratory syncytial virus (Cell)

Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies (Immunity)

An epithelial-immune circuit amplifies inflammasome and IL-6 responses to SARS-CoV-2 (Cell Host Microbe)

Efficacy of Antiviral Agents against Omicron Subvariants BQ.1.1 and XBB (NEJM)

Nearly 40 million children susceptible to measles due to COVID-19 disruptions (United Nations) note: the young girl in the photo is NOT receiving a measles vaccine; that is given by needle intramuscularly. The girl is receiving oral poliovirus vaccine. (vrr)

Vaccines are in short supply amid global cholera surge (Science)

Defining antigen targets to dissect vaccinia virus and monkeypox virus-specific T cell responses in humans (Cell Host Microbe)

SARS-CoV-2 viral load and shedding kinetics (Nat Rev Micro)

There is currently a measles outbreak in Ohio among unvaccinated children. This webpage has case details: Measles Public Report

Autopsy-based histopathological characterization of myocarditis after anti-SARS-CoV-2-vaccination (Clin Res Cardiol)

Low neutralization of SARS-CoV-2 Omicron BA.2.75.2, BQ.1.1, and XBB.1 by parental mRNA vaccine or a BA.5-bivalent booster (Nat Med)

Immunogenicity and safety of a 4^th homologous booster dose of a SARS-CoV-2 recombinant spike protein vaccine (NVX-CoV2373): a phase 2, randomized, placebo-controlled trial (medRxiv)

Observed versus expected rates of myocarditis after SARS-CoV-2 vaccination: a population-based cohort study (Can Med Assoc J)

Distinct Neutralizing Antibody Escape of SARS-CoV-2 Omicron Subvariants BQ.1, BQ.1.1, BA.4.6, BF.7 and BA.2.75.2 (bioRxiv)

Bulk IgG Glycosylation Predicts COVID-19 Severity and Vaccine Antibody Response (Cell Rep)

Cross-neutralization of Omicron subvariants after heterologous NVX-CoV2373 boosters: Comparison between prior SARS-CoV-2-infected and infection-naive individuals (J Infect)

Characterisation of SARS-CoV-2 genomic variation in response to molnupiravir treatment in the AGILE Phase IIa clinical trial (Nat Comm)

Fc mediated pan-sarbecovirus protection after alphavirus vector vaccination (bioRxiv)

Cross-reaction of current available SARS-CoV-2 MAbs against the pangolin-origin coronavirus GX/P2V/2017 (Cell Rep)

Cross-reactive SARS-CoV-2 epitope targeted across donors informs immunogen design (Cell Rep Med)

Differential mosquito attraction to humans is associated with skin-derived carboxylic acid levels (Cell)

Pathogen spillover driven by rapid changes in bat ecology (Nature)

Retrotransposon activation during Drosophila metamorphosis conditions adult antiviral responses (Nat Genet)

Longitudinal analysis of serum neutralization of SARS-CoV-2 Omicron BA.2, BA.4 and BA.5 in patients receiving monoclonal antibodies (Cell Rep Med)

Functional proteomic profiling links deficient DNA clearance with increased mortality in individuals with severe COVID-19 pneumonia (Immunity)

CD8 T cells contribute to vaccine protection against SARS-CoV-2 in macaques (Science)

Cross-reactive SARS-CoV-2 epitope targeted across donors informs immunogen design (Cell Rep Med)

Chlamydia repurposes the actin-binding protein EPS8 to disassemble epithelial tight junctions and promote infection (Cell Host Microbe)

Human type I IFN deficiency does not impair B cell response to SARS-CoV-2 mRNA vaccination (J Exp Med)

Selective retention of virus-specific tissue-resident T cells in healed skin after recovery from herpes zoster (Nat Comm)

Divergent SARS-CoV-2 variant emerges in white-tailed deer with deer-to-human transmission (Nat Micro)

Chances of finding COVID-virus ancestor ‘almost nil’, say virologists (Nature)

Associations between indoor relative humidity and global COVID-19 outcomes (J R Soc Interface)

The Paxlovid Rebound Study: A Prospective Cohort Study to Evaluate Viral and Symptom Rebound Differences Between Paxlovid and Untreated COVID-19 Participants (medRxiv)

SARS-CoV-2 Genomic Diversity in Households Highlights the Challenges of Sequence-Based Transmission Inference (mSphere)

Effectiveness of a third BNT162b2 mRNA COVID-19 vaccination during pregnancy: a national observational study in Israel (Nat Comm)

T follicular helper cells and the germinal centre are required for memory B cell formation and humoral immunity after ChAdOx1 nCoV-19 vaccination (Cell Rep Med)

Immune correlates analysis of the ENSEMBLE single Ad26.COV2.S dose vaccine efficacy clinical trial (Nat Micro)

Antiviral innate immunity is diminished in the upper respiratory tract of severe COVID-19 patients (medRxiv)

Acute and postacute sequelae associated with SARS-CoV-2 reinfection (Nat Med)

Tecovirimat is effective against human monkeypox virus in vitro at nanomolar concentrations (Nat Micro)

Lifting Universal Masking in Schools – Covid-19 Incidence among Students and Staff (NEJM)

Neutralization of SARS-CoV-2 Omicron sublineages by 4 doses of the original mRNA vaccine (Cell Rep)

Intranasal pediatric parainfluenza virus-vectored SARS-CoV-2 vaccine is protective in macaques (Cell)

Comparative Risk of Myocarditis/Pericarditis Following Second Doses of BNT162b2 and mRNA-1273 Coronavirus Vaccines (JACC)

Nirmatrelvir and the Risk of Post-Acute Sequelae of COVID-19 (medRxiv)

Shared genetic influences between blood analyte levels and risk of severe COVID-19 (Cell Rep)

Can SARS-CoV-2 trigger new onset of autoimmune disease in adults? A case-based review (Heliyon)

Humoral responses against SARS-CoV-2 Omicron BA.2.11, BA.2.12.1 and BA.2.13 from vaccine and BA.1 serum (Cell Discovery)

mRNA bivalent booster enhances neutralization against BA.2.75.2 and BQ.1.1 (bioRxiv)

Humoral responses against SARS-CoV-2 Omicron BA.2.11, BA.2.12.1 and BA.2.13 from vaccine and BA.1 serum (Cell Discovery)

Extensive neutralization against SARS-CoV-2 variants elicited by Omicron-specific subunit vaccine as a heterologous booster (iScience)

Immunogenicity and protective efficacy of a rhesus adenoviral vaccine targeting conserved COVID-19 replication transcription complex (NPJ Vaccines)

Immunogenicity of the BA.5 Bivalent mRNA Vaccine Boosters (bioRxiv)

Antibody responses to Omicron BA.4/BA.5 bivalent mRNA vaccine booster shot (bioRxiv)

Sterilizing immunity: Understanding COVID-19 (Immunity)

Bivalent SARS-CoV-2 mRNA vaccines increase breadth of neutralization and protect against the BA.5 Omicron variant in mice (Nat Med)

Myocarditis after BNT162b2 mRNA Vaccine against Covid-19 in Israel (NEJM)

Heart risks, data gaps fuel debate over COVID-19 boosters for young people (Science)

The Pfizer COVID-19 vaccine doesn’t prevent transmission: Antivax disinformation goes viral again (Science Based Medicine)

Severe COVID-19 outcomes after full vaccination of primary schedule and initial boosters: pooled analysis of national prospective cohort studies of 30 million individuals in England, Northern Ireland, Scotland, and Wales (Lancet)

Human leukocyte antigen alleles associate with COVID-19 vaccine immunogenicity and risk of breakthrough infection (Nat Med)

New vaccine to protect people in the EU and worldwide against dengue (European Medicines Agency)

Risk of Myocarditis and Pericarditis Following Coronavirus Disease 2019 Messenger RNA Vaccination—A Nationwide Study (medRxiv)

Prediction of upcoming global infection burden of influenza seasons after relaxation of public health and social measures during the COVID-19 pandemic: a modelling study (Lancet Glob Health)

Outcomes among confirmed cases and a matched comparison group in the Long-COVID in Scotland study (Nat Comm)

Tolerability and immunogenicity of an intranasally-administered adenovirus-vectored COVID-19 vaccine: An open-label partially-randomised ascending dose phase I trial (eBioMedicine)

Safety, immunogenicity and antibody persistence of a bivalent Beta-containing booster vaccine against COVID-19: a phase 2/3 trial (Nat Med)

Boosting with updated COVID-19 mRNA vaccines (Nat Med)

The neurobiology of long COVID (Neuron)

Seasonality of Common Human Coronaviruses, United States, 2014–2021 (Emerg Inf Dis)

A comparative characterization of SARS-CoV-2-specific T cells induced by mRNA or inactive virus COVID-19 vaccines (Cell Rep Med)

A boost with SARS-CoV-2 BNT162b2 mRNA vaccine elicits strong humoral responses independently of the interval between the first two doses (Cell Rep)

SARS-CoV-2 Omicron variant emerged under immune selection (Nat Micr)