The SARS-CoV-2 B.1.617 lineage was identified in October 2020 in India.sup.1-5. Since then, it has become dominant in some regions of India and in the UK, and has spread to many other ...countries.sup.6. The lineage includes three main subtypes (B1.617.1, B.1.617.2 and B.1.617.3), which contain diverse mutations in the N-terminal domain (NTD) and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein that may increase the immune evasion potential of these variants. B.1.617.2--also termed the Delta variant--is believed to spread faster than other variants. Here we isolated an infectious strain of the Delta variant from an individual with COVID-19 who had returned to France from India. We examined the sensitivity of this strain to monoclonal antibodies and to antibodies present in sera from individuals who had recovered from COVID-19 (hereafter referred to as convalescent individuals) or who had received a COVID-19 vaccine, and then compared this strain with other strains of SARS-CoV-2. The Delta variant was resistant to neutralization by some anti-NTD and anti-RBD monoclonal antibodies, including bamlanivimab, and these antibodies showed impaired binding to the spike protein. Sera collected from convalescent individuals up to 12 months after the onset of symptoms were fourfold less potent against the Delta variant relative to the Alpha variant (B.1.1.7). Sera from individuals who had received one dose of the Pfizer or the AstraZeneca vaccine had a barely discernible inhibitory effect on the Delta variant. Administration of two doses of the vaccine generated a neutralizing response in 95% of individuals, with titres three- to fivefold lower against the Delta variant than against the Alpha variant. Thus, the spread of the Delta variant is associated with an escape from antibodies that target non-RBD and RBD epitopes of the spike protein.
Coronavirus disease 2019 (COVID-19) is characterized by distinct patterns of disease progression that suggest diverse host immune responses. We performed an integrated immune analysis on a cohort of ...50 COVID-19 patients with various disease severity. A distinct phenotype was observed in severe and critical patients, consisting of a highly impaired interferon (IFN) type I response (characterized by no IFN-β and low IFN-α production and activity), which was associated with a persistent blood viral load and an exacerbated inflammatory response. Inflammation was partially driven by the transcriptional factor nuclear factor-κB and characterized by increased tumor necrosis factor-α and interleukin-6 production and signaling. These data suggest that type I IFN deficiency in the blood could be a hallmark of severe COVID-19 and provide a rationale for combined therapeutic approaches.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) B.1.1.7 and B.1.351 variants were first identified in the United Kingdom and South Africa, respectively, and have since spread to many ...countries. These variants harboring diverse mutations in the gene encoding the spike protein raise important concerns about their immune evasion potential. Here, we isolated infectious B.1.1.7 and B.1.351 strains from acutely infected individuals. We examined sensitivity of the two variants to SARS-CoV-2 antibodies present in sera and nasal swabs from individuals infected with previously circulating strains or who were recently vaccinated, in comparison with a D614G reference virus. We utilized a new rapid neutralization assay, based on reporter cells that become positive for GFP after overnight infection. Sera from 58 convalescent individuals collected up to 9 months after symptoms, similarly neutralized B.1.1.7 and D614G. In contrast, after 9 months, convalescent sera had a mean sixfold reduction in neutralizing titers, and 40% of the samples lacked any activity against B.1.351. Sera from 19 individuals vaccinated twice with Pfizer Cominarty, longitudinally tested up to 6 weeks after vaccination, were similarly potent against B.1.1.7 but less efficacious against B.1.351, when compared to D614G. Neutralizing titers increased after the second vaccine dose, but remained 14-fold lower against B.1.351. In contrast, sera from convalescent or vaccinated individuals similarly bound the three spike proteins in a flow cytometry-based serological assay. Neutralizing antibodies were rarely detected in nasal swabs from vaccinees. Thus, faster-spreading SARS-CoV-2 variants acquired a partial resistance to neutralizing antibodies generated by natural infection or vaccination, which was most frequently detected in individuals with low antibody levels. Our results indicate that B1.351, but not B.1.1.7, may increase the risk of infection in immunized individuals.
The severe acute respiratory syndrome coronavirus 2 Omicron BA.1 sublineage has been supplanted in many countries by the BA.2 sublineage. BA.2 differs from BA.1 by about 21 mutations in its spike. In ...this study, we first compared the sensitivity of BA.1 and BA.2 to neutralization by nine therapeutic monoclonal antibodies (mAbs). In contrast to BA.1, BA.2 was sensitive to cilgavimab, partly inhibited by imdevimab and resistant to adintrevimab and sotrovimab. We then analyzed sera from 29 immunocompromised individuals up to 1 month after administration of Ronapreve (casirivimab and imdevimab) and/or Evusheld (cilgavimab and tixagevimab) antibody cocktails. All treated individuals displayed elevated antibody levels in their sera, which efficiently neutralized the Delta variant. Sera from Ronapreve recipients did not neutralize BA.1 and weakly inhibited BA.2. Neutralization of BA.1 and BA.2 was detected in 19 and 29 out of 29 Evusheld recipients, respectively. As compared to the Delta variant, neutralizing titers were more markedly decreased against BA.1 (344-fold) than BA.2 (nine-fold). We further report four breakthrough Omicron infections among the 29 individuals, indicating that antibody treatment did not fully prevent infection. Collectively, BA.1 and BA.2 exhibit noticeable differences in their sensitivity to therapeutic mAbs. Anti-Omicron neutralizing activity of Ronapreve and, to a lesser extent, that of Evusheld is reduced in patients' sera.
Convergent evolution of SARS-CoV-2 Omicron BA.2, BA.4, and BA.5 lineages has led to the emergence of several new subvariants, including BA.2.75.2, BA.4.6. and BQ.1.1. The subvariant BQ.1.1 became ...predominant in many countries in December 2022. The subvariants carry an additional and often redundant set of mutations in the spike, likely responsible for increased transmissibility and immune evasion. Here, we established a viral amplification procedure to easily isolate Omicron strains. We examined their sensitivity to 6 therapeutic monoclonal antibodies (mAbs) and to 72 sera from Pfizer BNT162b2-vaccinated individuals, with or without BA.1/BA.2 or BA.5 breakthrough infection. Ronapreve (Casirivimab and Imdevimab) and Evusheld (Cilgavimab and Tixagevimab) lose antiviral efficacy against BA.2.75.2 and BQ.1.1, whereas Xevudy (Sotrovimab) remaine weakly active. BQ.1.1 is also resistant to Bebtelovimab. Neutralizing titers in triply vaccinated individuals are low to undetectable against BQ.1.1 and BA.2.75.2, 4 months after boosting. A BA.1/BA.2 breakthrough infection increases these titers, which remains about 18-fold lower against BA.2.75.2 and BQ.1.1, than against BA.1. Reciprocally, a BA.5 breakthrough infection increases more efficiently neutralization against BA.5 and BQ.1.1 than against BA.2.75.2. Thus, the evolution trajectory of novel Omicron subvariants facilitates their spread in immunized populations and raises concerns about the efficacy of most available mAbs.
•There is an urgent need for independent validation of available antigen-detecting rapid diagnostic tests designed for direct detection of SARS-CoV-2 viral proteins produced by replicating virus in ...respiratory secretions.•The SIENNA™ COVID-19 Antigen test demonstrates excellent analytical performances for viral loads ≤33 Ct, corresponding to situations of symptomatic COVID-19 and/or proven contagiousness.•The SIENNA™ COVID-19 Antigen test can be recommended for routine clinical use in most diagnostic indications of SARS-CoV-2 infection.
We herein assessed the analytical performances of the antigen-rapid diagnostic test (Ag-RDT) SIENNA™ COVID-19 Antigen Rapid Test Cassette (Nasopharyngeal Swab) (Salofa Oy, Salo, Finland), targeting the SARS-CoV-2 N nucleocapsid protein, for the diagnosis of COVID-19 in hospitalized patients with suspected SARS-CoV-2 infection, by reference to real-time RT-PCR (rRT-PCR).
Nasopharyngeal swabs were collected from patients with COVID-19-like illness during the second epidemic wave in Paris, France, among which 100 and 50 were positive and negative for SARS-CoV-2 RNA, respectively.
Overall, the Ag-RDT showed high sensitivity, specificity, positive and negative predictive values of 90.0%, 100.0%, 100.0% and 98.1%, respectively, as well as high or almost perfect agreement (93.3%), reliability assessed by Cohen’s κ coefficient (0.86), and accuracy assessed by Youden’s J index (90%) to detect SARS-CoV-2. The analytical performances of the Ag-RDT remained high in the event of significant viral excretion (i.e., N gene Ct values ≤33 by reference rtRT-PCR), while the sensitivity of the Ag-RDT dropped to 69.6% with low or very low viral shedding (Ct > 33).
The SIENNA™ Ag-RDT presents excellent analytical performances for viral loads ≤33 Ct, classically corresponding to situations of symptomatic COVID-19 and/or proven contagiousness.
Virus infection is sensed by pattern recognition receptors (PRRs) detecting virus nucleic acids and initiating an innate immune response. DNA-dependent protein kinase (DNA-PK) is a PRR that binds ...cytosolic DNA and is antagonized by vaccinia virus (VACV) protein C16. Here, VACV protein C4 is also shown to antagonize DNA-PK by binding to Ku and blocking Ku binding to DNA, leading to a reduced production of cytokines and chemokines in vivo and a diminished recruitment of inflammatory cells. C4 and C16 share redundancy in that a double deletion virus has reduced virulence not seen with single deletion viruses following intradermal infection. However, non-redundant functions exist because both single deletion viruses display attenuated virulence compared to wild-type VACV after intranasal infection. It is notable that VACV expresses two proteins to antagonize DNA-PK, but it is not known to target other DNA sensors, emphasizing the importance of this PRR in the response to infection in vivo.
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•DNA-PK is a pattern recognition receptor that binds cytosolic DNA•Vaccinia virus proteins C4 and C16 antagonize DNA-PK by blocking DNA binding•C4 and C16 inhibit IRF3 signaling, cytokine production, and immune cell recruitment•C4 and C16 share redundant and non-redundant functions in vivo
DNA-PK is a pattern recognition receptor (PRR) that binds cytosolic DNA and stimulates IRF3 signaling. Scutts et al. show that vaccinia virus antagonizes this DNA sensor with two proteins, C4 and C16, which both block DNA binding.
We aimed to determine whether pretherapeutic assessment of HPV circulating tumoral DNA (HPV ctDNA) by droplet‐based digital PCR (ddPCR) could constitute a predictive and prognostic biomarker for ...HPV‐associated oropharyngeal squamous cell carcinoma (OPSCC). A mono‐institutional prospective biomarker study on 66 patients with p16+/HPV16‐positive oropharyngeal squamous cell carcinoma (OPSCC) was conducted in European Georges Pompidou Hospital, Paris, France. Blood samples were collected at the time of diagnosis before any treatment. Optimized digital PCR assays were used to quantify HPV16 ctDNA. Forty‐seven (71%) patients showed a positive pretherapeutic HPV ctDNA at time of diagnosis. Interestingly, the quantity of HPV16 ctDNA at baseline, as assessed by ddPCR, was significantly correlated with the T/N/M status or OPSCC stages according to the 2018 new staging criteria for high‐risk human papillomavirus (HR HPV) related OPSCC from American Joint Committee on Cancer (AJCC). Moreover, all recurrences and the majority (83%) of death reported events occurred in patients with positive HPV16 ctDNA at baseline. Finally, when posttreatment blood samples were available (n = 6), the kinetic of pretreatment/posttreatment HPV16 ctDNA was clearly associated with treatment success or failure. HPV ctDNA monitoring by ddPCR could constitute a useful and noninvasive dynamic biomarker to select HR HPV‐related OPSCC patients eligible for potential treatment de‐escalation and to monitor treatment response.
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Circulating tumor DNA represents a tantalizing avenue for non‐invasive diagnostic and prognostic testing. Here, the authors investigated whether HPV16 ctDNA correlated with disease stage and outcome in oropharyngeal squamous cell carcinoma (OPSCC). Using digital PCR, they tested 66 blood samples collected at diagnosis, before treatment began. 71% of the patients tested positive for HPV ctDNA, and those patients tended to have more advanced disease than those with undetectable HPV ctDNA. Outcomes also appeared linked with the marker, as 83% of deaths occurred among patients with HPV ctDNA. Finally, post‐treatment assessment of ctDNA levels in 6 patients correlated with treatment response.
Highlights • Vaccinia virus encodes several proteins that inhibit programmed cell death. • These are related to cellular proteins from which they may have evolved. • Each is made early during ...infection and has a different mechanism of action. • These proteins affects virus virulence and the host response to infection. • Their deletion may enhance vaccinia potency as a vaccine or oncolytic agent.
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