Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization.

The SARS-CoV-2 B.1.617 lineage was identified in October 2020 in India1-5. Since then, it has become dominant in some regions of India and in the UK, and has spread to many other countries6. 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.

Circulating Ubiquitous RNA, A Highly Predictive and Prognostic Biomarker in Hospitalized Coronavirus Disease 2019 (COVID-19) Patients.

BACKGROUND: Approximately 15-30% of hospitalized coronavirus disease 2019 (COVID-19) patients develop acute respiratory distress syndrome, systemic tissue injury, and/or multi-organ failure leading to death in around 45% of cases. There is a clear need for biomarkers that quantify tissue injury, predict clinical outcomes, and guide the clinical management of hospitalized COVID-19 patients. METHODS: We herein report the quantification by droplet-based digital polymerase chain reaction (ddPCR) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNAemia and the plasmatic release of a ubiquitous human intracellular marker, the ribonuclease P (RNase P) in order to evaluate tissue injury and cell lysis in the plasma of 139 COVID-19 hospitalized patients at admission. RESULTS: We confirmed that SARS-CoV-2 RNAemia was associated with clinical severity of COVID-19 patients. In addition, we showed that plasmatic RNase P RNAemia at admission was also highly correlated with disease severity (P < .001) and invasive mechanical ventilation status (P < .001) but not with pulmonary severity. Altogether, these results indicate a consequent cell lysis process in severe and critical patients but not systematically due to lung cell death. Finally, the plasmatic RNase P RNA value was also significantly associated with overall survival. CONCLUSIONS: Viral and ubiquitous blood biomarkers monitored by ddPCR could be useful for the clinical monitoring and the management of hospitalized COVID-19 patients. Moreover, these results could pave the way for new and more personalized circulating biomarkers in COVID-19, and more generally in infectious diseases, specific from each patient organ injury profile.

Severe relapse of SARS-CoV-2 infection in a kidney transplant recipient with negative nasopharyngeal SARS-CoV-2 RT-PCR after rituximab.

Immunocompromised patients may experience prolonged viral shedding after their initial SARS-CoV-2 infection, however, symptomatic relapses after remission currently remain rare. We herein describe a severe COVID-19 relapse case of a kidney transplant recipient (KTR) following rituximab therapy, 3 months after a moderate COVID-19 infection, despite viral clearance after recovery of the first episode. During the clinical relapse, the diagnosis was established on a broncho-alveolar lavage specimen (BAL) by RT-PCR. The infectivity of the BAL sample was confirmed on a cell culture assay. Whole genome sequencing confirmed the presence of an identical stain (Clade 20A). However, it had an acquired G142D mutation and a larger deletion of 3-amino-acids at position 143-145. These mutations located within the N-terminal domain are suggested to play a role in viral entry. The diagnosis of a COVID-19 relapse should be considered in the setting of unexplained persistent fever and/or respiratory symptoms in KTRs (especially for those after rituximab therapy), even in patients with previous negative naso-pharyngeal SARS-CoV-2 PCR.

Review of authorship for COVID-19 research conducted during the 2020 first-wave epidemic in Africa reveals emergence of promising African biomedical research and persisting asymmetry of international collaborations.

OBJECTIVES: The contribution of African authors to the biomedical literature is small. We evaluated the African and non-African scientific production published in the international literature on the COVID-19 in Africa during the first year of the epidemic (2020). METHODS: Papers on COVID-19 in Africa were extracted from the Medline (PubMed) database for bibliometric analysis including the proportions of three leading and last authors by study type, study country, authors' and laboratories/institutions' countries of affiliation and journal ranking. RESULTS: A total of 160 articles fulfilling the inclusion criteria were analysed. The majority (91.3%) was produced by half (53.7%) of African countries, with important regional disparities, and generally without sources of funding mentioned. The majority (>85.0) of authors in lead positions (first, second, third and last authors) were Africans. Only a small number (8.7%) of studies on COVID-19 in Africa were carried out by laboratories not on the African continent (mainly Europe, USA and China) and generally received funding. The last and first authors were more frequently of non-African origin in journals with an Impact Factor ranking ≥1, and more frequently of African origin in journals with a lower ranking (< 1). The first and last non-African authors tended to report their studies in high ranking ≥1 journals. CONCLUSIONS: Our study demonstrates that the emergence of promising African research capable of publishing in indexed but low-impact factor medical journals and reveals the persistence of a North-South asymmetry in international cooperation in biomedical research with Africa.

Analytical performance of the point-of-care BIOSYNEX COVID-19 Ag BSS for the detection of SARS-CoV-2 nucleocapsid protein in nasopharyngeal swabs: a prospective field evaluation during the COVID-19 third wave in France.

BACKGROUND: The accuracy and reliability of rapid diagnostic tests are critical for monitoring and diagnosing SARS-CoV-2 infection in the general population. This study aimed to evaluate the analytical performance of the BIOSYNEX COVID-19 Ag BSS (Biosynex Swiss SA, Fribourg, Switzerland) antigen rapid diagnostic test (BIOSYNEX Ag-RDT), which targets the SARS-CoV-2 N-nucleocapsid protein for the diagnosis of COVID-19. The Ag-RDT was compared with a real-time RT-PCR (rtRT-PCR) as gold standard for performance measurement. METHODS: Two nasopharyngeal flocked swabs were prospectively collected simultaneously in March and April 2021 from 967 individuals aged ≥ 18 years tested for SARS-CoV-2 in two private laboratories, Paris, France. RESULTS: Overall, the Ag-RDT demonstrated high sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of 81.8%, 99.6%, 96.6%, and 97.5%, respectively. The agreement (97.0%), reliability assessed using Cohen's κ-coefficient (0.87), and accuracy evaluated using Youden index (J) (81.6%) in detecting SARS-CoV-2 were high. The analytical performance of the Ag-RDT remained high when there was significant viral shedding (i.e., N gene Ct values ≤ 33 on reference RT-PCR). The sensitivity was only 55.2% in case of low or very low viral excretion (Ct > 33). CONCLUSIONS: The BIOSYNEX Ag-RDT is a promising, potentially simple diagnostic tool, especially in symptomatic COVID-19 patients with substantial viral excretion in the nasopharynx.

Highly Sensitive Quantification of Plasma Severe Acute Respiratory Syndrome Coronavirus 2 RNA Sheds Light on its Potential Clinical Value.

BACKGROUND: Coronavirus disease 2019 (COVID-19) is a global public health problem that has already caused more than 662 000 deaths worldwide. Although the clinical manifestations of COVID-19 are dominated by respiratory symptoms, some patients present other severe damage such as cardiovascular, renal and liver injury, and/or multiple organ failure, suggesting a spread of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in blood. Recent ultrasensitive polymerase chain reaction (PCR) technology now allows absolute quantification of nucleic acids in plasma. We intend to use the droplet-based digital PCR technology to obtain sensitive detection and precise quantification of plasma SARS-CoV-2 viral load (SARS-CoV-2 RNAemia) in hospitalized COVID-19 patients. METHODS: Fifty-eight consecutive COVID-19 patients with pneumonia 8 to 12 days after onset of symptoms and 12 healthy controls were analyzed. Disease severity was categorized as mild to moderate in 17 patients, severe in 16, and critical in 26. Plasma SARS-CoV-2 RNAemia was quantified by droplet digital Crystal Digital PCR next-generation technology (Stilla Technologies, Villejuif, France). RESULTS: Overall, SARS-CoV-2 RNAemia was detected in 43 (74.1%) patients. Prevalence of positive SARS-CoV-2 RNAemia correlated with disease severity, ranging from 53% in mild-to-moderate patients to 88% in critically ill patients (P = .036). Levels of SARS-CoV-2 RNAemia were associated with severity (P = .035). Among 9 patients who experienced clinical deterioration during follow-up, 8 had positive SARS-CoV-2 RNAemia at baseline, whereas only 1 critical patient with undetectable SARS-CoV-2 RNAemia at the time of analysis died at day 27. CONCLUSION: SARS-CoV-2 RNAemia measured by droplet-based digital PCR constitutes a promising prognosis biomarker in COVID-19 patients.

Performances of the VitaPCR™ SARS-CoV-2 Assay during the second wave of the COVID-19 epidemic in France.

To assess the practicability (usability and satisfaction) and analytical performances of the VitaPCR™ SARS-CoV-2 Assay (Credo Diagnostics Biomedical Pte. Ltd.), a rapid point-of-care nucleic acid amplification test (NAAT), by reference to real-time reverse-transcription polymerase chain reaction (rRT-PCR) for respiratory viruses. The practicability of the VitaPCR™ Assay and Instrument was assessed from usability evaluation and a satisfaction questionnaire. Nasopharyngeal swabs were collected from 239 patients with coronavirus disease 2019 (COVID-19)-like illness during the second epidemic wave, in Paris, France. Overall, the usability of the VitaPCR™ Instrument was high. The satisfaction questionnaire indicated a high appreciation of the VitaPCR™ NAAT mainly for the short duration of analysis in only 20 min. A total of 140 and 99 samples were positive and negative for SARS-CoV-2 RNA by rRT-PCR, respectively. In the event of significant viral load (i.e., N gene Ct values 33), the platform's analytical performances dropped significantly, with lower sensitivity, concordance, and accuracy, while its specificity remained high. The VitaPCR™ SARS-CoV-2 Assay is an accurate rapid point-of-care NAAT, suitable for clinical practice for the rapid diagnosis of COVID-19, especially in patients with COVID-19-suspected symptoms.

Unexpected high frequency of unspecific reactivities by testing pre-epidemic blood specimens from Europe and Africa with SARS-CoV-2 IgG-IgM antibody rapid tests points to IgM as the Achilles heel.

We aimed to evaluate the rates of false-positive test results of three rapid diagnostic tests (RDTs) for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-specific immunoglobulin G (IgG) and IgM detection. Two serum panels from patients hospitalized in Paris, France, and from patients living in Bangui, Central African Republic, acquired before the 2019 COVID-19 outbreak, were tested by 3 CE IVD-labeled RDTs for SARS-CoV-2 serology (BIOSYNEX® COVID-19 BSS [IgG/IgM]; SIENNA™ COVID-19 IgG/IgM Rapid Test Cassette; NG-Test® IgG-IgM COVID-19). Detectable IgG or IgM reactivities could be observed in 31 (3.43%) of the 902 IgG and IgM bands of the 3 RDTs used with all pre-epidemic sera. The frequencies of IgG/IgM reactivities were similar for European (3.20%) and African (3.55%) sera. IgM reactivities were observed in 9 European and 14 African sera, while IgG reactivity was observed in only 1 African serum (15.1% vs. 0.66%). The test NG-Test® IgG-IgM COVID-19 showed the highest rates of IgG or IgM reactivities (6.12% [18/294]), while the test BIOSYNEX® COVID-19 BSS (IgG/IgM) showed the lowest rate (1.36% [4/294]). Some combinations of 2 RDTs in series allowed decreasing significantly the risk of false-positive test results. Our observations point to the risk of false-positive reactivities when using currently available RDT for SARS-CoV-2 serological screening, especially for the IgM band, even if the test is CE IVD-labeled and approved by national health authorities, and provide the rational basis for confirmatory testing by another RDT in case of positive initial screening.

HPV circulating tumoral DNA quantification by droplet-based digital PCR: A promising predictive and prognostic biomarker for HPV-associated oropharyngeal cancers.

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.

Comparison of practicability and effectiveness between unassisted HIV self-testing and directly assisted HIV self-testing in the Democratic Republic of the Congo: a randomized feasibility trial.

BACKGROUND: HIV self-testing (HIVST) can be performed using directly assisted and unassisted approaches in facilities or communities to reach different populations. The aim of this study was to compare the practicability and effectiveness of the two delivery approaches for HIVST, unassisted HIVST (UH) and directly assisted HIVST (DAH), in the field setting of Kisangani, the Democratic Republic of the Congo (DRC). METHODS: A randomized (1:1), non-blinded, non-inferiority trial using a blood-based and facility-based HIVST method was carried out in four facilities in Kisangani, the DRC, targeting populations at high risk for HIV infection. The primary outcome was the difference in the practicability of the HIV self-test between the two arms. Practicability was defined as successfully performing the test and correctly interpreting the result. Requests for assistance, positivity rate, linkage to care, and willingness to buy an HIV self-test kit constituted the secondary outcomes for HIVST effectiveness. The adjusted risk ratios (aRRs) were calculated using Poisson regression. RESULTS: The rate of successfully performing the test was same (93.2%) in the UH and DAH arms. The rate of correctly interpreting the results was 86.9% in the UH arm versus 93.2% in the DAH arm, for a difference of - 6.3%. After the follow-up 72 h later, participants in the UH arm had a significantly lower chance of correctly interpreting the test results than those in the DAH arm (aRR: 0.60; P = 0.019). Although the positivity rate was 3.4% among the participants in the DAH arm and 1.7% among those in the UH arm, no significant differences were found between the two arms in the positivity rate, requests for assistance, and linkage to care. Willingness to buy an HIV self-test was higher in the UH arm than in the DAH arm (92.3% versus 74.1%; aRR: 4.20; P < 0.001). CONCLUSION: The results of this study indicate that UH is as practicable and effective as DAH among individuals at high risk for HIV infection in Kisangani, the DRC. However, additional support tools need to be assessed to improve the interpretation of the self-test results when using the UH approach. TRIAL REGISTRATION: PACTR201904546865585. Registered 03 April 2019 - Retrospectively registered, https://pactr.samrc.ac.za/TrialDisplay.aspx?TrialID=6032.