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1.
BMJ Open ; 13(5): e064058, 2023 05 25.
Article in English | MEDLINE | ID: covidwho-20235059

ABSTRACT

INTRODUCTION: In the COVID-19 pandemic, healthcare workers (HCWs) were at high risk of infection due to their exposure to COVID infections. HCWs were the backbone of our healthcare response to this pandemic; every HCW withdrawn or lost due to infection had a substantial impact on our capacity to deliver care. Primary prevention was a key approach to reduce infection. Vitamin D insufficiency is highly prevalent in Canadians and worldwide. Vitamin D supplementation has been shown to significantly decrease the risk of respiratory infections. Whether this risk reduction would apply to COVID-19 infections remained to be determined. This study aimed to determine the impact of high-dose vitamin D supplementation on incidence of laboratory-confirmed COVID-19 infection rate and severity in HCWs working in high COVID incidence areas. METHODS AND ANALYSIS: PROTECT was a triple-blind, placebo-controlled, parallel-group multicentre trial of vitamin D supplementation in HCWs. Participants were randomly allocated in a 1:1 ratio in variable block size to intervention (one oral loading dose of 100 000 IU vitamin D3+10 000 IU weekly vitamin D3) or control (identical placebo loading dose+weekly placebo). The primary outcome was the incidence of laboratory-confirmed COVID-19 infection, documented by RT-qPCR on salivary (or nasopharyngeal) specimens obtained for screening or diagnostic purposes, as well as self-obtained salivary specimens and COVID-19 seroconversion at endpoint. Secondary outcomes included disease severity; duration of COVID-19-related symptoms; COVID-19 seroconversion documented at endpoint; duration of work absenteeism; duration of unemployment support; and adverse health events. The trial was terminated prematurely, due to recruitment difficulty. ETHICS AND DISSEMINATION: This study involves human participants and was approved by the Research Ethics Board (REB) of the Centre hospitalier universitaire (CHU) Sainte-Justine serving as central committee for participating institutions (#MP-21-2021-3044). Participants provided written informed consent to participate in the study before taking part. Results are being disseminated to the medical community via national/international conferences and publications in peer-reviewed journals. TRIAL REGISTRATION NUMBER: https://clinicaltrials.gov/ct2/show/NCT04483635.


Subject(s)
COVID-19 , Humans , SARS-CoV-2 , Pandemics/prevention & control , Canada/epidemiology , Vitamin D/therapeutic use , Vitamins/therapeutic use , Treatment Outcome , Randomized Controlled Trials as Topic , Multicenter Studies as Topic
2.
Antimicrob Steward Healthc Epidemiol ; 3(1): e45, 2023.
Article in English | MEDLINE | ID: covidwho-2282217

ABSTRACT

Objectives: We evaluated the added value of infection control-guided, on demand, and locally performed severe acute respiratory coronavirus virus 2 (SARS-CoV-2) genomic sequencing to support outbreak investigation and control in acute-care settings. Design and setting: This 18-month prospective molecular epidemiology study was conducted at a tertiary-care hospital in Montreal, Canada. When nosocomial transmission was suspected by local infection control, viral genomic sequencing was performed locally for all putative outbreak cases. Molecular and conventional epidemiology data were correlated on a just-in-time basis to improve understanding of coronavirus disease 2019 (COVID-19) transmission and reinforce or adapt control measures. Results: Between April 2020 and October 2021, 6 outbreaks including 59 nosocomial infections (per the epidemiological definition) were investigated. Genomic data supported 7 distinct transmission clusters involving 6 patients and 26 healthcare workers. We identified multiple distinct modes of transmission, which led to reinforcement and adaptation of infection control measures. Molecular epidemiology data also refuted (n = 14) suspected transmission events in favor of community acquired but institutionally clustered cases. Conclusion: SARS-CoV-2 genomic sequencing can refute or strengthen transmission hypotheses from conventional nosocomial epidemiological investigations, and guide implementation of setting-specific control strategies. Our study represents a template for prospective, on site, outbreak-focused SARS-CoV-2 sequencing. This approach may become increasingly relevant in a COVID-19 endemic state where systematic sequencing within centralized surveillance programs is not available. Trial registration: clinicaltrials.gov identifier: NCT05411562.

3.
Cell Rep Med ; 4(3): 100955, 2023 03 21.
Article in English | MEDLINE | ID: covidwho-2235229

ABSTRACT

Cellular immune defects associated with suboptimal responses to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mRNA vaccination in people receiving hemodialysis (HD) are poorly understood. We longitudinally analyze antibody, B cell, CD4+, and CD8+ T cell vaccine responses in 27 HD patients and 26 low-risk control individuals (CIs). The first two doses elicit weaker B cell and CD8+ T cell responses in HD than in CI, while CD4+ T cell responses are quantitatively similar. In HD, a third dose robustly boosts B cell responses, leads to convergent CD8+ T cell responses, and enhances comparatively more T helper (TH) immunity. Unsupervised clustering of single-cell features reveals phenotypic and functional shifts over time and between cohorts. The third dose attenuates some features of TH cells in HD (tumor necrosis factor alpha [TNFα]/interleukin [IL]-2 skewing), while others (CCR6, CXCR6, programmed cell death protein 1 [PD-1], and HLA-DR overexpression) persist. Therefore, a third vaccine dose is critical to achieving robust multifaceted immunity in hemodialysis patients, although some distinct TH characteristics endure.


Subject(s)
COVID-19 Vaccines , COVID-19 , Humans , SARS-CoV-2/genetics , COVID-19/prevention & control , CD4-Positive T-Lymphocytes
4.
iScience ; 26(1): 105904, 2023 Jan 20.
Article in English | MEDLINE | ID: covidwho-2210554

ABSTRACT

Spacing the first two doses of SARS-CoV-2 mRNA vaccines beyond 3-4 weeks raised initial concerns about vaccine efficacy. While studies have since shown that long-interval regimens induce robust antibody responses, their impact on B and T cell immunity is poorly known. Here, we compare SARS-CoV-2 naive donors B and T cell responses to two mRNA vaccine doses administered 3-4 versus 16 weeks apart. After boost, the longer interval results in a higher magnitude and a more mature phenotype of RBD-specific B cells. While the two geographically distinct cohorts present quantitative and qualitative differences in T cell responses at baseline and after priming, the second dose led to convergent features with overall similar magnitude, phenotype, and function of CD4+ and CD8+ T cell responses at post-boost memory time points. Therefore, compared to standard regimens, a 16-week interval has a favorable impact on the B cell compartment but minimally affects T cell immunity.

5.
Cell Rep ; 42(1): 111998, 2023 01 31.
Article in English | MEDLINE | ID: covidwho-2177163

ABSTRACT

Several severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron subvariants have recently emerged, becoming the dominant circulating strains in many countries. These variants contain a large number of mutations in their spike glycoprotein, raising concerns about vaccine efficacy. In this study, we evaluate the ability of plasma from a cohort of individuals that received three doses of mRNA vaccine to recognize and neutralize these Omicron subvariant spikes. We observed that BA.4/5 and BQ.1.1 spikes are markedly less recognized and neutralized compared with the D614G and other Omicron subvariant spikes tested. Also, individuals who have been infected before or after vaccination present better humoral responses than SARS-CoV-2-naive vaccinated individuals, thus indicating that hybrid immunity generates better humoral responses against these subvariants.


Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , COVID-19/prevention & control , Vaccines, Synthetic , Mutation , Antibodies, Viral , Antibodies, Neutralizing
6.
Trials ; 23(1): 1019, 2022 Dec 16.
Article in English | MEDLINE | ID: covidwho-2196408

ABSTRACT

BACKGROUND: The study objectives were to ascertain the efficacy of vitamin D supplementation in rapidly increasing serum vitamin D and of implementation of a hybrid (virtual and in-person) trial. METHODS: In a randomized triple-blind controlled trial, healthcare workers were allocated to receive an oral bolus of 100,000 IU with 10,000 IU/week of vitamin D3 or placebo. The co-primary outcomes were the change from baseline in serum 25-hydroxyvitamin D [(Δ) 25(OH)D] and proportion with vitamin D sufficiency (25(OH)D ≥ 75 nmol/L), at endpoint. Adherence to supplements and procedures as well as adverse event rates were documented. RESULTS: Thirty-four (19 intervention, 15 control) subjects were randomized, with 28 (41%) virtual visits. After 44.78 ± 11.00 days from baseline, a significant adjusted group difference of 44.2 (34.7, 53.8) nmol/L was observed in the Δ 25(OH)D (95% CI) in favor of supplementation; 77.8% of intervention, and 13.3% of control, patients were vitamin D sufficient (OR:6.11, 95% CI:1.6, 22.9). The adherence to intervention was 94.7% in the intervention and 100% in the control groups. Irrespective of visit type, high adherence was observed in sampling procedures and completion of fortnightly online questionnaire. No adverse events attributable to vitamin D were reported. CONCLUSION: The vitamin D supplementation rapidly and safely raised 25(OH)D levels to sufficient levels for a biological effect. Similarly high adherence to study procedures was observed with virtual and in-person participation. TRIAL REGISTRATION: This trial was registered at https://clinicaltrials.gov on July 23, 2020 (# NCT04483635 ).


Subject(s)
Vitamin D Deficiency , Vitamin D , Humans , Double-Blind Method , Calcifediol , Cholecalciferol/adverse effects , Vitamins , Dietary Supplements/adverse effects , Patient Care Team , Vitamin D Deficiency/diagnosis , Vitamin D Deficiency/drug therapy
7.
Vaccines (Basel) ; 11(2)2023 Jan 21.
Article in English | MEDLINE | ID: covidwho-2200989

ABSTRACT

The Omicron BQ.1.1 variant is now the major SARS-CoV-2 circulating strain in many countries. Because of the many mutations present in its Spike glycoprotein, this variant is resistant to humoral responses elicited by monovalent mRNA vaccines. With the goal to improve immune responses against Omicron subvariants, bivalent mRNA vaccines have recently been approved in several countries. In this study, we measure the capacity of plasma from vaccinated individuals, before and after a fourth dose of mono- or bivalent mRNA vaccine, to recognize and neutralize the ancestral (D614G) and the BQ.1.1 Spikes. Before and after the fourth dose, we observe a significantly better recognition and neutralization of the ancestral Spike. We also observe that fourth-dose vaccinated individuals who have been recently infected better recognize and neutralize the BQ.1.1 Spike, independently of the mRNA vaccine used, than donors who have never been infected or have an older infection. Our study supports that hybrid immunity, generated by vaccination and a recent infection, induces higher humoral responses than vaccination alone, independently of the mRNA vaccine used.

8.
Cell Rep ; 41(4): 111554, 2022 10 25.
Article in English | MEDLINE | ID: covidwho-2104502

ABSTRACT

Due to the recrudescence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections worldwide, mainly caused by the Omicron variant of concern (VOC) and its sub-lineages, several jurisdictions are administering an mRNA vaccine boost. Here, we analyze humoral responses induced after the second and third doses of an mRNA vaccine in naive and previously infected donors who received their second dose with an extended 16-week interval. We observe that the extended interval elicits robust humoral responses against VOCs, but this response is significantly diminished 4 months after the second dose. Administering a boost to these individuals brings back the humoral responses to the same levels obtained after the extended second dose. Interestingly, we observe that administering a boost to individuals that initially received a short 3- to 4-week regimen elicits humoral responses similar to those observed in the long interval regimen. Nevertheless, humoral responses elicited by the boost in naive individuals do not reach those present in previously infected vaccinated individuals.


Subject(s)
COVID-19 , Viral Vaccines , Humans , SARS-CoV-2 , BNT162 Vaccine , COVID-19/prevention & control , Antibodies, Viral , COVID-19 Vaccines , Vaccination
9.
J Int AIDS Soc ; 25(9): e25994, 2022 09.
Article in English | MEDLINE | ID: covidwho-2085049

ABSTRACT

INTRODUCTION: Men who have sex with men (MSM) and people who inject drugs (PWID) are disproportionately impacted by the HIV epidemic in Canada. Having the second-highest provincial diagnosis rate, an improved understanding of the epidemic among these populations in Québec could aid ongoing elimination efforts. We estimated HIV incidence and other epidemic indicators among MSM and PWID in Montréal and across Québec using a back-calculation model synthesizing surveillance data. METHODS: We developed a deterministic, compartmental mathematical model stratified by age, HIV status and disease progression, and clinical care stages. Using AIDS and HIV diagnoses data, including self-reported time since the last negative test and laboratory results of CD4 cell count at diagnosis, we estimated HIV incidence in each population over 1975-2020 by modelling a cubic M-spline. The prevalence, undiagnosed fraction, fraction diagnosed that started antiretroviral treatment (ART) and median time to diagnosis were also estimated. Since the COVID-19 pandemic disrupted testing, we excluded 2020 data and explored this in sensitivity analyses. RESULTS: HIV incidence in all populations peaked early in the epidemic. In 2020, an estimated 97 (95% CrI: 33-227) and 266 (95% CrI: 103-508) HIV acquisitions occurred among MSM in Montréal and Québec, respectively. Among PWID, we estimated 2 (95% CrI: 0-14) and 6 (95% CrI: 1-26) HIV acquisitions in those same regions. With 2020 data, unless testing rates were reduced by 50%, these estimates decreased, except among Québec PWID, whose increased. Among all, the median time to diagnosis shortened to <2 years before 2020 and the undiagnosed fraction decreased to <10%. This fraction was higher in younger MSM, with 22% of 15-24 year-olds living with HIV in Montréal (95% CrI: 9-39%) and 31% in Québec (95% CrI: 17-48%) undiagnosed by 2020 year-end. Finally, ART access neared 100% in all diagnosed populations. CONCLUSIONS: HIV incidence has drastically decreased in MSM and PWID across Québec, alongside significant improvements in diagnosis and treatment coverage-and the 2013 introduction of pre-exposure prophylaxis. Despite this, HIV transmission continued. Effective efforts to halt this transmission and rapidly diagnose people who acquired HIV, especially among younger MSM, are needed to achieve elimination. Further, as the impacts of the COVID-19 pandemic on HIV transmission are understood, increased efforts may be needed to overcome these.


Subject(s)
COVID-19 , HIV Infections , Sexual and Gender Minorities , Substance Abuse, Intravenous , COVID-19/epidemiology , HIV Infections/diagnosis , HIV Infections/drug therapy , HIV Infections/epidemiology , Homosexuality, Male , Humans , Male , Models, Theoretical , Pandemics , Quebec/epidemiology , Substance Abuse, Intravenous/epidemiology
10.
Cell reports ; 2022.
Article in English | EuropePMC | ID: covidwho-2046858

ABSTRACT

Due to the recrudescence of SARS-CoV-2 infections worldwide, mainly caused by Omicron variant of concern (VOC) and its sub-lineages, several jurisdictions are administering a mRNA vaccine boost. Here, we analyze humoral responses induced after the second and third doses of mRNA vaccine in naïve and previously-infected donors who received their second dose with an extended 16-week interval. We observe that the extended interval elicits robust humoral responses against VOCs, but this response is significantly diminished 4 months after the second dose. Administering a boost to these individuals brings back the humoral responses to the same levels obtained after the extended second dose. Interestingly, we observe that administering a boost to individuals that initially received a short 3-4 weeks regimen elicits humoral responses similar to those observed in the long interval regimen. Nevertheless, humoral responses elicited by the boost in naïve individuals do not reach those present in previously-infected vaccinated individuals. Graphical In this study, Tauzin et al. report that the third dose of SARS-CoV-2 mRNA vaccine elicits strong humoral responses against VOCs in naïve individuals, regardless of the interval between the first two doses. However, these responses remain lower than those induced by hybrid immunity.

11.
iScience ; 25(9): 104990, 2022 Sep 16.
Article in English | MEDLINE | ID: covidwho-1996293

ABSTRACT

Although SARS-CoV-2 mRNA vaccination has been shown to be safe and effective in the general population, immunocompromised solid organ transplant recipients (SOTRs) were reported to have impaired immune responses after one or two doses of vaccine. In this study, we examined humoral responses induced after the second and the third dose of mRNA vaccine in different SOTR (kidney, liver, lung, and heart). Compared to a cohort of SARS-CoV-2 naïve immunocompetent health care workers (HCWs), the second dose induced weak humoral responses in SOTRs, except for the liver recipients. The third dose boosted these responses but they did not reach the same level as in HCW. Interestingly, although the neutralizing activity against Delta and Omicron variants remained very low after the third dose, Fc-mediated effector functions in SOTR reached similar levels as in the HCW cohort. Whether these responses will suffice to protect SOTR from severe outcome remains to be determined.

12.
Cell Rep ; 39(13): 111013, 2022 06 28.
Article in English | MEDLINE | ID: covidwho-1885674

ABSTRACT

Spacing of BNT162b2 mRNA doses beyond 3 weeks raises concerns about vaccine efficacy. We longitudinally analyze B cell, T cell, and humoral responses to two BNT162b2 mRNA doses administered 16 weeks apart in 53 SARS-CoV-2 naive and previously infected donors. This regimen elicits robust RBD-specific B cell responses whose kinetics differs between cohorts, the second dose leading to increased magnitude in naive participants only. While boosting does not increase magnitude of CD4+ T cell responses further compared with the first dose, unsupervised clustering of single-cell features reveals phenotypic and functional shifts over time and between cohorts. Integrated analysis shows longitudinal immune component-specific associations, with early T helper responses post first dose correlating with B cell responses after the second dose, and memory T helper generated between doses correlating with CD8 T cell responses after boosting. Therefore, boosting elicits a robust cellular recall response after the 16-week interval, indicating functional immune memory.


Subject(s)
COVID-19 , Viral Vaccines , Antibodies, Viral , BNT162 Vaccine , Humans , Immunity, Humoral , RNA, Messenger , SARS-CoV-2
13.
Vaccine ; 40(26): 3633-3637, 2022 06 09.
Article in English | MEDLINE | ID: covidwho-1819620

ABSTRACT

INTRODUCTION: COVID-19 vaccine efficacy has been evaluated in large clinical trials and in real-world situation. Although they have proven to be very effective in the general population, little is known about their efficacy in immunocompromised patients. HIV-infected individuals' response to vaccine may vary according to the type of vaccine and their level of immunosuppression. We evaluated immunogenicity of an mRNA anti-SARS CoV-2 vaccine in HIV-positive individuals. METHODS: HIV-positive individuals (n = 121) were recruited from HIV clinics in Montreal and stratified according to their CD4 counts. A control group of 20 health care workers naïve to SARS CoV-2 was used. The participants' Anti-RBD IgG responses were measured by ELISA at baseline and 3-4 weeks after receiving the first dose of an mRNA vaccine). RESULTS: Eleven of 121 participants had anti-COVID-19 antibodies at baseline, and a further 4 had incomplete data for the analysis. Mean anti-RBD IgG responses were similar between the HIV negative control group (n = 20) and the combined HIV+ group (n = 106) (p = 0.72). However, these responses were significantly lower in the group with <250 CD4 cells/mm3. (p < 0.0001). Increasing age was independently associated with decreased immunogenicity. CONCLUSION: HIV-positive individuals with CD4 counts over 250 cells/mm3 have an anti-RBD IgG response similar to the general population. However, HIV-positive individuals with the lowest CD4 counts (<250 cells/mm3) have a weaker response. These data would support the hypothesis that a booster dose might be needed in this subgroup of HIV-positive individuals, depending on their response to the second dose.


Subject(s)
COVID-19 , HIV Seropositivity , HIV-1 , Antibodies, Viral , COVID-19/prevention & control , COVID-19 Vaccines , Humans , Immunogenicity, Vaccine , Immunoglobulin G , Vaccines, Synthetic , mRNA Vaccines
14.
Cell Rep ; 38(9): 110429, 2022 03 01.
Article in English | MEDLINE | ID: covidwho-1734242

ABSTRACT

Continuous emergence of SARS-CoV-2 variants of concern (VOCs) is fueling the COVID-19 pandemic. Omicron (B.1.1.529) rapidly spread worldwide. The large number of mutations in its Spike raise concerns about a major antigenic drift that could significantly decrease vaccine efficacy and infection-induced immunity. A long interval between BNT162b2 mRNA doses elicits antibodies that efficiently recognize Spikes from different VOCs. Here, we evaluate the recognition of Omicron Spike by plasma from a cohort of SARS-CoV-2 naive and previously infected individuals who received their BNT162b2 mRNA vaccine 16 weeks apart. Omicron Spike is recognized less efficiently than D614G, Alpha, Beta, Gamma, and Delta Spikes. We compare with plasma activity from participants receiving a short (4 weeks) interval regimen. Plasma from individuals of the long-interval cohort recognize and neutralize better the Omicron Spike compared with those who received a short interval. Whether this difference confers any clinical benefit against Omicron remains unknown.


Subject(s)
Antibodies, Neutralizing/blood , BNT162 Vaccine/administration & dosage , Immunization Schedule , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , Adult , Aged , Antibodies, Neutralizing/analysis , Antibodies, Neutralizing/immunology , Antibodies, Viral/analysis , Antibodies, Viral/blood , Antibodies, Viral/immunology , BNT162 Vaccine/immunology , Cohort Studies , Female , HEK293 Cells , Humans , Immunization, Secondary/methods , Male , Middle Aged , Quebec , SARS-CoV-2/pathogenicity , Time Factors , Vaccination/methods , Vaccine Potency , Vaccines, Synthetic/administration & dosage , Vaccines, Synthetic/immunology , Young Adult , mRNA Vaccines/administration & dosage , mRNA Vaccines/immunology
15.
Cell Host Microbe ; 30(1): 97-109.e5, 2022 01 12.
Article in English | MEDLINE | ID: covidwho-1549683

ABSTRACT

The standard regimen of the BNT162b2 mRNA vaccine for SARS-CoV-2 includes two doses administered three weeks apart. However, some public health authorities spaced these doses, raising questions about efficacy. We analyzed longitudinal humoral responses against the D614G strain and variants of concern for SARS-CoV-2 in a cohort of SARS-CoV-2-naive and previously infected individuals who received the BNT162b2 mRNA vaccine with sixteen weeks between doses. While administering a second dose to previously infected individuals did not significantly improve humoral responses, these responses significantly increased in naive individuals after a 16-week spaced second dose, achieving similar levels as in previously infected individuals. Comparing these responses to those elicited in individuals receiving a short (4-week) dose interval showed that a 16-week interval induced more robust responses among naive vaccinees. These findings suggest that a longer interval between vaccine doses does not compromise efficacy and may allow greater flexibility in vaccine administration.


Subject(s)
BNT162 Vaccine/immunology , COVID-19 Vaccines/immunology , COVID-19/immunology , Immunity, Humoral/immunology , SARS-CoV-2/immunology , Spike Glycoprotein, Coronavirus/immunology , Vaccines, Synthetic/immunology , mRNA Vaccines/immunology , Adult , Aged , Antibodies, Neutralizing/immunology , Antibodies, Viral/immunology , COVID-19/virology , Female , Humans , Male , Middle Aged , Vaccination/methods , Young Adult
16.
Viruses ; 13(9)2021 09 02.
Article in English | MEDLINE | ID: covidwho-1390788

ABSTRACT

3D-printed alternatives to standard flocked swabs were rapidly developed to provide a response to the unprecedented and sudden need for an exponentially growing amount of diagnostic tools to fight the COVID-19 pandemic. In light of the anticipated shortage, a hospital-based 3D-printing platform was implemented in our institution for the production of swabs for nasopharyngeal and oropharyngeal sampling based on the freely available, open-source design provided to the community by University of South Florida's Health Radiology and Northwell Health System teams as a replacement for locally used commercial swabs. Validation of our 3D-printed swabs was performed with a head-to-head diagnostic accuracy study of the 3D-printed "Northwell model" with the cobas PCR Media® swab sample kit. We observed an excellent concordance (total agreement 96.8%, Kappa 0.936) in results obtained with the 3D-printed and flocked swabs, indicating that the in-house 3D-printed swab could be used reliably in the context of a shortage of flocked swabs. To our knowledge, this is the first study to report on autonomous hospital-based production and clinical validation of 3D-printed swabs.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , COVID-19/virology , SARS-CoV-2 , COVID-19 Testing/instrumentation , Disease Management , Humans , Nasopharynx/virology , Polymerase Chain Reaction/methods , Printing, Three-Dimensional , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Specimen Handling/methods
17.
Diagn Microbiol Infect Dis ; 101(4): 115521, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1363964

ABSTRACT

SARS-CoV-2 whole genome sequencing is a molecular biology tool performed to support many aspects of the response to the pandemic. Freezing of primary clinical nasopharyngeal swabs and shipment to reference laboratories is usually required for sequencing. Cobas PCR Media transport medium facilitates high throughput SARS-CoV-2 RT-PCR analyses on cobas platforms. The manufacturer doesn't recommend freezing this transport medium because of risks of degrading molecular templates and impairing test results. Our objective was to compare the quality and results of SARS-CoV-2 genomic sequencing when performed on fresh or frozen samples in cobas PCR Media. Viral genome sequencing was performed using Oxford Nanopore Technologies MinION platform. Sequencing performance, quality and results did not significantly differ between fresh and frozen samples (n = 10). Freezing of cobas PCR Media does not negatively affect SARS-CoV-2 RNA sequencing results and it is therefore a suitable transport medium for outsourcing sequencing analyses to reference laboratories.


Subject(s)
COVID-19 Testing/methods , COVID-19/diagnosis , Freezing , Polymerase Chain Reaction/methods , SARS-CoV-2/isolation & purification , Whole Genome Sequencing/methods , COVID-19/virology , Cryopreservation , Genome, Viral , Humans , Molecular Diagnostic Techniques/methods , Nasopharynx/virology , RNA, Viral/genetics , SARS-CoV-2/genetics
18.
Cell Rep Med ; 2(6): 100290, 2021 06 15.
Article in English | MEDLINE | ID: covidwho-1307252

ABSTRACT

With the recent approval of highly effective coronavirus disease 2019 (COVID-19) vaccines, functional and lasting immunity to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently under investigation as antibody levels in plasma were shown to decline during convalescence. Since the absence of antibodies does not equate to absence of immune memory, we evaluate the presence of SARS-CoV-2-specific memory B cells in convalescent individuals. Here, we report a longitudinal assessment of humoral immune responses on 32 donors up to 8 months post-symptom onset. Our observations indicate that anti-Spike and anti-receptor binding domain (RBD) immunoglobulin M (IgM) in plasma decay rapidly, whereas the reduction of IgG is less prominent. Neutralizing activity also declines rapidly when compared to Fc-effector functions. Concomitantly, the frequencies of RBD-specific IgM+ B cells wane significantly when compared to RBD-specific IgG+ B cells, which remain stable. Our results add to the current understanding of immune memory following SARS-CoV-2 infection, which is critical for secondary infection prevention and vaccine efficacy.

19.
Cell Host Microbe ; 29(7): 1137-1150.e6, 2021 07 14.
Article in English | MEDLINE | ID: covidwho-1252574

ABSTRACT

While the standard regimen of the BNT162b2 mRNA vaccine for SARS-CoV-2 includes two doses administered 3 weeks apart, some public health authorities are spacing these doses, raising concerns about efficacy. However, data indicate that a single dose can be up to 90% effective starting 14 days post-administration. To assess the mechanisms contributing to protection, we analyzed humoral and T cell responses three weeks after a single BNT162b2 dose. We observed weak neutralizing activity elicited in SARS-CoV-2 naive individuals but strong anti-receptor binding domain and spike antibodies with Fc-mediated effector functions and cellular CD4+ T cell responses. In previously infected individuals, a single dose boosted all humoral and T cell responses, with strong correlations between T helper and antibody immunity. Our results highlight the potential role of Fc-mediated effector functions and T cell responses in vaccine efficacy. They also provide support for spacing doses to vaccinate more individuals in conditions of vaccine scarcity.


Subject(s)
Antibodies, Viral/immunology , COVID-19 Vaccines/administration & dosage , COVID-19 Vaccines/immunology , COVID-19/immunology , SARS-CoV-2/immunology , T-Lymphocytes/immunology , Adult , Antibodies, Neutralizing/immunology , Antibodies, Viral/chemistry , BNT162 Vaccine , Betacoronavirus , COVID-19/prevention & control , Carrier Proteins , Female , Humans , Immunity , Immunoglobulin Fc Fragments , Male , Middle Aged , Vaccination , Vaccines, Synthetic/immunology , Young Adult
20.
mBio ; 11(5)2020 10 16.
Article in English | MEDLINE | ID: covidwho-873469

ABSTRACT

In the absence of effective vaccines and with limited therapeutic options, convalescent plasma is being collected across the globe for potential transfusion to coronavirus disease 2019 (COVID-19) patients. The therapy has been deemed safe, and several clinical trials assessing its efficacy are ongoing. While it remains to be formally proven, the presence of neutralizing antibodies is thought to play a positive role in the efficacy of this treatment. Indeed, neutralizing titers of ≥1:160 have been recommended in some convalescent plasma trials for inclusion. Here, we performed repeated analyses at 1-month intervals on 31 convalescent individuals to evaluate how the humoral responses against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Spike glycoprotein, including neutralization, evolve over time. We observed that the levels of receptor-binding-domain (RBD)-specific IgG and IgA slightly decreased between 6 and 10 weeks after the onset of symptoms but that RBD-specific IgM levels decreased much more abruptly. Similarly, we observed a significant decrease in the capacity of convalescent plasma to neutralize pseudoparticles bearing wild-type SARS-CoV-2 S or its D614G variant. If neutralization activity proves to be an important factor in the clinical efficacy of convalescent plasma transfer, our results suggest that plasma from convalescent donors should be recovered rapidly after resolution of symptoms.IMPORTANCE While waiting for an efficient vaccine to protect against SARS-CoV-2 infection, alternative approaches to treat or prevent acute COVID-19 are urgently needed. Transfusion of convalescent plasma to treat COVID-19 patients is currently being explored; neutralizing activity in convalescent plasma is thought to play a central role in the efficacy of this treatment. Here, we observed that plasma neutralization activity decreased a few weeks after the onset of the symptoms. If neutralizing activity is required for the efficacy of convalescent plasma transfer, our results suggest that convalescent plasma should be recovered rapidly after the donor recovers from active infection.


Subject(s)
Betacoronavirus/immunology , Convalescence , Coronavirus Infections/immunology , Immunity, Humoral , Pneumonia, Viral/immunology , Spike Glycoprotein, Coronavirus/immunology , Adult , Aged , Antibodies, Neutralizing/blood , Antibodies, Viral/blood , COVID-19 , Coronavirus Infections/blood , Cross Reactions , Female , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/blood , SARS-CoV-2 , Spike Glycoprotein, Coronavirus/chemistry , Young Adult
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