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1.
Nat Rev Microbiol ; 2022 Oct 28.
Article in English | MEDLINE | ID: covidwho-2096724

ABSTRACT

Monoclonal antibodies (mAbs) offer a treatment option for individuals with severe COVID-19 and are especially important in high-risk individuals where vaccination is not an option. Given the importance of understanding the evolution of resistance to mAbs by SARS-CoV-2, we reviewed the available in vitro neutralization data for mAbs against live variants and viral constructs containing spike mutations of interest. Unfortunately, evasion of mAb-induced protection is being reported with new SARS-CoV-2 variants. The magnitude of neutralization reduction varied greatly among mAb-variant pairs. For example, sotrovimab retained its neutralization capacity against Omicron BA.1 but showed reduced efficacy against BA.2, BA.4 and BA.5, and BA.2.12.1. At present, only bebtelovimab has been reported to retain its efficacy against all SARS-CoV-2 variants considered here. Resistance to mAb neutralization was dominated by the action of epitope single amino acid substitutions in the spike protein. Although not all observed epitope mutations result in increased mAb evasion, amino acid substitutions at non-epitope positions and combinations of mutations also contribute to evasion of neutralization. This Review highlights the implications for the rational design of viral genomic surveillance and factors to consider for the development of novel mAb therapies.

3.
Emerg Microbes Infect ; 11(1): 2724-2734, 2022 Dec.
Article in English | MEDLINE | ID: covidwho-2087655

ABSTRACT

The development of safe and effective vaccines to respond to COVID-19 pandemic/endemic remains a priority. We developed a novel subunit protein-peptide COVID-19 vaccine candidate (UB-612) composed of: (i) receptor binding domain of SARS-CoV-2 spike protein fused to a modified single-chain human IgG1 Fc; (ii) five synthetic peptides incorporating conserved helper and cytotoxic T lymphocyte (Th/CTL) epitopes derived from SARS-CoV-2 structural proteins (three from S2 subunit, one from membrane and one from nucleocapsid), and one universal Th peptide; (iii) aluminum phosphate as adjuvant. The immunogenicity and protective immunity induced by UB-612 vaccine were evaluated in four animal models: Sprague-Dawley rats, AAV-hACE2 transduced BALB/c mice, rhesus and cynomolgus macaques. UB-612 vaccine induced high levels of neutralizing antibody and T-cell responses, in all animals. The immune sera from vaccinated animals neutralized the SARS-CoV-2 original wild-type strains and multiple variants of concern, including Delta and Omicron. The vaccination significantly reduced viral loads, lung pathology scores, and disease progression after intranasal and intratracheal challenge with SARS-CoV-2 in mice, rhesus and cynomolgus macaques. UB-612 has been tested in primary regimens in Phase 1 and Phase 2 clinical studies and is currently being evaluated in a global pivotal Phase 3 clinical study as a single dose heterologous booster.


Subject(s)
COVID-19 , Viral Vaccines , Rats , Mice , Humans , Animals , SARS-CoV-2 , COVID-19 Vaccines , Broadly Neutralizing Antibodies , Pandemics/prevention & control , COVID-19/prevention & control , Rats, Sprague-Dawley , Spike Glycoprotein, Coronavirus , Antibodies, Neutralizing , Vaccines, Subunit/genetics , Mice, Inbred BALB C , Macaca mulatta , Antibodies, Viral
4.
FEBS J ; 2022 Oct 20.
Article in English | MEDLINE | ID: covidwho-2078462

ABSTRACT

Antiviral therapies are integral in the fight against SARS-CoV-2 (i.e. severe acute respiratory syndrome coronavirus 2), the causative agent of COVID-19. Antiviral therapeutics can be divided into categories based on how they combat the virus, including viral entry into the host cell, viral replication, protein trafficking, post-translational processing, and immune response regulation. Drugs that target how the virus enters the cell include: Evusheld, REGEN-COV, bamlanivimab and etesevimab, bebtelovimab, sotrovimab, Arbidol, nitazoxanide, and chloroquine. Drugs that prevent the virus from replicating include: Paxlovid, remdesivir, molnupiravir, favipiravir, ribavirin, and Kaletra. Drugs that interfere with protein trafficking and post-translational processing include nitazoxanide and ivermectin. Lastly, drugs that target immune response regulation include interferons and the use of anti-inflammatory drugs such as dexamethasone. Antiviral therapies offer an alternative solution for those unable or unwilling to be vaccinated and are a vital weapon in the battle against the global pandemic. Learning more about these therapies helps raise awareness in the general population about the options available to them with respect to aiding in the reduction of the severity of COVID-19 infection. In this 'A Guide To' article, we provide an in-depth insight into the development of antiviral therapeutics against SARS-CoV-2 and their ability to help fight COVID-19.

5.
J Infect Dis ; 226(8): 1401-1406, 2022 Oct 17.
Article in English | MEDLINE | ID: covidwho-2077781

ABSTRACT

The highly transmissible severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant has caused high rates of breakthrough infections in those previously vaccinated with ancestral strain coronavirus disease 2019 (COVID-19) vaccines. Here, we demonstrate that a booster dose of UB-612 vaccine candidate delivered 7-9 months after primary vaccination increased neutralizing antibody levels by 131-, 61-, and 49-fold against ancestral SARS-CoV-2 and the Omicron BA.1 and BA.2 variants, respectively. Based on the receptor-binding domain protein binding antibody responses, the UB-612 third-dose booster may lead to an estimated approximately 95% efficacy against symptomatic COVID-19 caused by the ancestral strain. Our results support UB-612 as a potential potent booster against current and emerging SARS-CoV-2 variants.


Subject(s)
COVID-19 , Viral Vaccines , Antibodies, Neutralizing , Antibodies, Viral , COVID-19/prevention & control , Humans , SARS-CoV-2
6.
Cannabis Cannabinoid Res ; 2022 Oct 14.
Article in English | MEDLINE | ID: covidwho-2077549

ABSTRACT

Introduction: Coronavirus Disease 2019 (COVID-19) causes a wide range of symptoms, including death. As persons recover, some continue to experience symptoms described as Post-Acute COVID-19 Syndrome (PACS). The objectives of this study were to measure the efficacy of Formula C™, a cannabidiol (CBD)-rich, whole-flower terpene-rich preparation in managing PACS symptoms. Materials and Methods: This randomized, placebo-controlled, single-blind, open-label crossover study was conducted in 2021. Informed consent was obtained from participants, and they were randomized to two treatment groups. Group 1 (n=15) received blinded active product for 28 days, and Group 2 (n=16) received blinded placebo for 28 days (Treatment Period 1). Both groups crossed over to open-label active product for 28 days (Treatment Period 2) with a safety assessment at day 70. Patient-Reported Outcomes Measurement Information System (PROMIS®) scores and the Patient Global Impression of Change (PGIC) score were used to assess primary and secondary objectives. Safety assessments were also done at each visit. Results: Twenty-four participants completed study, with 8 withdrawals, none related to study product. PGIC and PROMIS scores improved across both groups at day 28. This raised questions about the placebo. A reanalysis of the placebo confirmed absence of CBD and unexpected medical concentration of terpenes. The study continued despite no longer having a true placebo. The improved scores on outcome measures were maintained across the open label treatment period. There were no safety events reported throughout the study. Discussion: For persons with PACS who are nonresponsive to conventional therapies, this study demonstrated symptom improvement for participants utilizing Formula C. In addition, the benefits seen in Group 2 suggest the possibility that non-CBD formulations rich in antioxidants, omega-3, and omega-6 fatty acids, gamma-linoleic acid, and terpenes may also have contributed to the overall improvement of the partial active group through the study. Conclusion: Given that both groups demonstrated improvement, both formulations may be contributing to these findings. Limitations include the small number of participants, the lack of a true placebo, and limited time on study products. Additional studies are warranted to explore both CBD-rich hemp products and hempseed oil as treatment options for PACS. Trial Registration ClinicalTrials.gov Identifier: NCT04828668.

7.
JAMA ; 328(15): 1523-1533, 2022 10 18.
Article in English | MEDLINE | ID: covidwho-2074838

ABSTRACT

Importance: Data on the epidemiology of mild to moderately severe COVID-19 are needed to inform public health guidance. Objective: To evaluate associations between 2 or 3 doses of mRNA COVID-19 vaccine and attenuation of symptoms and viral RNA load across SARS-CoV-2 viral lineages. Design, Setting, and Participants: A prospective cohort study of essential and frontline workers in Arizona, Florida, Minnesota, Oregon, Texas, and Utah with COVID-19 infection confirmed by reverse transcriptase-polymerase chain reaction testing and lineage classified by whole genome sequencing of specimens self-collected weekly and at COVID-19 illness symptom onset. This analysis was conducted among 1199 participants with SARS-CoV-2 from December 14, 2020, to April 19, 2022, with follow-up until May 9, 2022, reported. Exposures: SARS-CoV-2 lineage (origin strain, Delta variant, Omicron variant) and COVID-19 vaccination status. Main Outcomes and Measures: Clinical outcomes included presence of symptoms, specific symptoms (including fever or chills), illness duration, and medical care seeking. Virologic outcomes included viral load by quantitative reverse transcriptase-polymerase chain reaction testing along with viral viability. Results: Among 1199 participants with COVID-19 infection (714 [59.5%] women; median age, 41 years), 14.0% were infected with the origin strain, 24.0% with the Delta variant, and 62.0% with the Omicron variant. Participants vaccinated with the second vaccine dose 14 to 149 days before Delta infection were significantly less likely to be symptomatic compared with unvaccinated participants (21/27 [77.8%] vs 74/77 [96.1%]; OR, 0.13 [95% CI, 0-0.6]) and, when symptomatic, those vaccinated with the third dose 7 to 149 days before infection were significantly less likely to report fever or chills (5/13 [38.5%] vs 62/73 [84.9%]; OR, 0.07 [95% CI, 0.0-0.3]) and reported significantly fewer days of symptoms (10.2 vs 16.4; difference, -6.1 [95% CI, -11.8 to -0.4] days). Among those with Omicron infection, the risk of symptomatic infection did not differ significantly for the 2-dose vaccination status vs unvaccinated status and was significantly higher for the 3-dose recipients vs those who were unvaccinated (327/370 [88.4%] vs 85/107 [79.4%]; OR, 2.0 [95% CI, 1.1-3.5]). Among symptomatic Omicron infections, those vaccinated with the third dose 7 to 149 days before infection compared with those who were unvaccinated were significantly less likely to report fever or chills (160/311 [51.5%] vs 64/81 [79.0%]; OR, 0.25 [95% CI, 0.1-0.5]) or seek medical care (45/308 [14.6%] vs 20/81 [24.7%]; OR, 0.45 [95% CI, 0.2-0.9]). Participants with Delta and Omicron infections who received the second dose 14 to 149 days before infection had a significantly lower mean viral load compared with unvaccinated participants (3 vs 4.1 log10 copies/µL; difference, -1.0 [95% CI, -1.7 to -0.2] for Delta and 2.8 vs 3.5 log10 copies/µL, difference, -1.0 [95% CI, -1.7 to -0.3] for Omicron). Conclusions and Relevance: In a cohort of US essential and frontline workers with SARS-CoV-2 infections, recent vaccination with 2 or 3 mRNA vaccine doses less than 150 days before infection with Delta or Omicron variants, compared with being unvaccinated, was associated with attenuated symptoms, duration of illness, medical care seeking, or viral load for some comparisons, although the precision and statistical significance of specific estimates varied.


Subject(s)
COVID-19 Vaccines , COVID-19 , Vaccination , Viral Load , Adult , Female , Humans , Male , COVID-19/diagnosis , COVID-19/genetics , COVID-19/prevention & control , COVID-19/virology , COVID-19 Vaccines/administration & dosage , COVID-19 Vaccines/therapeutic use , Prospective Studies , RNA, Viral/analysis , RNA, Viral/genetics , RNA-Directed DNA Polymerase , SARS-CoV-2/genetics , Vaccination/statistics & numerical data , United States/epidemiology , Viral Load/drug effects , Viral Load/genetics , Viral Load/statistics & numerical data , Whole Genome Sequencing , Asymptomatic Infections/epidemiology , Asymptomatic Infections/therapy , Time Factors , Patient Acceptance of Health Care/statistics & numerical data
9.
Open Forum Infect Dis ; 9(10): ofac490, 2022 Oct.
Article in English | MEDLINE | ID: covidwho-2062949

ABSTRACT

Although numerous studies have evaluated severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection using cycle threshold (Ct) values as a surrogate of viral ribonucleic acid (RNA) load, few studies have used standardized, quantitative methods. We validated a quantitative SARS-CoV-2 digital polymerase chain reaction assay normalized to World Health Organization International Units and correlated viral RNA load with symptoms and disease severity.

10.
Investigative Ophthalmology and Visual Science ; 63(7):1084-A0179, 2022.
Article in English | EMBASE | ID: covidwho-2057445

ABSTRACT

Purpose : Moorfields Eye Hospital, London, is a centre of excellence for ophthalmic research, education and patient care. During the COVID-19 pandemic, medical students' clinical education exposure and patients' multidisciplinary care were greatly affected. Telepresence robots have been suggested as a solution to reduce the impact of COVID-19. We present the results of a trial used to evaluate the capabilities of a telepresence robot in improving clinical education for undergraduate medical students, and the possibility to deliver multidisciplinary clinical patient care via a telepresence robot. Methods : In a two-day trial period, the telepresence robot was used in four tasks: 1) to livestream an adnexal surgery to students off-site;2) autonomously navigating patients from clinic to pharmacy;3) by a clinician to remotely review patients with an ophthalmologist who was consulting the patient face to face;4) and to deliver a teaching session to medical students. Feedback was gathered using a questionnaire and in a group discussion together with clinicians, patients, students, robot specialists and IT specialists. Results : 15 patients of a wide age range and 5 medical students were surveyed. The vast majority of both groups were unaware of telepresence robots. The mean rating given by both groups was 6/10 (with a range of 1-10/10 and 3-8/10) respectively. The groups praised the innovation, felt it could support clinical pressures, and improve their involvement. However, there were concerns about impersonality and technical limitations, and each offered ideas for improvements. All students felt there was potential to improve medical education using the robot. Qualitative feedback during the group discussion highlighted the importance of adapting the currently available hardware and software to enhance its use in education and patient care. Conclusions : This trial provided a greater understanding into the practicalities of incorporating a telepresence robot, in its current form, to clinical medical care and education. While there are challenges with the technical specification of the telepresence robot, the proposition of using such a device has drawn positive engagement from students, patients and clinicians thus validating further research.

11.
2022 Annual Modeling and Simulation Conference, ANNSIM 2022 ; : 126-139, 2022.
Article in English | Scopus | ID: covidwho-2056827

ABSTRACT

Organizations are struggling to ensure business continuity without compromising on delivery excellence in the face of Covid19 pandemic related uncertainties. The uncertainty exists along multiple dimensions such as virus mutations, infectivity and severity of new mutants, efficacy of vaccines against new mutants, waning of vaccine induced immunity over time, and lockdown / opening-up policies effected by city authorities. Moreover, this uncertainty plays out in a non-uniform manner across nations, states, cities, and even within the cities thus leading to highly heterogeneous evolution of pandemic. While Work From Home (WFH) strategy has served well to meet ever-increasing business demands without compromising on individual health safety, there has been an undeniable reduction in social capital. With Covid19 pandemic showing definite waning trends, organizations are considering the possibility of safe transition from WFH to Work From Office (WFO) or a hybrid mode of operation. An effective strategy needs to score equally well on possibly interfering dimensions such as risk of infection, project delivery, and employee wellness. As large organizations will typically have a large number of offices spread across a geography, the problem of arriving at office-specific strategies becomes non-trivial. Moreover, the strategies need to adapt over time to changes that cannot be deduced upfront. This calls for an approach that is amenable to quick and easy adaptation. Our contribution in this regard is constructing a Digital Twin by leveraging various modelling techniques to realistically represent the above mentioned aspects of interest that can be subjected to what-if scenario analysis. We further demonstrate its efficacy using a case study from a large organization. © 2022 SCS.

13.
Preprint in English | bioRxiv | ID: ppbiorxiv-509649

ABSTRACT

Exposure to different mutagens leaves distinct mutational patterns that can allow prediction of pathogen replication niches (Ruis 2022). We therefore hypothesised that analysis of SARS-CoV-2 mutational spectra might show lineage-specific differences, dependant on the dominant site(s) of replication and onwards transmission, and could therefore rapidly infer virulence of emergent variants of concern (VOC; Konings 2021). Through mutational spectrum analysis, we found a significant reduction in G>T mutations in Omicron, which replicates in the upper respiratory tract (URT), compared to other lineages, which replicate in both upper and lower respiratory tracts (LRT). Mutational analysis of other viruses and bacteria indicates a robust, generalisable association of high G>T mutations with replication within the LRT. Monitoring G>T mutation rates over time, we found early separation of Omicron from Beta, Gamma and Delta, while the mutational burden in Alpha varied consistent with changes in transmission source as social restrictions were lifted. This supports the use of mutational spectra to infer niches of established and emergent pathogens.

15.
Preprint in English | bioRxiv | ID: ppbiorxiv-508299

ABSTRACT

Several sublineages of omicron have emerged with additional mutations that may afford further antibody evasion. Here, we characterise the sensitivity of emerging omicron sublineages BA.2.75.2, BA.4.6, and BA.2.10.4 to antibody-mediated neutralisation, and identify extensive escape by BA.2.75.2. BA.2.75.2 was resistant to neutralisation by Evusheld (tixagevimab + cilgavimab), but remained sensitive to bebtelovimab. In recent serum samples from blood donors in Stockholm, Sweden, BA.2.75.2 was neutralised, on average, at titers approximately 6.5-times lower than BA.5, making BA.2.75.2 the most neutralisation resistant variant evaluated to date. These data raise concerns that BA.2.75.2 may effectively evade humoral immunity in the population.

17.
Virus evolution ; 8(2), 2022.
Article in English | EuropePMC | ID: covidwho-1999627

ABSTRACT

Long-term severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in immunodeficient patients are an important source of variation for the virus but are understudied. Many case studies have been published which describe one or a small number of long-term infected individuals but no study has combined these sequences into a cohesive dataset. This work aims to rectify this and study the genomics of this patient group through a combination of literature searches as well as identifying new case series directly from the COVID-19 Genomics UK (COG-UK) dataset. The spike gene receptor-binding domain and N-terminal domain (NTD) were identified as mutation hotspots. Numerous mutations associated with variants of concern were observed to emerge recurrently. Additionally a mutation in the envelope gene, T30I was determined to be the second most frequent recurrently occurring mutation arising in persistent infections. A high proportion of recurrent mutations in immunodeficient individuals are associated with ACE2 affinity, immune escape, or viral packaging optimisation. There is an apparent selective pressure for mutations that aid cell–cell transmission within the host or persistence which are often different from mutations that aid inter-host transmission, although the fact that multiple recurrent de novo mutations are considered defining for variants of concern strongly indicates that this potential source of novel variants should not be discounted.

18.
J Womens Health (Larchmt) ; 31(8): 1097-1102, 2022 08.
Article in English | MEDLINE | ID: covidwho-1992076

ABSTRACT

Background: Some studies have suggested minor changes in the menstrual cycle after COVID-19 vaccination, but more detailed analyses of the menstrual cycle are needed to evaluate more specific changes in the menstrual cycle that are not affected by survey-based recall bias. Materials and Methods: Using a pretest-post-test quasi-experimental evaluation of menstrual cycle parameters before and after COVID-19 vaccination, we conducted an anonymous online survey of two groups of North American women who prospectively monitor their menstrual cycle parameters daily including bleeding patterns, urinary hormone levels using the ClearBlue Fertility Monitor, or cervical mucus observations. The primary outcome measures were cycle length, length of menses, menstrual volume, estimated day of ovulation (EDO), luteal phase length, and signs of ovulation. Perceived (subjective) menstrual cycle changes and stressors were also evaluated in this study as secondary outcome measures. Results: Of the 279 women who initiated the survey, 76 met the inclusion criteria and provided 588 cycles for analysis (227 pre-vaccine cycles, 145 vaccine cycles, 216 post-vaccine cycles). Although 22% of women subjectively identified changes in their menstrual cycle, there were no significant differences in menstrual cycle parameters (cycle length, length of menses, EOD, and luteal phase length) between the pre-vaccine, vaccine, and post-vaccine cycles. Conclusions: COVID-19 vaccines were not associated with significant changes in menstrual cycle parameters. Perceived changes by an individual woman must be compared with statistical changes to avoid confirmation bias.


Subject(s)
COVID-19 Vaccines , COVID-19 , COVID-19/prevention & control , Female , Humans , Luteal Phase/urine , Menstrual Cycle , Progesterone , Vaccination
19.
Nature ; 610(7930): 154-160, 2022 10.
Article in English | MEDLINE | ID: covidwho-1991629

ABSTRACT

The SARS-CoV-2 Delta (Pango lineage B.1.617.2) variant of concern spread globally, causing resurgences of COVID-19 worldwide1,2. The emergence of the Delta variant in the UK occurred on the background of a heterogeneous landscape of immunity and relaxation of non-pharmaceutical interventions. Here we analyse 52,992 SARS-CoV-2 genomes from England together with 93,649 genomes from the rest of the world to reconstruct the emergence of Delta and quantify its introduction to and regional dissemination across England in the context of changing travel and social restrictions. Using analysis of human movement, contact tracing and virus genomic data, we find that the geographic focus of the expansion of Delta shifted from India to a more global pattern in early May 2021. In England, Delta lineages were introduced more than 1,000 times and spread nationally as non-pharmaceutical interventions were relaxed. We find that hotel quarantine for travellers reduced onward transmission from importations; however, the transmission chains that later dominated the Delta wave in England were seeded before travel restrictions were introduced. Increasing inter-regional travel within England drove the nationwide dissemination of Delta, with some cities receiving more than 2,000 observable lineage introductions from elsewhere. Subsequently, increased levels of local population mixing-and not the number of importations-were associated with the faster relative spread of Delta. The invasion dynamics of Delta depended on spatial heterogeneity in contact patterns, and our findings will inform optimal spatial interventions to reduce the transmission of current and future variants of concern, such as Omicron (Pango lineage B.1.1.529).


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/transmission , COVID-19/virology , Cities/epidemiology , Contact Tracing , England/epidemiology , Genome, Viral/genetics , Humans , Quarantine/legislation & jurisprudence , SARS-CoV-2/genetics , SARS-CoV-2/growth & development , SARS-CoV-2/isolation & purification , Travel/legislation & jurisprudence
20.
EJHaem ; 2022.
Article in English | EuropePMC | ID: covidwho-1980349

ABSTRACT

Large granular lymphocyte leukemia is a rare chronic lymphoproliferative disorder of cytotoxic cells. Other hematological malignancies such as CLL and multiple myeloma have been associated with poor vaccination response and markedly increased severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) mortality rates, specifically in patients who have undergone immunosuppressive therapy. Given the immunosuppressive therapies often used to treat the disease, large granular lymphocytic (LGL) patients may be especially vulnerable to SARS‐CoV‐2 infection. A questionnaire was sent to all patients in the LGL Leukemia Registry at the University of Virginia (UVA) to obtain information on vaccination status, type of vaccine received, side effects of vaccination, patient treatment status before, during, and after vaccination, antibody testing, history of coronavirus disease 2019 (COVID‐19) infection, and presence or absence of booster vaccination. Antibody testing of 27 patients who had quantitative SARS‐CoV‐2 Spike Protein IgG levels determined by University of Virginia medical laboratories via the Abbott Architect SARS‐CoV‐2 IgG II assay were collected. The assay was scored as reactive at a threshold of ≥50.0 AU/mL or nonreactive with a threshold of <50.0 AU/mL. LGL patients without treatment as well as patients who held treatment prior to their vaccination have a robust humoral response to SARS‐CoV‐2 vaccines. Patients who did not hold their immunosuppressive treatments have signifigantly diminished vaccine response compared to those who held their immunosuppressive treatment. Our findings support a dual strategy of pausing immunotherapy during the vaccination window and administration of the SARS‐CoV‐2 booster to all LGL leukemia patients to maximize protective antibodies.

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