51
|
Alizon S, Sofonea MT. SARS-CoV-2 virulence evolution: Avirulence theory, immunity and trade-offs. J Evol Biol 2021; 34:1867-1877. [PMID: 34196431 PMCID: PMC8447366 DOI: 10.1111/jeb.13896] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/15/2021] [Accepted: 06/21/2021] [Indexed: 12/21/2022]
Abstract
The COVID-19 pandemic has led to a resurgence of the debate on whether host-parasite interactions should evolve towards avirulence. In this review, we first show that SARS-CoV-2 virulence is evolving, before explaining why some expect the mortality caused by the epidemic to converge towards that of human seasonal alphacoronaviruses. Leaning on existing theory, we then include viral evolution into the picture and discuss hypotheses explaining why the virulence has increased since the beginning of the pandemic. Finally, we mention some potential scenarios for the future.
Collapse
Affiliation(s)
- Samuel Alizon
- MIVEGECCNRS, IRD, Univ. MontpellierMontpellierFrance
| | | |
Collapse
|
52
|
Yaniv K, Ozer E, Lewis Y, Kushmaro A. RT-qPCR assays for SARS-CoV-2 variants of concern in wastewater reveals compromised vaccination-induced immunity. WATER RESEARCH 2021; 207:117808. [PMID: 34753092 PMCID: PMC8551083 DOI: 10.1016/j.watres.2021.117808] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 05/02/2023]
Abstract
SARS-CoV-2 variants of concern, demonstrating higher infection rate and lower vaccine effectiveness as compared with the original virus, are important factors propelling the ongoing COVID-19 global outbreak. Therefore, prompt identification of these variants in the environment is essential for pandemic assessment and containment efforts. One well established tool for such viral monitoring is the use of wastewater systems. Here, we describe continuous monitoring of traces of SARS-CoV-2 viruses in the municipal wastewater of a large city in Israel. By observing morbidity fluctuations (during three main COVID-19 surges) occurring in parallel with Pfizer-BioNTech COVID-19 vaccine vaccination rate, compromised immunity was revealed in the current morbidity peak. RT-qPCR assays for the Original (D614G), Alpha and Beta variants had been previously developed and are being employed for wastewater surveillance. In the present study we developed a sensitive RT-qPCR assay designed for the rapid, direct detection of Gamma and Delta variants of concern. Sensitive quantification and detection of the various variants showed the prevalence of the original variant during the first morbidity peak. The dominance of the Alpha variant over the original variant correlated with the second morbidity peak. These variants decreased concurrently with an increase in vaccinations (Feb-March 2021) and the observed decrease in morbidity. The appearance and subsequent rise of the Delta variant became evident and corresponded to the third morbidity peak (June-August 2021). These results suggest a high vaccine neutralization efficiency towards the Alpha variant compared to its neutralization efficiency towards the Delta variant. Moreover, the third vaccination dose (booster) seems to regain neutralization efficiency towards the Delta variant. The developed assays and wastewater-based epidemiology are important tools aiding in morbidity surveillance and disclosing vaccination efforts and immunity dynamics in the community.
Collapse
Affiliation(s)
- Karin Yaniv
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben- Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Eden Ozer
- Department of Life Sciences, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | | | - Ariel Kushmaro
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben- Gurion University of the Negev, Beer-Sheva 84105, Israel; The Ilse Katz Center for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel; School of Sustainability and Climate Change, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel.
| |
Collapse
|
53
|
Toscano S, Chisari CG, Patti F. Multiple Sclerosis, COVID-19 and Vaccines: Making the Point. Neurol Ther 2021; 10:627-649. [PMID: 34625925 PMCID: PMC8500471 DOI: 10.1007/s40120-021-00288-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/22/2021] [Indexed: 12/15/2022] Open
Abstract
On 11 March 2020, the World Health Organization declared the coronavirus disease 19 (COVID-19) outbreak a pandemic. In this context, several studies and clinical trials have been conducted since then, and many are currently ongoing, leading to the development of several COVID-19 vaccines with different mechanisms of action. People affected by multiple sclerosis (MS) have been considered high-risk subjects in most countries and prioritized for COVID-19 vaccination. However, the management of MS during the COVID-19 pandemic has represented a new challenge for MS specialists, particularly because of the initial lack of guidelines and differing recommendations. Despite an initial hesitation in prescribing disease-modifying drugs (DMDs) in naïve and already treated patients with MS, most national neurology associations and organizations agree on not stopping treatment. However, care is needed especially for patients treated with immune-depleting drugs, which also require some attentions in programming vaccine administration. Many discoveries and new research results have accumulated in a short time on COVID-19, resulting in a need for summarizing the existing evidence on this topic. In this review, we describe the latest research results on the immunological aspects of SARS-CoV-2 infection speculating about their impact on COVID-19 vaccines' mechanisms of action and focused on the management of MS during the COVID pandemic according to the most recent guidelines and recommendations. Finally, the efficacy of COVID-19 and other well-known vaccines against infectious disease in patients with MS on DMDs is discussed.
Collapse
Affiliation(s)
- Simona Toscano
- Department G. F. Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Clara G Chisari
- Department G. F. Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy
| | - Francesco Patti
- Department G. F. Ingrassia, Section of Neurosciences, University of Catania, Via Santa Sofia 78, 95123, Catania, Italy.
| |
Collapse
|
54
|
Prates-Syed WA, Chaves LCS, Crema KP, Vuitika L, Lira A, Côrtes N, Kersten V, Guimarães FEG, Sadraeian M, Barroso da Silva FL, Cabral-Marques O, Barbuto JAM, Russo M, Câmara NOS, Cabral-Miranda G. VLP-Based COVID-19 Vaccines: An Adaptable Technology against the Threat of New Variants. Vaccines (Basel) 2021; 9:1409. [PMID: 34960155 PMCID: PMC8708688 DOI: 10.3390/vaccines9121409] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 12/23/2022] Open
Abstract
Virus-like particles (VLPs) are a versatile, safe, and highly immunogenic vaccine platform. Recently, there are developmental vaccines targeting SARS-CoV-2, the causative agent of COVID-19. The COVID-19 pandemic affected humanity worldwide, bringing out incomputable human and financial losses. The race for better, more efficacious vaccines is happening almost simultaneously as the virus increasingly produces variants of concern (VOCs). The VOCs Alpha, Beta, Gamma, and Delta share common mutations mainly in the spike receptor-binding domain (RBD), demonstrating convergent evolution, associated with increased transmissibility and immune evasion. Thus, the identification and understanding of these mutations is crucial for the production of new, optimized vaccines. The use of a very flexible vaccine platform in COVID-19 vaccine development is an important feature that cannot be ignored. Incorporating the spike protein and its variations into VLP vaccines is a desirable strategy as the morphology and size of VLPs allows for better presentation of several different antigens. Furthermore, VLPs elicit robust humoral and cellular immune responses, which are safe, and have been studied not only against SARS-CoV-2 but against other coronaviruses as well. Here, we describe the recent advances and improvements in vaccine development using VLP technology.
Collapse
Affiliation(s)
- Wasim A. Prates-Syed
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Institute of Research and Education in Child Health (PENSI), São Paulo 01228200, SP, Brazil
| | - Lorena C. S. Chaves
- Department of Microbiology and Immunology, School of Medicine, Emory University, Claudia Nance Rollins Building, Atlanta, GA 30329, USA;
| | - Karin P. Crema
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Institute of Research and Education in Child Health (PENSI), São Paulo 01228200, SP, Brazil
| | - Larissa Vuitika
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
| | - Aline Lira
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Institute of Research and Education in Child Health (PENSI), São Paulo 01228200, SP, Brazil
| | - Nelson Côrtes
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Institute of Research and Education in Child Health (PENSI), São Paulo 01228200, SP, Brazil
| | - Victor Kersten
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
| | | | - Mohammad Sadraeian
- São Carlos Institute of Physics, IFSC-USP, São Carlos 13566590, SP, Brazil; (F.E.G.G.); (M.S.)
- Institute for Biomedical Materials & Devices (IBMD), Faculty of Science, University of Technology, Sydney, NSW 2007, Australia
| | - Fernando L. Barroso da Silva
- Department of Biomolecular Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto 14040903, SP, Brazil;
- Department of Chemical and Biomolecular Engeneering, North Carolina State University, Raleigh, NC 27695, USA
| | - Otávio Cabral-Marques
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Department of Clinical and Toxicological Analyses, School of Pharmaceutical Sciences, University of São Paulo, São Paulo 05508000, SP, Brazil
- Network of Immunity in Infection, Malignancy and Autoimmunity (NIIMA), Universal Scientific Education and Research Network (USERN), Children’s Medical Center, Tehran 1419733151, Iran
| | - José A. M. Barbuto
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Laboratory of Medical Investigation in Pathogenesis and Targeted Therapy in Onco-Immuno-Hematology (LIM-31), Department of Hematology, Hospital das Clínicas HCFMUSP, Faculdade de Medicina, Universidade de São Paulo, São Paulo 0124690, SP, Brazil
| | - Momtchilo Russo
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
| | - Niels O. S. Câmara
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
| | - Gustavo Cabral-Miranda
- Department of Immunology, Institute of Biomedical Sciences, University of São Paulo (ICB/USP), São Paulo 05508000, SP, Brazil; (W.A.P.-S.); (K.P.C.); (L.V.); (A.L.); (N.C.); (V.K.); (O.C.-M.); (J.A.M.B.); (M.R.); (N.O.S.C.)
- Institute of Research and Education in Child Health (PENSI), São Paulo 01228200, SP, Brazil
| |
Collapse
|
55
|
Gussarow D, Bonifacius A, Cossmann A, Stankov MV, Mausberg P, Tischer-Zimmermann S, Gödecke N, Kalinke U, Behrens GMN, Blasczyk R, Eiz-Vesper B. Long-Lasting Immunity Against SARS-CoV-2: Dream or Reality? Front Med (Lausanne) 2021; 8:770381. [PMID: 34901085 PMCID: PMC8656217 DOI: 10.3389/fmed.2021.770381] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 10/29/2021] [Indexed: 12/14/2022] Open
Abstract
Since its declaration as a pandemic in March 2020, SARS-CoV-2 has infected more than 217 million people worldwide and despite mild disease in the majority of the cases, more than 4.5 million cases of COVID-19-associated death have been reported as of September 2021. The question whether recovery from COVID-19 results in prevention of reinfection can be answered with a "no" since cases of reinfections have been reported. The more important question is whether during SARS-CoV-2 infection, a protective immunity is built and maintained afterwards in a way which protects from possibly severe courses of disease in case of a reinfection. A similar question arises with respect to vaccination: as of September 2021, globally, more than 5.2 billion doses of vaccines have been administered. Therefore, it is of utmost importance to study the cellular and humoral immunity toward SARS-CoV-2 in a longitudinal manner. In this study, reconvalescent COVID-19 patients have been followed up for more than 1 year after SARS-CoV-2 infection to characterize in detail the long-term humoral as well as cellular immunity. Both SARS-CoV-2-specific T cells and antibodies could be detected for a period of more than 1 year after infection, indicating that the immune protection established during initial infection is maintained and might possibly protect from severe disease in case of reinfection or infection with novel emerging variants. Moreover, these data demonstrate the opportunity for immunotherapy of hospitalized COVID-19 patients via adoptive transfer of functional antiviral T cells isolated from reconvalescent individuals.
Collapse
Affiliation(s)
- Daniel Gussarow
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hanover, Germany
| | - Agnes Bonifacius
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hanover, Germany
| | - Anne Cossmann
- Department of Rheumatology and Clinical Immunology, Hannover Medical School, Hanover, Germany
| | - Metodi V. Stankov
- Department of Rheumatology and Clinical Immunology, Hannover Medical School, Hanover, Germany
| | - Philip Mausberg
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hanover, Germany
| | - Sabine Tischer-Zimmermann
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hanover, Germany
| | - Nina Gödecke
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hanover, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Helmholtz Centre for Infection Research and Hannover Medical School, Hanover, Germany
- Cluster of Excellence - Resolving Infection Susceptibility (RESIST, EXC 2155), Hannover Medical School, Hanover, Germany
| | - Georg M. N. Behrens
- Department of Rheumatology and Clinical Immunology, Hannover Medical School, Hanover, Germany
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, A Joint Venture Between the Helmholtz Centre for Infection Research and the Hannover Medical School, Hanover, Germany
| | - Rainer Blasczyk
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hanover, Germany
| | - Britta Eiz-Vesper
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Hanover, Germany
| |
Collapse
|
56
|
Ward T, Glaser A, Johnsen A, Xu F, Hall I, Pellis L. Growth, reproduction numbers and factors affecting the spread of SARS-CoV-2 novel variants of concern in the UK from October 2020 to July 2021: a modelling analysis. BMJ Open 2021; 11:e056636. [PMID: 34819293 PMCID: PMC8613669 DOI: 10.1136/bmjopen-2021-056636] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 10/18/2021] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES Importations of novel variants of concern (VOC), particularly B.1.617.2, have become the impetus behind recent outbreaks of SARS-CoV-2. Concerns around the impact on vaccine effectiveness, transmissibility and severity are now driving the public health response to these variants. This paper analyses the patterns of growth in hospitalisations and confirmed cases for novel VOCs by age groups, geography and ethnicity in the context of changing behaviour, non-pharmaceutical interventions (NPIs) and the UK vaccination programme. We seek to highlight where strategies have been effective and periods that have facilitated the establishment of new variants. DESIGN We have algorithmically linked the most complete testing and hospitalisation data in England to create a data set of confirmed infections and hospitalisations by SARS-CoV-2 genomic variant. We have used these linked data sets to analyse temporal, geographic and demographic distinctions. SETTING AND PARTICIPANTS The setting is England from October 2020 to July 2021. Participants included all COVID-19 tests that included RT-PCR CT gene target data or underwent sequencing and hospitalisations that could be linked to these tests. METHODS To calculate the instantaneous growth rate for VOCs we have developed a generalised additive model fit to multiple splines and varying day of the week effects. We have further modelled the instantaneous reproduction number Rt for the B.1.1.7 and B.1.617.2 variants and included a doubly interval censored model to temporally adjust the confirmed variant cases. RESULTS We observed a clear replacement of the predominant B.1.1.7 by the B.1.617.2 variant without observing sustained exponential growth in other novel variants. Modelled exponential growth of RT PCR gene target triple-positive cases was initially detected in the youngest age groups, although we now observe across all ages a very small doubling time of 10.7 (95% CI 9.1 to 13.2) days and 8 (95% CI 6.9 to 9.1) days for cases and hospitalisations, respectively. We observe that growth in RT PCR gene target triple-positive cases was first detected in the Indian ethnicity group in late February, with a peak of 0.06 (95% CI 0.07 to 0.05) in the instantaneous growth rate, but is now maintained by the white ethnicity groups, observing a doubling time of 6.8 (95% CI 4.9 to 11) days. Rt analysis indicates a reproduction number advantage of 0.45 for B.1.617.2 relative to B.1.1.7, with the Rt value peaking at 1.85 for B.1.617.2. CONCLUSIONS Our results illustrate a clear transmission advantage for the B.1.617.2 variant and the growth in hospitalisations illustrates that this variant is able to maintain exponential growth within age groups that are largely doubly vaccinated. There are concerning signs of intermittent growth in the B.1.351 variant, reaching a 28-day doubling time peak in March 2021, although this variant is presently not showing any evidence of a transmission advantage over B.1.617.2. Step 1b of the UK national lockdown easing was sufficient to precipitate exponential growth in B.1.617.2 cases for most regions and younger adult age groups. The final stages of NPI easing appeared to have a negligible impact on the growth of B.1.617.2 with every region experiencing sustained exponential growth from step 2. Nonetheless, early targeted local NPIs appeared to markedly reduced growth of B.1.617.2. Later localised interventions, at a time of higher prevalence and greater geographic dispersion of this variant, appeared to have a negligible impact on growth.
Collapse
Affiliation(s)
| | - Alex Glaser
- Department of Health and Social Care, London, UK
| | | | - Feng Xu
- The University of Manchester, Manchester, UK
| | - Ian Hall
- Department of Mathematics, University of Manchester, Manchester, UK
| | | |
Collapse
|
57
|
Yang W, Shaman J. COVID-19 pandemic dynamics in India, the SARS-CoV-2 Delta variant, and implications for vaccination. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.06.21.21259268. [PMID: 34845460 PMCID: PMC8629204 DOI: 10.1101/2021.06.21.21259268] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
BACKGROUND The COVID-19 Delta pandemic wave in India surged and declined within 3 months; cases then remained low despite the continued spread of Delta elsewhere. Here we aim to estimate key epidemiological characteristics of the Delta variant based on data from India and examine the underpinnings of its dynamics. METHODS We utilize multiple datasets and model-inference methods to reconstruct COVID-19 pandemic dynamics in India during March 2020 - June 2021. We further use model estimates to retrospectively predict cases and deaths during July - mid-Oct 2021, under various vaccination and vaccine effectiveness (VE) settings to estimate the impact of vaccination and VE for non-Delta-infection recoverees. FINDINGS We estimate that Delta escaped immunity in 34.6% (95% CI: 0 - 64.2%) of individuals with prior wildtype infection and was 57.0% (95% CI: 37.9 - 75.6%) more infectious than wildtype SARS-CoV-2. Models assuming higher VE among those with prior non-Delta infection, particularly after the 1 st dose, generated more accurate predictions than those assuming no such increases (best-performing VE setting: 90/95% vs. 30/67% baseline for the 1 st /2 nd dose). Counterfactual modeling indicates that high vaccination coverage for 1 st vaccine-dose in India (∼50% by mid-Oct 2021) combined with the boosting of VE among recoverees averted around 60% of infections during July - mid-Oct 2021. INTERPRETATION Non-pharmaceutical interventions, infection seasonality, and high coverage of 1-dose vaccination likely all contributed to pandemic dynamics in India during 2021. Given the shortage of COVID-19 vaccines globally and boosting of VE, for populations with high prior infection rates, prioritizing the first vaccine-dose may protect more people. RESEARCH IN CONTEXT Evidence before this study: We searched PubMed for studies published through Nov 3, 2021 on the Delta (B.1.617.2) SARS-CoV-2 variant that focused on three areas: 1) transmissibility [search terms: ("Delta variant" OR "B.1.617") AND ("transmission rate" OR "growth rate" OR "secondary attack rate" OR "transmissibility")]; 2) immune response ([search terms: ("Delta variant" OR "B.1.617") AND ("immune evas" OR "immune escape")]; and 3) vaccine effectiveness ([search terms: ("Delta variant" OR "B.1.617") AND ("vaccine effectiveness" OR "vaccine efficacy" OR "vaccination")]. Our search returned 256 papers, from which we read the abstracts and identified 54 relevant studies.Forty-two studies addressed immune evasion and/or vaccine effectiveness. Around half (n=19) of these studies measured the neutralizing ability of convalescent sera and/or vaccine sera against Delta and most reported some reduction (around 2-to 8-fold) compared to ancestral variants. The remainder (n=23) used field observations (often with a test-negative or cohort-design) and reported lower VE against infection but similar VE against hospitalization or death. Together, these laboratory and field observations consistently indicate that Delta can evade preexisting immunity. In addition, five studies reported higher B-cell and/or T-cell vaccine-induced immune response among recovered vaccinees than naïve vaccinees, suggesting potential boosting of pre-existing immunity; however, all studies were based on small samples (n = 10 to 198 individuals).Sixteen studies examined transmissibility, including 1) laboratory experiments (n=6) showing that Delta has higher affinity to the cell receptor, fuses membranes more efficiently, and/or replicates faster than other SARS-CoV-2 variants, providing biological mechanisms for its higher transmissibility; 2) field studies (n=5) showing higher rates of breakthrough infections by Delta and/or higher viral load among Delta infections than other variants; and 3) modeling/mixed studies (n=5) using genomic or case data to estimate the growth rate or reproduction number, reporting a 60-120% increase. Only one study jointly estimated the increase in transmissibility (1.3-1.7-fold, 50% CI) and immune evasion (10-50%, 50% CI); this study also reported a 27.5% (25/91) reinfection rate by Delta.Added value of this study: We utilize observed pandemic dynamics and the differential vaccination coverage for two vaccine doses in India, where the Delta variant was first identified, to estimate the epidemiological properties of Delta and examine the impact of prior non-Delta infection on immune boosting at the population level. We estimate that Delta variant can escape immunity from prior wildtype infection roughly one-third of the time and is around 60% more infectious than wildtype SARS-CoV-2. In addition, our analysis suggests the large increase in population receiving their first vaccine dose (∼50% by end of Oct 2021) combined with the boosting effect of vaccination for non-Delta infection recoverees likely mitigated epidemic intensity in India during July - Oct 2021.Implications of all the available evidence: Our analysis reconstructs the interplay and effects of non-pharmaceutical interventions, infection seasonality, Delta variant emergence, and vaccination on COVID-19 pandemic dynamics in India. Modeling findings support prioritizing the first vaccine dose in populations with high prior infection rates, given vaccine shortages.
Collapse
|
58
|
Deb P, Molla MMA, Saif-Ur-Rahman KM, Das MC, Das D. A review of epidemiology, clinical features and disease course, transmission dynamics, and neutralization efficacy of SARS-CoV-2 variants. THE EGYPTIAN JOURNAL OF BRONCHOLOGY 2021. [PMCID: PMC8571979 DOI: 10.1186/s43168-021-00090-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Background After the first detection in November 2019, SARS-CoV-2 has spread rapidly over the continents and started the pandemic of the millennium. In addition to several novels and repurposed monoclonal antibodies (mAbs) as a therapeutic option against COVID-19, scientists from across the world have developed several candidate vaccines, developed mainly targeting the Wuhan strain, with very promising results to combat this pandemic. Unfortunately like any RNA viruses, SARS CoV-2 has also gone through the accumulation of hundreds and thousands of mutations in their genome lead to the development of several variants of concerns (VOC) and variants of interests (VOI), resulting in increased transmissibility and virulence of the virus, along with their capacity to escape cross-protection. Seemingly, the main hindrance of containing this pandemic right now is the effectiveness of currently available vaccines and mAbs against newly emerging variants. Therefore, it is important to monitor variants epidemiology, transmission dynamics, clinical characteristics, as well as their immune evasion capacity to implement appropriate vaccine strategy and other containment measures. Body In this review, we tried to focus on variants characteristics and to what extent they can escape immunity, provided by both available vaccinated sera and convalescent sera. A stringent literature review was performed using various databases, mentioned in the methodology portion. The current geographical distribution of these variants of SARS CoV-2 has been presented using a heat map. Findings from published articles comparing these variants, in terms of genome epidemiology, transmissibility, viral load dynamics, and association with different waves have been described briefly. Due strength was given while describing variants neutralization potency against current vaccines, mAbs, and also against convalescent sera. Data from both clinical trials and in vitro/ex-vivo studies have been discussed here. Comparative findings from several articles were brought into one concise paper. After careful reviewing of all the available data, it was clear that, without hesitation, we should strengthen our vaccination strategy, because the severity of COVID 19 is reasonably lower, irrespective of variants and vaccine used. Conclusion We hope that many falsified myths and beliefs regarding vaccine immunity and emerging variants will be clarified in light of this available evidence, which we summarized in our paper.
Collapse
|
59
|
Mlcochova P, Kemp SA, Dhar MS, Papa G, Meng B, Ferreira IATM, Datir R, Collier DA, Albecka A, Singh S, Pandey R, Brown J, Zhou J, Goonawardane N, Mishra S, Whittaker C, Mellan T, Marwal R, Datta M, Sengupta S, Ponnusamy K, Radhakrishnan VS, Abdullahi A, Charles O, Chattopadhyay P, Devi P, Caputo D, Peacock T, Wattal C, Goel N, Satwik A, Vaishya R, Agarwal M, Mavousian A, Lee JH, Bassi J, Silacci-Fegni C, Saliba C, Pinto D, Irie T, Yoshida I, Hamilton WL, Sato K, Bhatt S, Flaxman S, James LC, Corti D, Piccoli L, Barclay WS, Rakshit P, Agrawal A, Gupta RK. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 2021; 599:114-119. [PMID: 34488225 DOI: 10.1101/2021.05.08.443253] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/23/2021] [Indexed: 05/23/2023]
Abstract
The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.
Collapse
Affiliation(s)
- Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | | | - Guido Papa
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Dami A Collier
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | - Anna Albecka
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Sujeet Singh
- National Centre for Disease Control, Delhi, India
| | - Rajesh Pandey
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Jonathan Brown
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Jie Zhou
- Department of Infectious Diseases, Imperial College London, London, UK
| | | | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Thomas Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | | | | | - Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Priti Devi
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Tom Peacock
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | - Joo Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Takashi Irie
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Isao Yoshida
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Kei Sato
- Division of Systems Virology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Samir Bhatt
- National Centre for Disease Control, Delhi, India
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Leo C James
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Wendy S Barclay
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | - Anurag Agrawal
- CSIR Institute of Genomics and Integrative Biology, Delhi, India.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, Durban, South Africa.
| |
Collapse
|
60
|
Mlcochova P, Kemp SA, Dhar MS, Papa G, Meng B, Ferreira IATM, Datir R, Collier DA, Albecka A, Singh S, Pandey R, Brown J, Zhou J, Goonawardane N, Mishra S, Whittaker C, Mellan T, Marwal R, Datta M, Sengupta S, Ponnusamy K, Radhakrishnan VS, Abdullahi A, Charles O, Chattopadhyay P, Devi P, Caputo D, Peacock T, Wattal C, Goel N, Satwik A, Vaishya R, Agarwal M, Mavousian A, Lee JH, Bassi J, Silacci-Fegni C, Saliba C, Pinto D, Irie T, Yoshida I, Hamilton WL, Sato K, Bhatt S, Flaxman S, James LC, Corti D, Piccoli L, Barclay WS, Rakshit P, Agrawal A, Gupta RK. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature 2021; 599:114-119. [PMID: 34488225 PMCID: PMC8566220 DOI: 10.1038/s41586-021-03944-y] [Citation(s) in RCA: 849] [Impact Index Per Article: 283.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/23/2021] [Indexed: 12/26/2022]
Abstract
The B.1.617.2 (Delta) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified in the state of Maharashtra in late 2020 and spread throughout India, outcompeting pre-existing lineages including B.1.617.1 (Kappa) and B.1.1.7 (Alpha)1. In vitro, B.1.617.2 is sixfold less sensitive to serum neutralizing antibodies from recovered individuals, and eightfold less sensitive to vaccine-elicited antibodies, compared with wild-type Wuhan-1 bearing D614G. Serum neutralizing titres against B.1.617.2 were lower in ChAdOx1 vaccinees than in BNT162b2 vaccinees. B.1.617.2 spike pseudotyped viruses exhibited compromised sensitivity to monoclonal antibodies to the receptor-binding domain and the amino-terminal domain. B.1.617.2 demonstrated higher replication efficiency than B.1.1.7 in both airway organoid and human airway epithelial systems, associated with B.1.617.2 spike being in a predominantly cleaved state compared with B.1.1.7 spike. The B.1.617.2 spike protein was able to mediate highly efficient syncytium formation that was less sensitive to inhibition by neutralizing antibody, compared with that of wild-type spike. We also observed that B.1.617.2 had higher replication and spike-mediated entry than B.1.617.1, potentially explaining the B.1.617.2 dominance. In an analysis of more than 130 SARS-CoV-2-infected health care workers across three centres in India during a period of mixed lineage circulation, we observed reduced ChAdOx1 vaccine effectiveness against B.1.617.2 relative to non-B.1.617.2, with the caveat of possible residual confounding. Compromised vaccine efficacy against the highly fit and immune-evasive B.1.617.2 Delta variant warrants continued infection control measures in the post-vaccination era.
Collapse
Affiliation(s)
- Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | | | - Guido Papa
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Dami A Collier
- Department of Medicine, University of Cambridge, Cambridge, UK
- University College London, London, UK
| | - Anna Albecka
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Sujeet Singh
- National Centre for Disease Control, Delhi, India
| | - Rajesh Pandey
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | - Jonathan Brown
- Department of Infectious Diseases, Imperial College London, London, UK
| | - Jie Zhou
- Department of Infectious Diseases, Imperial College London, London, UK
| | | | - Swapnil Mishra
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Charles Whittaker
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Thomas Mellan
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | - Robin Marwal
- National Centre for Disease Control, Delhi, India
| | - Meena Datta
- National Centre for Disease Control, Delhi, India
| | | | | | | | - Adam Abdullahi
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | | | | | - Priti Devi
- CSIR Institute of Genomics and Integrative Biology, Delhi, India
| | | | - Tom Peacock
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | | | | | | | | | | | - Joo Hyeon Lee
- Wellcome-MRC Cambridge Stem Cell Institute, Cambridge, UK
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Takashi Irie
- Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Isao Yoshida
- Tokyo Metropolitan Institute of Public Health, Tokyo, Japan
| | | | - Kei Sato
- Division of Systems Virology, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- CREST, Japan Science and Technology Agency, Saitama, Japan
| | - Samir Bhatt
- National Centre for Disease Control, Delhi, India
- Section of Epidemiology, Department of Public Health, University of Copenhagen, Copenhagen, Denmark
| | - Seth Flaxman
- Department of Computer Science, University of Oxford, Oxford, UK
| | - Leo C James
- MRC - Laboratory of Molecular Biology, Cambridge, UK
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Wendy S Barclay
- Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Jameel Institute, School of Public Health, Imperial College London, London, UK
| | | | - Anurag Agrawal
- CSIR Institute of Genomics and Integrative Biology, Delhi, India.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, Durban, South Africa.
| |
Collapse
|
61
|
Mandal S, Arinaminpathy N, Bhargava B, Panda S. Plausibility of a third wave of COVID-19 in India: A mathematical modelling based analysis. Indian J Med Res 2021; 153:522-532. [PMID: 34643562 PMCID: PMC8555606 DOI: 10.4103/ijmr.ijmr_1627_21] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
BACKGROUND & OBJECTIVES In the context of India's ongoing resurgence of COVID-19 (second wave since mid-February 2021, following the subsiding of the first wave in September 2020), there has been increasing speculation on the possibility of a future third wave of infection, posing a burden on the healthcare system. Using simple mathematical models of the transmission dynamics of SARS-CoV-2, this study examined the conditions under which a serious third wave could occur. METHODS Using a deterministic, compartmental model of SARS-CoV-2 transmission, four potential mechanisms for a third wave were examined: (i) waning immunity restores previously exposed individuals to a susceptible state, (ii) emergence of a new viral variant that is capable of escaping immunity to previously circulating strains, (iii) emergence of a new viral variant that is more transmissible than the previously circulating strains, and (iv) release of current lockdowns affording fresh opportunities for transmission. RESULTS Immune-mediated mechanisms (waning immunity, or viral evolution for immune escape) are unlikely to drive a severe third wave if acting on their own, unless such mechanisms lead to a complete loss of protection among those previously exposed. Likewise, a new, more transmissible variant would have to exceed a high threshold (R0>4.5) to cause a third wave on its own. However, plausible mechanisms for a third wave include: (i) a new variant that is more transmissible and at the same time capable of escaping prior immunity, and (ii) lockdowns that are highly effective in limiting transmission and subsequently released. In both cases, any third wave seems unlikely to be as severe as the second wave. Rapid scale-up of vaccination efforts could play an important role in mitigating these and future waves of the disease. INTERPRETATION & CONCLUSIONS This study demonstrates plausible mechanisms by which a substantial third wave could occur, while also illustrating that it is unlikely for any such resurgence to be as large as the second wave. Model projections are, however, subject to several uncertainties, and it remains important to scale up vaccination coverage to mitigate against any eventuality. Preparedness planning for any potential future wave will benefit by drawing upon the projected numbers based on the present modelling exercise.
Collapse
Affiliation(s)
- Sandip Mandal
- Clinical Studies, Projection & Policy Unit, Indian Council of Medical Research, New Delhi, India
| | - Nimalan Arinaminpathy
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, UK
| | | | - Samiran Panda
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India
- ICMR-National AIDS Research Institute, Pune, India
| |
Collapse
|
62
|
Haddadi S, Mirsaeidi M. Commentary: Meta-Analysis and Structural Dynamics of the Emergence of Genetic Variants of SARS-CoV-2. Front Med (Lausanne) 2021; 8:747109. [PMID: 34631759 PMCID: PMC8494943 DOI: 10.3389/fmed.2021.747109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sara Haddadi
- Department of Medicine, Division of Pulmonary, Critical Care, Sleep and Allergy, University of Miami Miller School of Medicine, Miami, FL, United States
| | - Mehdi Mirsaeidi
- Division of Pulmonary, Critical Care, and Sleep Medicine, College of Medicine, University of Florida, Jacksonville, FL, United States
| |
Collapse
|
63
|
Amatya B, Pandey P, Dawadi S, Manandhar S. COVID-19 in fully vaccinated Everest trekkers in Nepal. J Travel Med 2021; 28:6316239. [PMID: 34230969 PMCID: PMC8344616 DOI: 10.1093/jtm/taab098] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 11/12/2022]
Abstract
COVID-19 in a fully mRNA-1273 vaccinated aspiring Everest summiteer and an Everest trekker who had two doses of ChAdOx1nCoV-19 are presented. Delta B.1.617.2 variant was sequenced in one of the cases. Travellers should be wary of starting up travel to under-vaccinated regions, particularly if they are at high risk for severe disease.
Collapse
Affiliation(s)
- Bhawana Amatya
- CIWEC Hospital and Travel Medicine Center, Lainchaur, Kathmandu, Nepal
| | - Prativa Pandey
- CIWEC Hospital and Travel Medicine Center, Lainchaur, Kathmandu, Nepal
| | - Suvash Dawadi
- CIWEC Hospital and Travel Medicine Center, Lainchaur, Kathmandu, Nepal
| | - Shanta Manandhar
- CIWEC Hospital and Travel Medicine Center, Lainchaur, Kathmandu, Nepal
| |
Collapse
|
64
|
Sharma P, Mishra S, Basu S, Kumar R, Tanwar N. Breakthrough Infection With Severe Acute Respiratory Syndrome Coronavirus 2 Among Healthcare Workers in Delhi: A Single-Institution Study. Cureus 2021; 13:e19070. [PMID: 34824945 PMCID: PMC8610433 DOI: 10.7759/cureus.19070] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/27/2021] [Indexed: 11/10/2022] Open
Abstract
Introduction This study aimed to determine the breakthrough infection rate of coronavirus disease 2019 (COVID-19) (severe acute respiratory syndrome coronavirus 2 {SARS-CoV-2}) infection in healthcare workers (HCWs) vaccinated with either BBV152 or AZD1222 (ChAdOx1-S) vaccine. Methods A cross-sectional analysis was conducted at a medical college and hospital complex in Delhi, India, through telephonic interviews among HCWs who had received at least one dose of a COVID-19 vaccine during January-March 2021. Breakthrough infections were operationally defined as the occurrence of COVID-19 infection ≥14 days after administration of two doses of either COVID-19 vaccine. Data were entered in Epidata 3.1 (Odense, Denmark: EpiData Association) (single entered) and analyzed with IBM SPSS version 25 (Armonk, NY: IBM Corp.). A p-value < 0.05 was considered statistically significant. Results We enrolled 325 HCWs with a mean (SD) age of 29.1 (9.9) years including 211 (64.9%) males and 114 (35.1%) females. A total of 37 (13.3%, 95% CI 9.8, 17.7) COVID-19 breakthrough infections were observed in the HCWs. Additionally, 20 (6.1%) non-breakthrough infections were reported in the HCWs who were vaccinated with at least a single dose of a COVID-19 vaccine, or both doses, but prior to 14 days since the administration of the second dose. Most breakthrough infections were mild without needing supplemental oxygen for recovery. Conclusion Nearly one in seven HCWs experienced a COVID-19 breakthrough infection in the present study. A history of SARS-CoV-2 natural infection followed by at least one dose of COVID-19 vaccination was associated with significant protection against breakthrough infections.
Collapse
Affiliation(s)
- Pragya Sharma
- Community Medicine, Maulana Azad Medical College, Delhi, IND
| | - Suruchi Mishra
- Community Medicine, Maulana Azad Medical College, Delhi, IND
| | - Saurav Basu
- Community Medicine, Maulana Azad Medical College, Delhi, IND
| | - Rajesh Kumar
- Community Medicine, Maulana Azad Medical College, Delhi, IND
| | - Neha Tanwar
- Community Medicine, Maulana Azad Medical College, Delhi, IND
| |
Collapse
|
65
|
Bittar C, Possebon FS, Ullmann LS, Geraldini DB, da Costa VG, de Almeida LGP, da S. Sanches PR, Nascimento-Júnior NM, Cilli EM, Artico Banho C, Campos GRF, Ferreira HL, Sacchetto L, da Silva GCD, Parra MCP, Moraes MM, da Costa PI, Vasconcelos ATR, Spilki FR, Nogueira ML, Rahal P, Araujo Jr JP. The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil. Front Public Health 2021; 9:745310. [PMID: 34660520 PMCID: PMC8517261 DOI: 10.3389/fpubh.2021.745310] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 09/07/2021] [Indexed: 12/28/2022] Open
Abstract
The emergence of several SARS-CoV-2 lineages presenting adaptive mutations is a matter of concern worldwide due to their potential ability to increase transmission and/or evade the immune response. While performing epidemiological and genomic surveillance of SARS-CoV-2 in samples from Porto Ferreira-São Paulo-Brazil, we identified sequences classified by pangolin as B.1.1.28 harboring Spike L452R mutation, in the RBD region. Phylogenetic analysis revealed that these sequences grouped into a monophyletic branch, with others from Brazil, mainly from the state of São Paulo. The sequences had a set of 15 clade defining amino acid mutations, of which six were in the Spike protein. A new lineage was proposed to Pango and it was accepted and designated P.4. In samples from the city of Porto Ferreira, P.4 lineage has been increasing in frequency since it was first detected in March 2021, corresponding to 34.7% of the samples sequenced in June, the second in prevalence after P.1. Also, it is circulating in 30 cities from the state of São Paulo, and it was also detected in one sample from the state of Sergipe and two from the state of Rio de Janeiro. Further studies are needed to understand whether P.4 should be considered a new threat.
Collapse
Affiliation(s)
- Cíntia Bittar
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp), São José do Rio Preto, Brazil
| | - Fábio Sossai Possebon
- Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Botucatu, Brazil
| | - Leila Sabrina Ullmann
- Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Botucatu, Brazil
| | - Dayla Bott Geraldini
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp), São José do Rio Preto, Brazil
| | - Vivaldo G. da Costa
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp), São José do Rio Preto, Brazil
| | - Luiz G. P. de Almeida
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil
| | - Paulo Ricardo da S. Sanches
- Laboratório de Síntese e Estudos de Biomoléculas (LaSEBio), Departamento de Bioquímica e Química Orgânica, Instituto de Química, Universidade Estadual Paulista (Unesp), Araraquara, Brazil
| | - Nailton M. Nascimento-Júnior
- Laboratório de Química Medicinal, Síntese Orgânica e Modelagem Molecular (LaQMedSOMM), Departamento de Bioquímica e Química Orgânica, Instituto de Química, Universidade Estadual Paulista (Unesp), Araraquara, Brazil
| | - Eduardo M. Cilli
- Laboratório de Síntese e Estudos de Biomoléculas (LaSEBio), Departamento de Bioquímica e Química Orgânica, Instituto de Química, Universidade Estadual Paulista (Unesp), Araraquara, Brazil
| | - Cecília Artico Banho
- Laboratório de Pesquisas em Virologia (LPV), Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Guilherme R. F. Campos
- Laboratório de Pesquisas em Virologia (LPV), Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Helena Lage Ferreira
- Laboratório de Medicina Veterinária Preventiva Aplicada, Departamento de Medicina Veterinária, Faculdade de Zootecnia e Engenharia de Alimentos (FZEA), Universidade de São Paulo (USP), Pirassununga, Brazil
| | - Lívia Sacchetto
- Laboratório de Pesquisas em Virologia (LPV), Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Gislaine C. D. da Silva
- Laboratório de Pesquisas em Virologia (LPV), Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Maisa C. P. Parra
- Laboratório de Pesquisas em Virologia (LPV), Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Marília M. Moraes
- Laboratório de Pesquisas em Virologia (LPV), Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Paulo Inácio da Costa
- Departamento de Análises Clínicas, Faculdade de Ciências Farmacêuticas (FCFAR), Universidade Estadual Paulista (Unesp), Araraquara, Brazil
| | - Ana Tereza R. Vasconcelos
- Laboratório de Bioinformática, Laboratório Nacional de Computação Científica (LNCC), Petrópolis, Brazil
| | - Fernando Rosado Spilki
- Laboratório de Microbiologia Molecular, Instituto de Ciências da Saúde, Universidade Feevale, Novo Hamburgo, Brazil
| | - Maurício L. Nogueira
- Laboratório de Pesquisas em Virologia (LPV), Departamento de Doenças Dermatológicas, Infecciosas e Parasitárias, Faculdade de Medicina de São José do Rio Preto (FAMERP), São José do Rio Preto, Brazil
| | - Paula Rahal
- Laboratório de Estudos Genômicos, Departamento de Biologia, Instituto de Biociências Letras e Ciências Exatas (IBILCE), Universidade Estadual Paulista (Unesp), São José do Rio Preto, Brazil
| | - João Pessoa Araujo Jr
- Instituto de Biotecnologia, Universidade Estadual Paulista (Unesp), Botucatu, Brazil
| |
Collapse
|
66
|
Nörz D, Grunwald M, Tang HT, Olearo F, Günther T, Robitaille A, Fischer N, Grundhoff A, Aepfelbacher M, Pfefferle S, Lütgehetmann M. Rapid Automated Screening for SARS-CoV-2 B.1.617 Lineage Variants (Delta/Kappa) through a Versatile Toolset of qPCR-Based SNP Detection. Diagnostics (Basel) 2021; 11:1818. [PMID: 34679517 PMCID: PMC8534837 DOI: 10.3390/diagnostics11101818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/23/2021] [Accepted: 09/25/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The recent emergence of distinct and highly successful SARS-CoV-2 lineages has substantial implications for individual patients and public health measures. While next-generation-sequencing is routinely performed for surveillance purposes, RT-qPCR can be used to rapidly rule-in or rule-out relevant variants, e.g., in outbreak scenarios. The objective of this study was to create an adaptable and comprehensive toolset for multiplexed Spike-gene SNP detection, which was applied to screen for SARS-CoV-2 B.1.617 lineage variants. METHODS We created a broad set of single nucleotide polymorphism (SNP)-assays including del-Y144/145, E484K, E484Q, P681H, P681R, L452R, and V1176F based on a highly specific multi-LNA (locked nucleic acid)-probe design to maximize mismatch discrimination. As proof-of-concept, a multiplex-test was compiled and validated (SCOV2-617VOC-UCT) including SNP-detection for L452R, P681R, E484K, and E484Q to provide rapid screening capabilities for the novel B.1.617 lineages. RESULTS For the multiplex-test (SCOV2-617VOC-UCT), the analytic lower limit of detection was determined as 182 IU/mL for L452R, 144 IU/mL for P681R, and 79 IU/mL for E484Q. A total of 233 clinical samples were tested with the assay, including various on-target and off-target sequences. All SNPs (179/179 positive) were correctly identified as determined by SARS-CoV-2 whole genome sequencing. CONCLUSION The recurrence of SNP locations and flexibility of methodology presented in this study allows for rapid adaptation to current and future variants. Furthermore, the ability to multiplex various SNP-assays into screening panels improves speed and efficiency for variant testing. We show 100% concordance with whole genome sequencing for a B.1.617.2 screening assay on the cobas6800 high-throughput system.
Collapse
Affiliation(s)
- Dominik Nörz
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Moritz Grunwald
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Hui Ting Tang
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Flaminia Olearo
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Thomas Günther
- Virus Genomics, Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
| | - Alexis Robitaille
- Virus Genomics, Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
| | - Nicole Fischer
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Adam Grundhoff
- Virus Genomics, Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany; (T.G.); (A.R.); (A.G.)
| | - Martin Aepfelbacher
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Susanne Pfefferle
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| | - Marc Lütgehetmann
- Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf (UKE), 20246 Hamburg, Germany; (D.N.); (M.G.); (H.T.T.); (F.O.); (N.F.); (M.A.); (S.P.)
| |
Collapse
|
67
|
Farinholt T, Doddapaneni H, Qin X, Menon V, Meng Q, Metcalf G, Chao H, Gingras MC, Avadhanula V, Farinholt P, Agrawal C, Muzny DM, Piedra PA, Gibbs RA, Petrosino J. Transmission event of SARS-CoV-2 delta variant reveals multiple vaccine breakthrough infections. BMC Med 2021; 19:255. [PMID: 34593004 PMCID: PMC8483940 DOI: 10.1186/s12916-021-02103-4] [Citation(s) in RCA: 117] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/18/2021] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND This study aims to identify the causative strain of SARS-CoV-2 in a cluster of vaccine breakthroughs. Vaccine breakthrough by a highly transmissible SARS-CoV-2 strain is a risk to global public health. METHODS Nasopharyngeal swabs from suspected vaccine breakthrough cases were tested for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) by qPCR (quantitative polymerase chain reaction) for Wuhan-Hu1 and alpha variant. Positive samples were then sequenced by Swift Normalase Amplicon Panels to determine the causal variant. GATK (genome analysis toolkit) variants were filtered with allele fraction ≥80 and min read depth 30x. RESULTS Viral sequencing revealed an infection cluster of 6 vaccinated patients infected with the delta (B.1.617.2) SARS-CoV-2 variant. With no history of vaccine breakthrough, this suggests the delta variant may possess immune evasion in patients that received the Pfizer BNT162b2, Moderna mRNA-1273, and Covaxin BBV152. CONCLUSIONS Delta variant may pose the highest risk out of any currently circulating SARS-CoV-2 variants, with previously described increased transmissibility over alpha variant and now, possible vaccine breakthrough. FUNDING Parts of this work was supported by the National Institute of Allergy and Infectious Diseases (1U19AI144297) and Baylor College of Medicine internal funding.
Collapse
Affiliation(s)
- Timothy Farinholt
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA.
| | - Harsha Doddapaneni
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Xiang Qin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Vipin Menon
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Qingchang Meng
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ginger Metcalf
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hsu Chao
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Marie-Claude Gingras
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Vasanthi Avadhanula
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Paige Farinholt
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Charu Agrawal
- Department of Medicine, Baylor College of Medicine, Houston, TX, USA
| | - Donna M Muzny
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Pedro A Piedra
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Joseph Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| |
Collapse
|
68
|
Wagner CE, Saad-Roy CM, Morris SE, Baker RE, Mina MJ, Farrar J, Holmes EC, Pybus OG, Graham AL, Emanuel EJ, Levin SA, Metcalf CJE, Grenfell BT. Vaccine nationalism and the dynamics and control of SARS-CoV-2. Science 2021; 373:eabj7364. [PMID: 34404735 PMCID: PMC9835930 DOI: 10.1126/science.abj7364] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 08/09/2021] [Indexed: 01/16/2023]
Abstract
Vaccines provide powerful tools to mitigate the enormous public health and economic costs that the ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues to exert globally, yet vaccine distribution remains unequal among countries. To examine the potential epidemiological and evolutionary impacts of “vaccine nationalism,” we extend previous models to include simple scenarios of stockpiling between two regions. In general, when vaccines are widely available and the immunity they confer is robust, sharing doses minimizes total cases across regions. A number of subtleties arise when the populations and transmission rates in each region differ, depending on evolutionary assumptions and vaccine availability. When the waning of natural immunity contributes most to evolutionary potential, sustained transmission in low-access regions results in an increased potential for antigenic evolution, which may result in the emergence of novel variants that affect epidemiological characteristics globally. Overall, our results stress the importance of rapid, equitable vaccine distribution for global control of the pandemic.
Collapse
Affiliation(s)
- Caroline E. Wagner
- Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Chadi M. Saad-Roy
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
- Princeton High Meadows Environmental Institute, Princeton University, Princeton, NJ 08540, USA
| | - Sinead E. Morris
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
| | - Rachel E. Baker
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
- Princeton High Meadows Environmental Institute, Princeton University, Princeton, NJ 08540, USA
| | - Michael J. Mina
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jeremy Farrar
- Department of Bioengineering, McGill University, Montreal, QC H3A 0C3, Canada
- The Wellcome Trust, London, UK
| | - Edward C. Holmes
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, Sydney, NSW, Australia
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- School of Medical Sciences, The University of Sydney, Sydney, NSW, Australia
| | - Oliver G. Pybus
- Department of Pathology and Cell Biology, Columbia University Medical Center, New York, NY 10032, USA
- Department of Zoology, University of Oxford, Oxford, UK
| | - Andrea L. Graham
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
- Princeton High Meadows Environmental Institute, Princeton University, Princeton, NJ 08540, USA
| | - Ezekiel J. Emanuel
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
- Department of Medical Ethics and Health Policy, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Simon A. Levin
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
- Princeton High Meadows Environmental Institute, Princeton University, Princeton, NJ 08540, USA
| | - C. Jessica E. Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
- Princeton High Meadows Environmental Institute, Princeton University, Princeton, NJ 08540, USA
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ 08540, USA
| | - Bryan T. Grenfell
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08540, USA
- Princeton High Meadows Environmental Institute, Princeton University, Princeton, NJ 08540, USA
- Princeton School of Public and International Affairs, Princeton University, Princeton, NJ 08540, USA
| |
Collapse
|
69
|
Hsieh WY, Lin CH, Lin TC, Lin CH, Chang HF, Tsai CH, Wu HT, Lin CS. Development and Efficacy of Lateral Flow Point-of-Care Testing Devices for Rapid and Mass COVID-19 Diagnosis by the Detections of SARS-CoV-2 Antigen and Anti-SARS-CoV-2 Antibodies. Diagnostics (Basel) 2021; 11:1760. [PMID: 34679458 PMCID: PMC8534532 DOI: 10.3390/diagnostics11101760] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/26/2021] [Accepted: 09/10/2021] [Indexed: 12/15/2022] Open
Abstract
The COVID-19 pandemic is an ongoing global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in 2020-2021. COVID-19 is becoming one of the most fatal pandemics in history and brings a huge challenge to the global healthcare system. Opportune detection, confinement, and early treatment of infected cases present the first step in combating COVID-19. Diagnosis via viral nucleic acid amplification tests (NAATs) is frequently employed and considered the standard procedure. However, with an increasing urge for point-of-care tests, rapid and cheaper immunoassays are widely utilized, such as lateral flow immunoassay (LFIA), which can be used for rapid, early, and large-scale detection of SARS-CoV-2 infection. In this narrative review, the principle and technique of LFIA applied in COVID-19 antigen and antibody detection are introduced. The diagnostic sensitivity and specificity of the commercial LFIA tests are outlined and compared. Generally, LFIA antigen tests for SARS-CoV-2 are less sensitive than viral NAATs, the "gold standard" for clinical COVID-19 diagnosis. However, antigen tests can be used for rapid and mass testing in high-risk congregate housing to quickly identify people with COVID-19, implementing infection prevention and control measures, thus preventing transmission. LFIA anti-SARS-CoV-2 antibody tests, IgM and/or IgG, known as serology tests, are used for identification if a person has previously been exposed to the virus or vaccine immunization. Notably, advanced techniques, such as LFT-based CRISPR-Cas9 and surface-enhanced Raman spectroscopy (SERS), have added new dimensions to the COVID-19 diagnosis and are also discussed in this review.
Collapse
Affiliation(s)
- Wen-Yeh Hsieh
- Department of Internal Medicine, Division of Chest Medicine, Hsinchu Mackay Memorial Hospital, Hsinchu 30068, Taiwan;
| | - Cheng-Han Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan; (C.-H.L.); (C.-H.L.); (H.-F.C.); (C.-H.T.)
| | - Tzu-Ching Lin
- Department of Pharmacy, College of Pharmacy, Taipei Medical University, Taipei 11031, Taiwan;
| | - Chao-Hsu Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan; (C.-H.L.); (C.-H.L.); (H.-F.C.); (C.-H.T.)
- Department of Pediatrics, Hsinchu Mackay Memorial Hospital, Hsinchu 30071, Taiwan
| | - Hui-Fang Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan; (C.-H.L.); (C.-H.L.); (H.-F.C.); (C.-H.T.)
- Department of Internal Medicine, Division of Endocrinology, Hsinchu Mackay Memorial Hospital, Hsinchu 30071, Taiwan
| | - Chin-Hung Tsai
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan; (C.-H.L.); (C.-H.L.); (H.-F.C.); (C.-H.T.)
- Department of Internal Medicine, Division of Pulmonary Medicine, Tungs’ Taichung Metro Harbor Hospital, Taichung 43503, Taiwan
| | - Hsi-Tien Wu
- Department of BioAgricultural Sciences, College of Agriculture, National Chiayi University, Chiayi 60004, Taiwan;
| | - Chih-Sheng Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan; (C.-H.L.); (C.-H.L.); (H.-F.C.); (C.-H.T.)
- Department of Biological Science and Technology, National Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| |
Collapse
|
70
|
Baden LR, El Sahly HM, Essink B, Follmann D, Neuzil KM, August A, Clouting H, Fortier G, Deng W, Han S, Zhao X, Leav B, Talarico C, Girard B, Paila YD, Tomassini JE, Schödel F, Pajon R, Zhou H, Das R, Miller J. Covid-19 in the Phase 3 Trial of mRNA-1273 During the Delta-variant Surge. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021. [PMID: 34611666 DOI: 10.1101/2021.09.17.21263624] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Background Following emergency use authorization in December 2020, the Coronavirus Efficacy (COVE) trial was amended to an open-label phase, where participants were unblinded and those randomized to placebo were offered vaccination. Emergence of the delta variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been associated with increased incidences of coronavirus disease 2019 (Covid-19) among unvaccinated and vaccinated persons. This exploratory analysis evaluated the incidence and genetic sequences of Covid-19 cases in the ongoing COVE trial during the open-label phase, with a focus on July-August 2021, when delta-variants surged in the US. Methods Covid-19 cases were identified in participants initially randomized to mRNA-1273 (vaccinated from July-December 2020) and those initially randomized to the placebo (vaccinated December 2020-April 2021) who received at least one dose and were SARS-CoV-2-negative at baseline in the modified-intent-to-treat population were analyzed. Included were Covid-19 cases occurring after 26-Mar-2021 with positive RT-PCR results in nasopharyngeal samples (central lab test) and reported Covid-19 symptoms. Genetic sequencing of Covid-19 cases was also performed. Results There were 14,746 participants in the earlier mRNA-1273 (mRNA-1273e) group and 11,431 in the later placebo-mRNA1273 (mRNA-1273p) group. Covid-19 cases increased from the start of the open-label phase to July-August 2021. During July and August, 162 Covid-19 cases occurred in the mRNA-1273e group and 88 in the mRNA-1273p group. Of the cases sequenced, 144/149 [97%]) in the mRNA-1273 and 86/88 (99%) in the mRNA-1273p groups were attributed to delta. The incidence rate of Covid-19 was lower for the mRNA-1273p (49.0/1000 person-years) versus mRNA-1273e (77.1/1000 person-years) group [36.4% (95% CI 17.1%-51.5%) reduction]. There were fewer severe Covid-19 cases in the mRNA-1273p (6; 6.2/1000 person-years) than mRNA-1273e (13; 3.3/1000 person-years) [46.0% (95% CI -52.4%-83.2%) reduction]. Three Covid-19 related hospitalizations occurred with two resulting deaths in the mRNA-1273e group. Conclusion Incidence rates of Covid-19 and severe Covid-19 were lower during the months when delta was the dominant variant (July/August 2021) among COVE participants vaccinated more recently. Analysis of COVID-19 cases from the open-label phase of the COVE study is ongoing.
Collapse
|
71
|
Braeye T, Cornelissen L, Catteau L, Haarhuis F, Proesmans K, De Ridder K, Djiena A, Mahieu R, De Leeuw F, Dreuw A, Hammami N, Quoilin S, Van Oyen H, Wyndham-Thomas C, Van Cauteren D. Vaccine effectiveness against infection and onwards transmission of COVID-19: Analysis of Belgian contact tracing data, January-June 2021. Vaccine 2021; 39:5456-5460. [PMID: 34454789 PMCID: PMC8373820 DOI: 10.1016/j.vaccine.2021.08.060] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 08/13/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022]
Abstract
In Belgium, high-risk contacts of an infected person were offered PCR-testing irrespective of their vaccination status. We estimated vaccine effectiveness (VE) against infection and onwards transmission, controlling for previous infections, household-exposure and temporal trends. We included 301,741 tests from 25 January to 24 June 2021. Full-schedule vaccination was associated with significant protection against infection. In addition, mRNA-vaccines reduced onward transmission: VE-estimates increased to >90% when index and contact were fully vaccinated. The small number of viral-vector vaccines included limited interpretability.
Collapse
Affiliation(s)
- Toon Braeye
- Department of Epidemiology and public health, Sciensano, Brussels, Belgium
| | - Laura Cornelissen
- Department of Epidemiology and public health, Sciensano, Brussels, Belgium
| | - Lucy Catteau
- Department of Epidemiology and public health, Sciensano, Brussels, Belgium
| | - Freek Haarhuis
- Department of Epidemiology and public health, Sciensano, Brussels, Belgium
| | | | - Karin De Ridder
- Department of Epidemiology and public health, Sciensano, Brussels, Belgium
| | | | - Romain Mahieu
- Common Community Commission Brussels, Brussels, Belgium
| | | | - Alex Dreuw
- Ministry of the German-speaking Community, Eupen, Belgium
| | - Naima Hammami
- Agency for Care and Health, Infection Prevention and Control, Flemish Community, Ghent, Belgium
| | - Sophie Quoilin
- Department of Epidemiology and public health, Sciensano, Brussels, Belgium
| | - Herman Van Oyen
- Department of Epidemiology and public health, Sciensano, Brussels, Belgium
| | | | | |
Collapse
|
72
|
Schaefer GO, Leland RJ, Emanuel EJ. Making Vaccines Available to Other Countries Before Offering Domestic Booster Vaccinations. JAMA 2021; 326:903-904. [PMID: 34382999 DOI: 10.1001/jama.2021.13226] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- G Owen Schaefer
- Centre for Biomedical Ethics, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - R J Leland
- Department of Philosophy, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Ezekiel J Emanuel
- Perelman School of Medicine, University of Pennsylvania, Philadelphia
| |
Collapse
|
73
|
Psichogiou M, Karabinis A, Poulakou G, Antoniadou A, Kotanidou A, Degiannis D, Pavlopoulou ID, Chaidaroglou A, Roussos S, Mastrogianni E, Eliadi I, Basoulis D, Petsios K, Leontis K, Kakalou E, Protopapas K, Jahaj E, Pratikaki M, Syrigos KN, Lagiou P, Gogas H, Tsiodras S, Magiorkinis G, Paraskevis D, Sypsa V, Hatzakis A. Comparative Immunogenicity of BNT162b2 mRNA Vaccine with Natural SARS-CoV-2 Infection. Vaccines (Basel) 2021; 9:1017. [PMID: 34579254 PMCID: PMC8471735 DOI: 10.3390/vaccines9091017] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/31/2021] [Accepted: 09/07/2021] [Indexed: 12/04/2022] Open
Abstract
BNT162b2 has proven to be highly effective, but there is a paucity of data regarding immunogenicity factors and comparison between response to vaccination and natural infection. This study included 871 vaccinated healthcare workers (HCW) and 181 patients with natural infection. Immunogenicity was assessed by measuring anti-SARS-CoV-2 against the RBD domain of the spike protein (anti-RBD). Samples were collected 1-2 weeks after vaccination or 15-59 days post-onset of symptoms. Post-vaccine anti-RBD concentrations were associated with age, gender, vaccination side-effects (VSE) and prior infection (Pr-CoV). Anti-RBD median levels (95%CI) were lower by 2466 (651-5583), 6228 (3254-9203) and 7651 (4479-10,823) AU/mL in 35-44, 45-54, 55-70 yrs, respectively, compared with the 18-34 yrs group. In females, the median levels were higher by 2823 (859-4787), 5024 (3122-6926) in individuals with VSE, and 9971 (5158-14,783) AU/mL in HCWs with Pr-CoV. The ratio of anti-RBD in vaccinated individuals versus those with natural infection varied from 1.0 to 19.4. The high immunogenicity of BNT162b2 is verified, although its sustainability has yet to be elucidated. The use of comparative data from natural infection serological panels, expressing the clinical heterogeneity of natural infection, may facilitate early decisions for candidate vaccines to be evaluated in clinical trials.
Collapse
Affiliation(s)
- Mina Psichogiou
- First Department of Internal Medicine, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.M.); (I.E.); (D.B.); (H.G.)
| | - Andreas Karabinis
- Onassis Cardiac Surgery Center, 17674 Athens, Greece; (A.K.); (D.D.); (A.C.)
| | - Garyphallia Poulakou
- 3rd Department of Internal Medicine, Sotiria General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (G.P.); (K.L.); (E.K.); (K.N.S.)
| | - Anastasia Antoniadou
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (A.A.); (K.P.); (S.T.)
| | - Anastasia Kotanidou
- 1st Department of Critical Care & Pulmonary Services, Medical School, National and Kapodistrian University of Athens, Evangelismos Hospital, 10676 Athens, Greece; (A.K.); (E.J.); (M.P.)
| | - Dimitrios Degiannis
- Onassis Cardiac Surgery Center, 17674 Athens, Greece; (A.K.); (D.D.); (A.C.)
| | - Ioanna D. Pavlopoulou
- Pediatric Research Laboratory, Faculty of Nursing, National and Kapodistrian University of Athens, 11527 Athens, Greece;
| | | | - Sotirios Roussos
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.R.); (P.L.); (G.M.); (D.P.); (V.S.); (A.H.)
| | - Elpida Mastrogianni
- First Department of Internal Medicine, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.M.); (I.E.); (D.B.); (H.G.)
| | - Irene Eliadi
- First Department of Internal Medicine, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.M.); (I.E.); (D.B.); (H.G.)
| | - Dimitrios Basoulis
- First Department of Internal Medicine, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.M.); (I.E.); (D.B.); (H.G.)
| | | | - Konstantinos Leontis
- 3rd Department of Internal Medicine, Sotiria General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (G.P.); (K.L.); (E.K.); (K.N.S.)
| | - Eleni Kakalou
- 3rd Department of Internal Medicine, Sotiria General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (G.P.); (K.L.); (E.K.); (K.N.S.)
| | - Konstantinos Protopapas
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (A.A.); (K.P.); (S.T.)
| | - Edison Jahaj
- 1st Department of Critical Care & Pulmonary Services, Medical School, National and Kapodistrian University of Athens, Evangelismos Hospital, 10676 Athens, Greece; (A.K.); (E.J.); (M.P.)
| | - Maria Pratikaki
- 1st Department of Critical Care & Pulmonary Services, Medical School, National and Kapodistrian University of Athens, Evangelismos Hospital, 10676 Athens, Greece; (A.K.); (E.J.); (M.P.)
| | - Konstantinos N. Syrigos
- 3rd Department of Internal Medicine, Sotiria General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (G.P.); (K.L.); (E.K.); (K.N.S.)
| | - Pagona Lagiou
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.R.); (P.L.); (G.M.); (D.P.); (V.S.); (A.H.)
| | - Helen Gogas
- First Department of Internal Medicine, Laiko General Hospital, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (E.M.); (I.E.); (D.B.); (H.G.)
| | - Sotirios Tsiodras
- 4th Department of Internal Medicine, Medical School, National and Kapodistrian University of Athens, 12462 Athens, Greece; (A.A.); (K.P.); (S.T.)
| | - Gkikas Magiorkinis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.R.); (P.L.); (G.M.); (D.P.); (V.S.); (A.H.)
| | - Dimitrios Paraskevis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.R.); (P.L.); (G.M.); (D.P.); (V.S.); (A.H.)
| | - Vana Sypsa
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.R.); (P.L.); (G.M.); (D.P.); (V.S.); (A.H.)
| | - Angelos Hatzakis
- Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, 11527 Athens, Greece; (S.R.); (P.L.); (G.M.); (D.P.); (V.S.); (A.H.)
- Hellenic Scientific Society for the Study of AIDS, Sexually Transmitted and Emerging Diseases, 11527 Athens, Greece
| |
Collapse
|
74
|
Khowaja SA, Khuwaja P, Dev K, D’Aniello G. VIRFIM: an AI and Internet of Medical Things-driven framework for healthcare using smart sensors. Neural Comput Appl 2021; 35:1-18. [PMID: 34493907 PMCID: PMC8412386 DOI: 10.1007/s00521-021-06434-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Accepted: 08/17/2021] [Indexed: 11/24/2022]
Abstract
After affecting the world in unexpected ways, the virus has started mutating which is evident with the insurgence of its new variants. The governments, hospitals, schools, industries, and humans, in general, are looking for a potential solution in the vaccine which will eventually be available, but its timeline for eradicating the virus is yet unknown. Several researchers have encouraged and recommended the use of good practices such as physical healthcare monitoring, immunity boosting, personal hygiene, mental healthcare, and contact tracing for slowing down the spread of the virus. In this article, we propose the use of smart sensors integrated with the Internet of Medical Things to cover the spectrum of good practices in an automated manner. We present hypothetical frameworks for each of the good practice modules and propose the VIrus Resistance Framework using the Internet of Medical Things (VIRFIM) to tie all the individual modules in a unified architecture. Furthermore, we validate the realization of VIRFIM framework with two case studies related to physical activity monitoring and stress detection services. We envision that VIRFIM would be influential in assisting people with the new normal for current and future pandemics as well as instrumental in halting the economic losses, respectively. We also provide potential challenges and their probable solutions in compliance with the proposed VIRFIM.
Collapse
Affiliation(s)
- Sunder Ali Khowaja
- Department of Telecommunication Engineering, Faculty of Engineering and Technology, University of Sindh, Jamshoro, Pakistan
| | - Parus Khuwaja
- Institute of Business Administration, University of Sindh, Jamshoro, Pakistan
| | - Kapal Dev
- Department of Institute of Intelligent systems, University of Johannesburg, Johannesburg, South Africa
| | - Giuseppe D’Aniello
- Department of Information and Electrical Engineering and Applied Mathematics, University of Salerno, Fisciano, Italy
| |
Collapse
|
75
|
Sharma K, Koirala A, Nicolopoulos K, Chiu C, Wood N, Britton PN. Vaccines for COVID-19: Where do we stand in 2021? Paediatr Respir Rev 2021; 39:22-31. [PMID: 34362666 PMCID: PMC8274273 DOI: 10.1016/j.prrv.2021.07.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 07/06/2021] [Indexed: 12/20/2022]
Abstract
As of July 2021, over 3 billion doses of a COVID-19 vaccines have been administered globally, and there are now 19 COVID-19 vaccines approved for use in at least one country. Several of these have been shown to be highly effective both in clinical trials and real-world observational studies, some of which have included special populations of interest. A small number of countries have approved a COVID-19 vaccine for use in adolescents or children. These are laudable achievements, but the global vaccination effort has been challenged by inequitable distribution of vaccines predominantly to high income countries, with only 0.9% of people in low-income countries having received at least one dose of a COVID-19 vaccine. Addressing this inequity is of critical importance and will result in better control of SARS-CoV-2 globally. Other challenges include: the reduced protection from COVID-19 vaccines against some strains of SARS-CoV-2, necessitating the development of variant specific vaccines; and uncertainties around the duration of protection from vaccine-induced immunity.
Collapse
Affiliation(s)
- Ketaki Sharma
- National Centre for Immunisation Research and Surveillance, Westmead, NSW, Australia; Sydney Medical School, The University of Sydney, NSW, Australia
| | - Archana Koirala
- National Centre for Immunisation Research and Surveillance, Westmead, NSW, Australia; Sydney Medical School, The University of Sydney, NSW, Australia; Department of Infectious Diseases, Nepean Hospital, Penrith, NSW, Australia
| | - Katrina Nicolopoulos
- National Centre for Immunisation Research and Surveillance, Westmead, NSW, Australia
| | - Clayton Chiu
- National Centre for Immunisation Research and Surveillance, Westmead, NSW, Australia; Sydney Medical School, The University of Sydney, NSW, Australia
| | - Nicholas Wood
- National Centre for Immunisation Research and Surveillance, Westmead, NSW, Australia; Sydney Medical School, The University of Sydney, NSW, Australia
| | - Philip N Britton
- Sydney Medical School, The University of Sydney, NSW, Australia; Department of Infectious Diseases and Microbiology, The Children's Hospital at Westmead, NSW, Australia.
| |
Collapse
|
76
|
Caldwell JM, Le X, McIntosh L, Meehan MT, Ogunlade S, Ragonnet R, O'Neill GK, Trauer JM, McBryde ES. Vaccines and variants: Modelling insights into emerging issues in COVID-19 epidemiology. Paediatr Respir Rev 2021; 39:32-39. [PMID: 34417121 PMCID: PMC8294600 DOI: 10.1016/j.prrv.2021.07.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 07/13/2021] [Indexed: 01/21/2023]
Abstract
Mathematical modelling has played a pivotal role in understanding the epidemiology of and guiding public health responses to the ongoing coronavirus disease of 2019 (COVID-19) pandemic. Here, we review the role of epidemiological models in understanding evolving epidemic characteristics, including the effects of vaccination and Variants of Concern (VoC). We highlight ways in which models continue to provide important insights, including (1) calculating the herd immunity threshold and evaluating its limitations; (2) verifying that nascent vaccines can prevent severe disease, infection, and transmission but may be less efficacious against VoC; (3) determining optimal vaccine allocation strategies under efficacy and supply constraints; and (4) determining that VoC are more transmissible and lethal than previously circulating strains, and that immune escape may jeopardize vaccine-induced herd immunity. Finally, we explore how models can help us anticipate and prepare for future stages of COVID-19 epidemiology (and that of other diseases) through forecasts and scenario projections, given current uncertainties and data limitations.
Collapse
Affiliation(s)
| | - Xuan Le
- Epidemiological Modelling Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Lorin McIntosh
- Epidemiological Modelling Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Michael T Meehan
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia
| | - Samson Ogunlade
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia
| | - Romain Ragonnet
- Epidemiological Modelling Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Genevieve K O'Neill
- Epidemiological Modelling Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - James M Trauer
- Epidemiological Modelling Unit, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Emma S McBryde
- Australian Institute of Tropical Health and Medicine, James Cook University, Townsville, Australia.
| |
Collapse
|
77
|
Salzberger B, Buder F, Lampl B, Ehrenstein B, Hitzenbichler F, Bauernfeind S, Holzmann T, Schmidt B, Hanses F. [Update on: SARS-CoV-2/COVID-19-epidemiology and prevention]. DER NEPHROLOGE 2021; 16:307-310. [PMID: 34426750 PMCID: PMC8374405 DOI: 10.1007/s11560-021-00529-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Accepted: 07/23/2021] [Indexed: 11/23/2022]
Affiliation(s)
- Bernd Salzberger
- Abt. Krankenhaushygiene und Infektiologie, Universitätsklinikum Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Deutschland
| | - Felix Buder
- Abt. Krankenhaushygiene und Infektiologie, Universitätsklinikum Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Deutschland
| | - Benedikt Lampl
- Sachgebiet Infektionsschutz und Hygiene, Gesundheitsamt Regensburg, Regensburg, Deutschland
| | - Boris Ehrenstein
- Klinik für Rheumatologie und Klinische Immunologie, Fachklinikum Bad Abbach, Bad Abbach, Deutschland
| | - Florian Hitzenbichler
- Abt. Krankenhaushygiene und Infektiologie, Universitätsklinikum Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Deutschland
| | - Stilla Bauernfeind
- Abt. Krankenhaushygiene und Infektiologie, Universitätsklinikum Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Deutschland
| | - Thomas Holzmann
- Abt. Krankenhaushygiene und Infektiologie, Universitätsklinikum Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Deutschland
| | - Barbara Schmidt
- Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinikum Regensburg, Regensburg, Deutschland
| | - Frank Hanses
- Abt. Krankenhaushygiene und Infektiologie, Universitätsklinikum Regensburg, Franz-Josef-Strauß-Allee 11, 93053 Regensburg, Deutschland
| |
Collapse
|
78
|
Huntingford C, Rawson T, Bonsall MB. Optimal COVID-19 Vaccine Sharing Between Two Nations That Also Have Extensive Travel Exchanges. Front Public Health 2021; 9:633144. [PMID: 34458218 PMCID: PMC8387873 DOI: 10.3389/fpubh.2021.633144] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 07/08/2021] [Indexed: 01/12/2023] Open
Abstract
Countries around the world have observed reduced infections from the SARS-CoV-2 virus, that causes COVID-19 illness, primarily due to non-pharmaceutical interventions (NPIs) such as lockdowns and social distancing measures designed to limit physical proximity between people. However, economies and societal interactions require restarting, and so lockdowns cannot continue indefinitely. Therefore, much hope is placed in using newly developed vaccines as a route back to normality, but this raises key questions about how they are shared. There are also emerging questions regarding travel. For instance, international business and trade necessitates at least some in-person exchanges, alongside restarting travel also for tourist purposes. By utilising a Susceptible-Infected-Recovered-Vaccinated (SIRV) mathematical model, we simulate the populations of two nations in parallel, where the first nation produces a vaccine and decides the extent to which it is shared with the second. Overlaying our mathematical structure is the virus-related effects of travel between the two nations. We find that even with extensive travel, nation one minimises its total number of deaths by simply retaining vaccines, aiming for full inoculation as fast as possible, suggesting that the risks posed by travel can be mitigated by rapidly vaccinating its own population. If instead we consider the total deaths i.e., sum of deaths of both nations, then such a policy of not sharing by nation one until full vaccination is highly sub-optimal. A policy of low initial sharing causes many more deaths in nation two than lives saved in nation one, raising important ethical issues. This imbalance in the health impact of vaccination provision must be considered as some countries begin to approach the point of extensive vaccination, while others lack the resources to do so.
Collapse
Affiliation(s)
| | - Thomas Rawson
- Mathematical Ecology Research Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Michael B. Bonsall
- Mathematical Ecology Research Group, Department of Zoology, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
79
|
Liu J, Liu Y, Xia H, Zou J, Weaver SC, Swanson KA, Cai H, Cutler M, Cooper D, Muik A, Jansen KU, Sahin U, Xie X, Dormitzer PR, Shi PY. BNT162b2-elicited neutralization of B.1.617 and other SARS-CoV-2 variants. Nature 2021; 596:273-275. [PMID: 34111888 DOI: 10.1038/s41586-021-03693-y] [Citation(s) in RCA: 244] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/04/2021] [Indexed: 12/31/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuing to evolve around the world, generating new variants that are of concern on the basis of their potential for altered transmissibility, pathogenicity, and coverage by vaccines and therapeutic agents1-5. Here we show that serum samples taken from twenty human volunteers, two or four weeks after their second dose of the BNT162b2 vaccine, neutralize engineered SARS-CoV-2 with a USA-WA1/2020 genetic background (a virus strain isolated in January 2020) and spike glycoproteins from the recently identified B.1.617.1, B.1.617.2, B.1.618 (all of which were first identified in India) or B.1.525 (first identified in Nigeria) lineages. Geometric mean plaque reduction neutralization titres against the variant viruses-particularly the B.1.617.1 variant-seemed to be lower than the titre against the USA-WA1/2020 virus, but all sera tested neutralized the variant viruses at titres of at least 1:40. The susceptibility of the variant strains to neutralization elicited by the BNT162b2 vaccine supports mass immunization as a central strategy to end the coronavirus disease 2019 (COVID-19) pandemic globally.
Collapse
Affiliation(s)
- Jianying Liu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
| | - Yang Liu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Scott C Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA
| | - Kena A Swanson
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Hui Cai
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - Mark Cutler
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | - David Cooper
- Pfizer Vaccine Research and Development, Pearl River, NY, USA
| | | | | | | | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | | | - Pei-Yong Shi
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
| |
Collapse
|
80
|
Chitsike L, Duerksen-Hughes P. Keep out! SARS-CoV-2 entry inhibitors: their role and utility as COVID-19 therapeutics. Virol J 2021; 18:154. [PMID: 34301275 PMCID: PMC8301738 DOI: 10.1186/s12985-021-01624-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 07/15/2021] [Indexed: 12/13/2022] Open
Abstract
The COVID-19 pandemic has put healthcare infrastructures and our social and economic lives under unprecedented strain. Effective solutions are needed to end the pandemic while significantly lessening its further impact on mortality and social and economic life. Effective and widely-available vaccines have appropriately long been seen as the best way to end the pandemic. Indeed, the current availability of several effective vaccines are already making a significant progress towards achieving that goal. Nevertheless, concerns have risen due to new SARS-CoV-2 variants that harbor mutations against which current vaccines are less effective. Furthermore, some individuals are unwilling or unable to take the vaccine. As health officials across the globe scramble to vaccinate their populations to reach herd immunity, the challenges noted above indicate that COVID-19 therapeutics are still needed to work alongside the vaccines. Here we describe the impact that neutralizing antibodies have had on those with early or mild COVID-19, and what their approval for early management of COVID-19 means for other viral entry inhibitors that have a similar mechanism of action. Importantly, we also highlight studies that show that therapeutic strategies involving various viral entry inhibitors such as multivalent antibodies, recombinant ACE2 and miniproteins can be effective not only for pre-exposure prophylaxis, but also in protecting against SARS-CoV-2 antigenic drift and future zoonotic sarbecoviruses.
Collapse
Affiliation(s)
- Lennox Chitsike
- Department of Basic Sciences, Loma Linda University School of Medicine, 11021 Campus Street, 101 Alumni Hall, Loma Linda, CA, 92354, USA
| | - Penelope Duerksen-Hughes
- Department of Basic Sciences, Loma Linda University School of Medicine, 11021 Campus Street, 101 Alumni Hall, Loma Linda, CA, 92354, USA.
| |
Collapse
|
81
|
Cherian S, Potdar V, Jadhav S, Yadav P, Gupta N, Das M, Rakshit P, Singh S, Abraham P, Panda S, Team NIC. SARS-CoV-2 Spike Mutations, L452R, T478K, E484Q and P681R, in the Second Wave of COVID-19 in Maharashtra, India. Microorganisms 2021; 9:1542. [PMID: 34361977 PMCID: PMC8307577 DOI: 10.3390/microorganisms9071542] [Citation(s) in RCA: 410] [Impact Index Per Article: 136.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/12/2021] [Accepted: 07/01/2021] [Indexed: 12/19/2022] Open
Abstract
As the global severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic expands, genomic epidemiology and whole genome sequencing are being used to investigate its transmission and evolution. Against the backdrop of the global emergence of "variants of concern" (VOCs) during December 2020 and an upsurge in a state in the western part of India since January 2021, whole genome sequencing and analysis of spike protein mutations using sequence and structural approaches were undertaken to identify possible new variants and gauge the fitness of the current circulating strains. Phylogenetic analysis revealed that newly identified lineages B.1.617.1 and B.1.617.2 were predominantly circulating. The signature mutations possessed by these strains were L452R, T478K, E484Q, D614G and P681R in the spike protein, including within the receptor-binding domain (RBD). Of these, the mutations at residue positions 452, 484 and 681 have been reported in other globally circulating lineages. The structural analysis of RBD mutations L452R, T478K and E484Q revealed that these may possibly result in increased ACE2 binding while P681R in the furin cleavage site could increase the rate of S1-S2 cleavage, resulting in better transmissibility. The two RBD mutations, L452R and E484Q, indicated decreased binding to select monoclonal antibodies (mAbs) and may affect their neutralization potential. Further in vitro/in vivo studies would help confirm the phenotypic changes of the mutant strains. Overall, the study revealed that the newly emerged variants were responsible for the second wave of COVID-19 in Maharashtra. Lineage B.1.617.2 has been designated as a VOC delta and B.1.617.1 as a variant of interest kappa, and they are being widely reported in the rest of the country as well as globally. Continuous monitoring of these and emerging variants in India is essential.
Collapse
Affiliation(s)
- Sarah Cherian
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Varsha Potdar
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Santosh Jadhav
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Pragya Yadav
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Nivedita Gupta
- Indian Council of Medical Research, New Delhi 110029, India; (N.G.); (S.P.)
| | - Mousumi Das
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Partha Rakshit
- National Centre for Disease Control, New Delhi 110054, India; (P.R.); (S.S.)
| | - Sujeet Singh
- National Centre for Disease Control, New Delhi 110054, India; (P.R.); (S.S.)
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune 411001, India; (S.C.); (V.P.); (S.J.); (P.Y.); (M.D.)
| | - Samiran Panda
- Indian Council of Medical Research, New Delhi 110029, India; (N.G.); (S.P.)
| | | |
Collapse
|
82
|
Imai N, Hogan AB, Williams L, Cori A, Mangal TD, Winskill P, Whittles LK, Watson OJ, Knock ES, Baguelin M, Perez-Guzman PN, Gaythorpe KA, Sonabend R, Ghani AC, Ferguson NM. Interpreting estimates of coronavirus disease 2019 (COVID-19) vaccine efficacy and effectiveness to inform simulation studies of vaccine impact: a systematic review. Wellcome Open Res 2021. [DOI: 10.12688/wellcomeopenres.16992.1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background: The multiple efficacious vaccines authorised for emergency use worldwide represent the first preventative intervention against coronavirus disease 2019 (COVID-19) that does not rely on social distancing measures. The speed at which data are emerging and the heterogeneities in study design, target populations, and implementation make it challenging to interpret and assess the likely impact of vaccine campaigns on local epidemics. We reviewed available vaccine efficacy and effectiveness studies to generate working estimates that can be used to parameterise simulation studies of vaccine impact. Methods: We searched MEDLINE, the World Health Organization’s Institutional Repository for Information Sharing, medRxiv, and vaccine manufacturer websites for studies that evaluated the emerging data on COVID-19 vaccine efficacy and effectiveness. Studies providing an estimate of the efficacy or effectiveness of a COVID-19 vaccine using disaggregated data against SARS-CoV-2 infection, symptomatic disease, severe disease, death, or transmission were included. We extracted information on study population, variants of concern (VOC), vaccine platform, dose schedule, study endpoints, and measures of impact. We applied an evidence synthesis approach to capture a range of plausible and consistent parameters for vaccine efficacy and effectiveness that can be used to inform and explore a variety of vaccination strategies as the COVID-19 pandemic evolves. Results: Of the 602 articles and reports identified, 53 were included in the analysis. The availability of vaccine efficacy and effectiveness estimates varied by vaccine and were limited for VOCs. Estimates for non-primary endpoints such as effectiveness against infection and onward transmission were sparse. Synthesised estimates were relatively consistent for the same vaccine platform for wild-type, but was more variable for VOCs. Conclusions: Assessment of efficacy and effectiveness of COVID-19 vaccines is complex. Simulation studies must acknowledge and capture the uncertainty in vaccine effectiveness to robustly explore and inform vaccination policies and policy around the lifting of non-pharmaceutical interventions.
Collapse
|
83
|
Chong WC, Chellappan DK, Shukla SD, Peterson GM, Patel RP, Jha NK, Eri RD, Dua K, Tambuwala MM, Shastri MD. An Appraisal of the Current Scenario in Vaccine Research for COVID-19. Viruses 2021; 13:1397. [PMID: 34372603 PMCID: PMC8310376 DOI: 10.3390/v13071397] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/13/2021] [Accepted: 07/16/2021] [Indexed: 12/15/2022] Open
Abstract
The recent coronavirus disease 2019 (COVID-19) outbreak has drawn global attention, affecting millions, disrupting economies and healthcare modalities. With its high infection rate, COVID-19 has caused a colossal health crisis worldwide. While information on the comprehensive nature of this infectious agent, SARS-CoV-2, still remains obscure, ongoing genomic studies have been successful in identifying its genomic sequence and the presenting antigen. These may serve as promising, potential therapeutic targets in the effective management of COVID-19. In an attempt to establish herd immunity, massive efforts have been directed and driven toward developing vaccines against the SARS-CoV-2 pathogen. This review, in this direction, is aimed at providing the current scenario and future perspectives in the development of vaccines against SARS-CoV-2.
Collapse
Affiliation(s)
- Wai Chin Chong
- Department of Molecular and Translational Science, Monash University, Clayton 3168, Australia;
| | - Dinesh K. Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University (IMU), Kuala Lumpur 57000, Malaysia;
| | - Shakti D. Shukla
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney 2007, Australia; (S.D.S.); (K.D.)
| | - Gregory M. Peterson
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart 7005, Australia; (G.M.P.); (R.P.P.)
| | - Rahul P. Patel
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart 7005, Australia; (G.M.P.); (R.P.P.)
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida 201310, UP, India;
| | - Rajaraman D. Eri
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston 7248, Australia;
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Sydney 2007, Australia; (S.D.S.); (K.D.)
| | - Murtaza M. Tambuwala
- School of Pharmacy and Pharmaceutical Science, Ulster University, Coleraine BT52 1SA, UK
| | - Madhur D. Shastri
- School of Pharmacy and Pharmacology, University of Tasmania, Hobart 7005, Australia; (G.M.P.); (R.P.P.)
- School of Health Sciences, College of Health and Medicine, University of Tasmania, Launceston 7248, Australia;
| |
Collapse
|
84
|
Trombetta CM, Marchi S, Viviani S, Manenti A, Benincasa L, Ruello A, Bombardieri E, Vicenti I, Zazzi M, Montomoli E. Serum Neutralizing Activity against B.1.1.7, B.1.351, and P.1 SARS-CoV-2 Variants of Concern in Hospitalized COVID-19 Patients. Viruses 2021; 13:1347. [PMID: 34372553 PMCID: PMC8310013 DOI: 10.3390/v13071347] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/01/2021] [Accepted: 07/08/2021] [Indexed: 11/17/2022] Open
Abstract
The recent spreading of new SARS-CoV-2 variants, carrying several mutations in the spike protein, could impact immune protection elicited by natural infection or conferred by vaccination. In this study, we evaluated the neutralizing activity against the viral variants that emerged in the United Kingdom (B.1.1.7), Brazil (P.1), and South Africa (B.1.351) in human serum samples from hospitalized patients infected by SARS-CoV-2 during the first pandemic wave in Italy in 2020. Of the patients studied, 59.5% showed a decrease (≥2 fold) in neutralizing antibody titer against B.1.1.7, 83.3% against P.1, and 90.5% against B.1.351 with respect to the original strain. The reduction in antibody titers against all analyzed variants, and in particular P.1 and B.1.351, suggests that previous symptomatic infection might be not fully protective against exposure to SARS-CoV-2 variants carrying a set of relevant spike mutations.
Collapse
Affiliation(s)
- Claudia Maria Trombetta
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (S.M.); (S.V.); (E.M.)
| | - Serena Marchi
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (S.M.); (S.V.); (E.M.)
| | - Simonetta Viviani
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (S.M.); (S.V.); (E.M.)
| | - Alessandro Manenti
- VisMederi srl, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy;
| | - Linda Benincasa
- VisMederi Research srl, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy;
| | - Antonella Ruello
- Humanitas Gavazzeni, Via Mauro Gavazzeni 21, 24125 Bergamo, Italy; (A.R.); (E.B.)
| | - Emilio Bombardieri
- Humanitas Gavazzeni, Via Mauro Gavazzeni 21, 24125 Bergamo, Italy; (A.R.); (E.B.)
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (M.Z.)
| | - Maurizio Zazzi
- Department of Medical Biotechnologies, University of Siena, 53100 Siena, Italy; (I.V.); (M.Z.)
| | - Emanuele Montomoli
- Department of Molecular and Developmental Medicine, University of Siena, 53100 Siena, Italy; (S.M.); (S.V.); (E.M.)
- VisMederi srl, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy;
- VisMederi Research srl, Strada del Petriccio e Belriguardo 35, 53100 Siena, Italy;
| |
Collapse
|
85
|
Salleh MZ, Derrick JP, Deris ZZ. Structural Evaluation of the Spike Glycoprotein Variants on SARS-CoV-2 Transmission and Immune Evasion. Int J Mol Sci 2021; 22:7425. [PMID: 34299045 PMCID: PMC8306177 DOI: 10.3390/ijms22147425] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 07/07/2021] [Accepted: 07/07/2021] [Indexed: 02/07/2023] Open
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents significant social, economic and political challenges worldwide. SARS-CoV-2 has caused over 3.5 million deaths since late 2019. Mutations in the spike (S) glycoprotein are of particular concern because it harbours the domain which recognises the angiotensin-converting enzyme 2 (ACE2) receptor and is the target for neutralising antibodies. Mutations in the S protein may induce alterations in the surface spike structures, changing the conformational B-cell epitopes and leading to a potential reduction in vaccine efficacy. Here, we summarise how the more important variants of SARS-CoV-2, which include cluster 5, lineages B.1.1.7 (Alpha variant), B.1.351 (Beta), P.1 (B.1.1.28/Gamma), B.1.427/B.1.429 (Epsilon), B.1.526 (Iota) and B.1.617.2 (Delta) confer mutations in their respective spike proteins which enhance viral fitness by improving binding affinity to the ACE2 receptor and lead to an increase in infectivity and transmission. We further discuss how these spike protein mutations provide resistance against immune responses, either acquired naturally or induced by vaccination. This information will be valuable in guiding the development of vaccines and other therapeutics for protection against the ongoing coronavirus disease 2019 (COVID-19) pandemic.
Collapse
Affiliation(s)
- Mohd Zulkifli Salleh
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Malaysia;
| | - Jeremy P. Derrick
- Lydia Becker Institute of Immunology and Inflammation, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, The University of Manchester, Oxford Road, Manchester M13 9PL, UK;
| | - Zakuan Zainy Deris
- Department of Medical Microbiology & Parasitology, School of Medical Sciences, Universiti Sains Malaysia Health Campus, Kubang Kerian 16150, Malaysia;
| |
Collapse
|
86
|
Planas D, Veyer D, Baidaliuk A, Staropoli I, Guivel-Benhassine F, Rajah MM, Planchais C, Porrot F, Robillard N, Puech J, Prot M, Gallais F, Gantner P, Velay A, Le Guen J, Kassis-Chikhani N, Edriss D, Belec L, Seve A, Courtellemont L, Péré H, Hocqueloux L, Fafi-Kremer S, Prazuck T, Mouquet H, Bruel T, Simon-Lorière E, Rey FA, Schwartz O. Reduced sensitivity of SARS-CoV-2 variant Delta to antibody neutralization. Nature 2021; 596:276-280. [PMID: 34237773 DOI: 10.1038/s41586-021-03777-9] [Citation(s) in RCA: 1423] [Impact Index Per Article: 474.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 06/29/2021] [Indexed: 12/27/2022]
Abstract
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.
Collapse
Affiliation(s)
- Delphine Planas
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Vaccine Research Institute, Creteil, France
| | - David Veyer
- INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, Paris, France.,Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Artem Baidaliuk
- G5 Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
| | - Isabelle Staropoli
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | | | - Maaran Michael Rajah
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France.,Université de Paris, Sorbonne Paris Cité, Paris, France
| | - Cyril Planchais
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, Paris, France
| | - Françoise Porrot
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Nicolas Robillard
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Julien Puech
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Matthieu Prot
- G5 Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
| | - Floriane Gallais
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Université de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
| | - Pierre Gantner
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Université de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
| | - Aurélie Velay
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Université de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
| | - Julien Le Guen
- Service de Gériatrie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Najiby Kassis-Chikhani
- Unité d'Hygiène Hospitalière, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Dhiaeddine Edriss
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Laurent Belec
- Laboratoire de Virologie, Service de Microbiologie, Hôpital Européen Georges Pompidou, Assistance Publique des Hôpitaux de Paris, Paris, France
| | - Aymeric Seve
- CHR d'Orléans, Service de Maladies Infectieuses, Orléans, France
| | | | - Hélène Péré
- INSERM, Functional Genomics of Solid Tumors (FunGeST), Centre de Recherche des Cordeliers, Université de Paris and Sorbonne Université, Paris, France
| | | | - Samira Fafi-Kremer
- CHU de Strasbourg, Laboratoire de Virologie, Strasbourg, France.,Université de Strasbourg, INSERM, IRM UMR_S 1109, Strasbourg, France
| | - Thierry Prazuck
- CHR d'Orléans, Service de Maladies Infectieuses, Orléans, France
| | - Hugo Mouquet
- Laboratory of Humoral Immunology, Department of Immunology, Institut Pasteur, INSERM U1222, Paris, France
| | - Timothée Bruel
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France. .,Vaccine Research Institute, Creteil, France.
| | - Etienne Simon-Lorière
- G5 Evolutionary Genomics of RNA Viruses, Department of Virology, Institut Pasteur, Paris, France
| | - Felix A Rey
- Structural Virology Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Olivier Schwartz
- Virus and Immunity Unit, Department of Virology, Institut Pasteur, CNRS UMR 3569, Paris, France. .,Vaccine Research Institute, Creteil, France.
| |
Collapse
|
87
|
Raman R, Patel KJ, Ranjan K. COVID-19: Unmasking Emerging SARS-CoV-2 Variants, Vaccines and Therapeutic Strategies. Biomolecules 2021; 11:993. [PMID: 34356617 PMCID: PMC8301790 DOI: 10.3390/biom11070993] [Citation(s) in RCA: 107] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the etiological agent of the coronavirus disease 2019 (COVID-19) pandemic, which has been a topic of major concern for global human health. The challenge to restrain the COVID-19 pandemic is further compounded by the emergence of several SARS-CoV-2 variants viz. B.1.1.7 (Alpha), B.1.351 (Beta), P1 (Gamma) and B.1.617.2 (Delta), which show increased transmissibility and resistance towards vaccines and therapies. Importantly, there is convincing evidence of increased susceptibility to SARS-CoV-2 infection among individuals with dysregulated immune response and comorbidities. Herein, we provide a comprehensive perspective regarding vulnerability of SARS-CoV-2 infection in patients with underlying medical comorbidities. We discuss ongoing vaccine (mRNA, protein-based, viral vector-based, etc.) and therapeutic (monoclonal antibodies, small molecules, plasma therapy, etc.) modalities designed to curb the COVID-19 pandemic. We also discuss in detail, the challenges posed by different SARS-CoV-2 variants of concern (VOC) identified across the globe and their effects on therapeutic and prophylactic interventions.
Collapse
Affiliation(s)
- Renuka Raman
- Department of Surgery, Weill Cornell Medical College, New York, NY 10065, USA;
| | - Krishna J. Patel
- Mount Sinai Innovation Partners, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Kishu Ranjan
- School of Medicine, Yale University, New Haven, CT 06519, USA
| |
Collapse
|
88
|
Duerr R, Crosse KM, Valero-Jimenez AM, Dittmann M. SARS-CoV-2 Portrayed against HIV: Contrary Viral Strategies in Similar Disguise. Microorganisms 2021; 9:1389. [PMID: 34198973 PMCID: PMC8307803 DOI: 10.3390/microorganisms9071389] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/06/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
SARS-CoV-2 and HIV are zoonotic viruses that rapidly reached pandemic scale, causing global losses and fear. The COVID-19 and AIDS pandemics ignited massive efforts worldwide to develop antiviral strategies and characterize viral architectures, biological and immunological properties, and clinical outcomes. Although both viruses have a comparable appearance as enveloped viruses with positive-stranded RNA and envelope spikes mediating cellular entry, the entry process, downstream biological and immunological pathways, clinical outcomes, and disease courses are strikingly different. This review provides a systemic comparison of both viruses' structural and functional characteristics, delineating their distinct strategies for efficient spread.
Collapse
Affiliation(s)
- Ralf Duerr
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA; (K.M.C.); (A.M.V.-J.); (M.D.)
| | | | | | | |
Collapse
|
89
|
Focosi D, Tuccori M, Baj A, Maggi F. SARS-CoV-2 Variants: A Synopsis of In Vitro Efficacy Data of Convalescent Plasma, Currently Marketed Vaccines, and Monoclonal Antibodies. Viruses 2021; 13:1211. [PMID: 34201767 PMCID: PMC8310233 DOI: 10.3390/v13071211] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/01/2021] [Accepted: 06/02/2021] [Indexed: 12/24/2022] Open
Abstract
We summarize here in vitro evidences of efficacy for convalescent plasma, currently approved vaccines and monoclonal antibodies against SARS-CoV-2 variants of concern (VOC: B.1.1.7, B.1.351, P.1, and B.1.617.2), variants of interest (VOI: B.1.427/B.1.429, P.2, B.1.525, P.3, B.1.526, and B.1.671.1), and other strains (B.1.1.298 and B.1.258delta). While waiting from real world clinical efficacy, these data provide guidance for the treating physician.
Collapse
Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, Via Paraisa 2, 56124 Pisa, Italy
| | - Marco Tuccori
- Division of Pharmacovigilance, Pisa University Hospital, Via Paradisa 2, 56124 Pisa, Italy
| | - Andreina Baj
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| | - Fabrizio Maggi
- Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy
| |
Collapse
|
90
|
COVID-19 variants in India: Potential role in second wave and impact on vaccination. Heart Lung 2021; 50:784-787. [PMID: 34217989 PMCID: PMC8173455 DOI: 10.1016/j.hrtlng.2021.05.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 12/01/2022]
|