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Demongeot J, Magal P. Data-driven mathematical modeling approaches for COVID-19: A survey. Phys Life Rev 2024; 50:166-208. [PMID: 39142261 DOI: 10.1016/j.plrev.2024.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2024] [Accepted: 08/02/2024] [Indexed: 08/16/2024]
Abstract
In this review, we successively present the methods for phenomenological modeling of the evolution of reported and unreported cases of COVID-19, both in the exponential phase of growth and then in a complete epidemic wave. After the case of an isolated wave, we present the modeling of several successive waves separated by endemic stationary periods. Then, we treat the case of multi-compartmental models without or with age structure. Eventually, we review the literature, based on 260 articles selected in 11 sections, ranging from the medical survey of hospital cases to forecasting the dynamics of new cases in the general population. This review favors the phenomenological approach over the mechanistic approach in the choice of references and provides simulations of the evolution of the number of observed cases of COVID-19 for 10 states (California, China, France, India, Israel, Japan, New York, Peru, Spain and United Kingdom).
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Affiliation(s)
- Jacques Demongeot
- Université Grenoble Alpes, AGEIS EA7407, La Tronche, F-38700, France.
| | - Pierre Magal
- Department of Mathematics, Faculty of Arts and Sciences, Beijing Normal University, Zhuhai, 519087, China; Univ. Bordeaux, IMB, UMR 5251, Talence, F-33400, France; CNRS, IMB, UMR 5251, Talence, F-33400, France
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2
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Prasad R, Ajith H, Kumar Chandrakumaran N, Dnyaneshwar Khangar P, Mohan A, Nelson-Sathi S. In silico study identifies peptide inhibitors that negate the effect of non-synonymous mutations in major drug targets of SARS-CoV-2 variants. J Biomol Struct Dyn 2023; 41:9551-9561. [PMID: 36377464 DOI: 10.1080/07391102.2022.2143426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 10/29/2022] [Indexed: 11/16/2022]
Abstract
Since its advent in December 2019, SARS-CoV-2 has diverged into multiple variants with differing levels of virulence owing to the accumulation of mutations in its genome. The structural changes induced by non-synonymous mutations in major drug targets of the virus are known to alter the binding of potential antagonistic inhibitors. Here, we analyzed the effects of non-synonymous mutations in major targets of SARS-CoV-2 in response to potential peptide inhibitors. We screened 12 peptides reported to have anti-viral properties against RBD and 5 peptides against Mpro of SARS-CoV-2 variants using molecular docking and simulation approaches. The mutational landscape of RBD among SARS-CoV-2 variants had 21 non-synonymous mutations across 18 distinct sites. Among these, 14 mutations were present in the RBM region directly interacting with the hACE2 receptor. However, Only 3 non-synonymous mutations were observed in Mpro. We found that LCB1 - a de novo-synthesized peptide has the highest binding affinity to RBD despite non-synonymous mutations in variants and engages key residues of RBD-hACE2 interaction such as K417, E484, N487, and N501. Similarly, an antimicrobial peptide; 2JOS, was identified against Mpro with high binding affinity as it interacts with key residues in dimerization sites such as E166 and F140 crucial for viral replication. MD simulations affirm the stability of RBD-LCB1 and Mpro-2JOS complexes with an average RMSD of 1.902 and 2.476 respectively. We ascertain that LCB1 and 2JOS peptides are promising inhibitors to combat emerging variants of SARS-CoV-2 and thus warrant further investigations using in-vitro and in-vivo analysis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Roshny Prasad
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Harikrishnan Ajith
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | | | | | - Anand Mohan
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
| | - Shijulal Nelson-Sathi
- Bioinformatics Laboratory, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, India
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de Mello Almeida Maziero L, Giovanetti M, Fonseca V, Zardin MCSU, de Castro Lichs GG, de Rezende Romera GR, Tsuha DH, Frias DFR, Escandolhero VC, Demarchi LH, Domingues Castilho L, Barbosa KF, Tebet DGM, Xavier J, Fritsch H, Lima M, de Oliveira C, Santos EV, Kashima S, Said RFDC, Rosewell A, Croda J, Alcantara LCJ, Cavalheiro Maymone Gonçalves C. Unveiling the Impact of the Omicron Variant: Insights from Genomic Surveillance in Mato Grosso do Sul, Midwest Brazil. Viruses 2023; 15:1604. [PMID: 37515290 PMCID: PMC10386548 DOI: 10.3390/v15071604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/15/2023] [Accepted: 07/20/2023] [Indexed: 07/30/2023] Open
Abstract
Genomic surveillance has emerged as a crucial tool in monitoring and understanding the dynamics of viral variants during the COVID-19 pandemic. In the Midwest region of Brazil, Mato Grosso do Sul has faced a significant burden from the SARS-CoV-2 epidemic, with a total of 613,000 confirmed cases as of June 2023. In collaboration with the Central Public Health Laboratory in the capital city of Campo Grande, we conducted a portable whole-genome sequencing and phylodynamic analysis to investigate the circulation of the Omicron variant in the region. The study aimed to uncover the genomic landscape and provide valuable insights into the prevalence and transmission patterns of this highly transmissible variant. Our findings revealed an increase in the number of cases within the region during 2022, followed by a gradual decline as a result of the successful impact of the vaccination program together with the capacity of this unpredictable and very transmissible variant to quickly affect the proportion of susceptible population. Genomic data indicated multiple introduction events, suggesting that human mobility played a differential role in the variant's dispersion dynamics throughout the state. These findings emphasize the significance of implementing public health interventions to mitigate further spread and highlight the powerful role of genomic monitoring in promptly tracking and uncovering the circulation of viral strains. Together those results underscore the importance of proactive surveillance, rapid genomic sequencing, and data sharing to facilitate timely public health responses.
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Affiliation(s)
- Lívia de Mello Almeida Maziero
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 9031-350, Brazil
- Universidade Federal de EMato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Marta Giovanetti
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Preto 30190-009, Brazil
- Sciences and Technologies for Sustainable Development and One Health, University of Campus Bio-Medico of Rome, 00128 Rome, Italy
| | - Vagner Fonseca
- Coordenação de Vigilância, Preparação e Resposta à Emergências e Desastres (PHE), Organização Pan-Americana da Saúde/Organização Mundial da Saúde (OPAS/OMS), Brasília 25045-002, Brazil
| | | | | | | | | | | | | | - Luiz Henrique Demarchi
- SES-MS-Laboratório Central de Saúde Pública de Mato Grosso do Sul, Campo Grande 79080-320, Brazil
| | - Larissa Domingues Castilho
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 9031-350, Brazil
- Universidade Federal de EMato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Karine Ferreira Barbosa
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 9031-350, Brazil
- Universidade Federal de EMato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Danielle Galindo Martins Tebet
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 9031-350, Brazil
- Universidade Federal de EMato Grosso do Sul, Campo Grande 79070-900, Brazil
| | - Joilson Xavier
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Preto 30190-009, Brazil
| | - Hegger Fritsch
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Preto 30190-009, Brazil
| | - Mauricio Lima
- Instituto Rene Rachou, Fundação Oswaldo Cruz, Preto 30190-009, Brazil
| | - Carla de Oliveira
- lnstituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro 21040-900, Brazil
| | | | - Simone Kashima
- Fundação Hemocentro de Ribeirão Preto, Rio de Janeiro 14015-160, Brazil
| | | | - Alexander Rosewell
- Organização Pan-Americana da Saúde/Organização Mundial da Saúde (OPAS/OMS), Brasilia 25045-002, Brazil
| | - Julio Croda
- Fundação Oswaldo Cruz, Universidade Federal de Mato Grosso do Sul-UFMS, Campo Grande 79081-746, Brazil
| | | | - Crhistinne Cavalheiro Maymone Gonçalves
- Secretaria de Estado de Saúde de Mato Grosso do Sul, Campo Grande 9031-350, Brazil
- Universidade Federal de EMato Grosso do Sul, Campo Grande 79070-900, Brazil
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Alongi A, D'Aiuto F, Montomoli C, Borrelli P. Impact of the First Year of the COVID-19 Pandemic on Pediatric Emergency Department Attendance in a Tertiary Center in South Italy: An Interrupted Time-Series Analysis. Healthcare (Basel) 2023; 11:healthcare11111638. [PMID: 37297778 DOI: 10.3390/healthcare11111638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 05/30/2023] [Accepted: 06/01/2023] [Indexed: 06/12/2023] Open
Abstract
BACKGROUND The evidence shows a reduction in pediatric emergency department (PED) flows during the early stages of the COVID-19 pandemic. Using interrupted time-series analysis, we evaluated the impact of different stages of the pandemic response on overall and cause-specific PED attendance at a tertiary hospital in south Italy. Our methods included evaluations of total visits, hospitalizations, accesses for critical illnesses and four etiological categories (transmissible and non-transmissible infectious diseases, trauma and mental-health) during March-December 2020, which were compared with analogous intervals from 2016 to 2019; the pandemic period was divided into three segments: the "first lockdown" (FL, 9 March-3 May), the "post-lockdown" (PL, 4 May-6 November) and the "second lockdown" (SL, 7 November-31 December). Our results showed that attendance dropped by a mean of 50.09% during the pandemic stages, while hospitalizations increased. Critical illnesses decreased during FL (incidence rate ratio -IRR- 0.37, 95% CI 0.13, 0.88) e SL (IRR 0.09, 95% CI 0.01, 0.74) and transmissible disease related visits reduced more markedly and persistently (FL: IRR 0.18, 95% CI 0.14, 0.24; PL: IRR 0.20, 95% CI 0.13, 0.31, SL: IRR 0.17, 95% CI 0.10, 0.29). Non-infectious diseases returned to pre-COVID-19 pandemic levels by PL. We concluded that that the results highlight the specific effect of the late 2020 containment measures on transmissible infectious diseases and their burden on pediatric emergency resources. This evidence can inform resource allocation and interventions to mitigate the impact of infectious diseases on pediatric populations and the health-care system.
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Affiliation(s)
- Alessandra Alongi
- Pediatric Emergency Unit, Di Cristina Hospital, Azienda Ospedaliera di Rilievo Nazionale e di Alta Specializzazione Civico Di Cristina e Benfratelli, 90127 Palermo, Italy
| | - Francesca D'Aiuto
- Pediatric Emergency Unit, Di Cristina Hospital, Azienda Ospedaliera di Rilievo Nazionale e di Alta Specializzazione Civico Di Cristina e Benfratelli, 90127 Palermo, Italy
| | - Cristina Montomoli
- Unit of Biostatistics and Clinical Epidemiology, Department of Public Health, Experimental and Forensic Medicine, University of Pavia, 27100 Pavia, Italy
| | - Paola Borrelli
- Laboratory of Biostatistics, Department of Medical, Oral and Biotechnological Sciences, G. d'Annunzio University of Chieti-Pescara, 66100 Chieti, Italy
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Rife Magalis B, Rich S, Tagliamonte MS, Mavian C, Cash MN, Riva A, Marini S, Amador DM, Zhang Y, Shapiro J, Horine A, Starostik P, Pieretti M, Vega S, Paula Lacombe A, Salinas J, Stevenson M, Myers P, Glenn Morris J, Lauzardo M, Prosperi M, Salemi M. Severe Acute Respiratory Syndrome Coronavirus 2 Delta Vaccine Breakthrough Transmissibility in Alachua County, Florida. Clin Infect Dis 2022; 75:1618-1627. [PMID: 35271704 PMCID: PMC9617581 DOI: 10.1093/cid/ciac197] [Citation(s) in RCA: 2] [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: 11/30/2021] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant has caused a dramatic resurgence in infections in the United Sates, raising questions regarding potential transmissibility among vaccinated individuals. METHODS Between October 2020 and July 2021, we sequenced 4439 SARS-CoV-2 full genomes, 23% of all known infections in Alachua County, Florida, including 109 vaccine breakthrough cases. Univariate and multivariate regression analyses were conducted to evaluate associations between viral RNA burden and patient characteristics. Contact tracing and phylogenetic analysis were used to investigate direct transmissions involving vaccinated individuals. RESULTS The majority of breakthrough sequences with lineage assignment were classified as Delta variants (74.6%) and occurred, on average, about 3 months (104 ± 57.5 days) after full vaccination, at the same time (June-July 2021) of Delta variant exponential spread within the county. Six Delta variant transmission pairs between fully vaccinated individuals were identified through contact tracing, 3 of which were confirmed by phylogenetic analysis. Delta breakthroughs exhibited broad viral RNA copy number values during acute infection (interquartile range, 1.2-8.64 Log copies/mL), on average 38% lower than matched unvaccinated patients (3.29-10.81 Log copies/mL, P < .00001). Nevertheless, 49% to 50% of all breakthroughs, and 56% to 60% of Delta-infected breakthroughs exhibited viral RNA levels above the transmissibility threshold (4 Log copies/mL) irrespective of time after vaccination. CONCLUSIONS Delta infection transmissibility and general viral RNA quantification patterns in vaccinated individuals suggest limited levels of sterilizing immunity that need to be considered by public health policies. In particular, ongoing evaluation of vaccine boosters should specifically address whether extra vaccine doses curb breakthrough contribution to epidemic spread.
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Affiliation(s)
- Brittany Rife Magalis
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, University of Florida, Gainesville, Florida, USA
| | - Shannan Rich
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
- Florida Department of Health, Alachua County, Gainesville, Florida, USA
| | - Massimiliano S Tagliamonte
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, University of Florida, Gainesville, Florida, USA
| | - Carla Mavian
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, University of Florida, Gainesville, Florida, USA
| | - Melanie N Cash
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, University of Florida, Gainesville, Florida, USA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Simone Marini
- Department of Pathology, University of Florida, Gainesville, Florida, USA
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
| | - David Moraga Amador
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, USA
| | - Jerne Shapiro
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
- Florida Department of Health, Alachua County, Gainesville, Florida, USA
| | - Amelia Horine
- Florida Department of Health, Alachua County, Gainesville, Florida, USA
| | - Petr Starostik
- Department of Pathology, University of Florida, Gainesville, Florida, USA
| | | | | | | | - Jessica Salinas
- University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Mario Stevenson
- University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Paul Myers
- Florida Department of Health, Alachua County, Gainesville, Florida, USA
| | - J Glenn Morris
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida
| | - Michael Lauzardo
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Florida Department of Health, Alachua County, Gainesville, Florida, USA
- Department of Medicine, College of Medicine, University of Florida, Gainesville, Florida
| | - Mattia Prosperi
- Department of Epidemiology, University of Florida, Gainesville, Florida, USA
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, Florida, USA
- Department of Pathology, University of Florida, Gainesville, Florida, USA
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Gut Microbiota and COVID-19: Potential Implications for Disease Severity. Pathogens 2022; 11:pathogens11091050. [PMID: 36145482 PMCID: PMC9503814 DOI: 10.3390/pathogens11091050] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 09/02/2022] [Accepted: 09/14/2022] [Indexed: 12/11/2022] Open
Abstract
The SARS-CoV-2 pandemic resulted in an unprecedented global crisis. SARS-CoV-2 primarily causes lung infection trough the binding of the virus with the ACE-2 cell receptor located on the surface of the alveolar epithelial cells. Notably, ACE-2 cell receptors are also expressed in the epithelial cells of the intestinal tract (GI). Recent data showed that the microbial communities of the GI might act as local and systematic inflammatory modulators. Gastrointestinal symptoms, including diarrhea, are frequently observed in infected individuals, and recent released data indicate that SARS-CoV-2 may also spread by fecal–oral transmission. Moreover, the gut microbiota’s ecosystem can regulate and be regulated by invading pathogens, including viruses, facilitating an effective immune response, which in turn results in less severe diseases. In this regard, increased SARS-CoV-2 mortality and morbidities appear to be frequently observed in elderly immunocompromised patients and in people with essential health problems, such as diabetes, who, indeed, tend to have a less diverse gut microbiota (dysbiosis). Therefore, it is important to understand how the interaction between the gut microbiota and SARS-CoV-2 might shape the intensity of the infection and different clinical outcomes. Here, we provide insights into the current knowledge of dysbiosis during SARS-CoV-2 infection and methods that may be used to re-establish a more correct microbiota composition.
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Flores-Alanis A, Delgado G, Espinosa-Camacho LF, Rodríguez-Gómez F, Cruz-Rangel A, Sandner-Miranda L, Cravioto A, Morales-Espinosa R. Two Years of Evolutionary Dynamics of SARS-CoV-2 in Mexico, With Emphasis on the Variants of Concern. Front Microbiol 2022; 13:886585. [PMID: 35865920 PMCID: PMC9294468 DOI: 10.3389/fmicb.2022.886585] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 06/07/2022] [Indexed: 01/09/2023] Open
Abstract
Background The advance of the COVID-19 pandemic and spread of SARS-CoV-2 around the world has generated the emergence of new genomic variants. Those variants with possible clinical and therapeutic implications have been classified as variants of concern (VOCs) and variants of interest (VOIs). Objective This study aims to describe the COVID-19 pandemic and build the evolutionary and demographic dynamics of SARS-CoV-2 populations in Mexico, with emphasis on VOCs. Methods 30,645 complete genomes of SARS-CoV-2 from Mexico were obtained from GISAID databases up to January 25, 2022. A lineage assignment and phylogenetic analysis was completed, and demographic history for Alpha, Gamma, Delta and Omicron VOCs, and the Mexican variant (B.1.1.519) was performed. Results 148 variants were detected among the 30,645 genomes analyzed with the Delta variant being the most prevalent in the country, representing 49.7% of all genomes. Conclusion The COVID-19 pandemic in Mexico was caused by several introductions of SARS-CoV-2, mainly from the United States of America and Europe, followed by local transmission. Regional molecular epidemiological surveillance must implement to detect emergence, introductions and spread of new variants with biologically important mutations.
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Affiliation(s)
- Alejandro Flores-Alanis
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Gabriela Delgado
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Luis F. Espinosa-Camacho
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Flor Rodríguez-Gómez
- Laboratorio de Análisis de la Biodiversidad y Genómica, Departamento de Bioingeniería Traslacional, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara, Mexico
| | - Armando Cruz-Rangel
- Laboratorio de Bioquímica de Enfermedades Crónicas, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Luisa Sandner-Miranda
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Alejandro Cravioto
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Rosario Morales-Espinosa
- Laboratorio de Genómica Bacteriana, Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City, Mexico
- *Correspondence: Rosario Morales-Espinosa,
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Magalis BR, Mavian C, Tagliamonte M, Rich SN, Cash M, Riva A, Loeb JC, Norris M, Amador DM, Zhang Y, Shapiro J, Starostik P, Marini S, Myers P, Ostrov DA, Lednicky JA, Glenn Morris J, Lauzardo M, Salemi M. Low-frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled-edged sword. J Med Virol 2022; 94:3192-3202. [PMID: 35307848 PMCID: PMC9325371 DOI: 10.1002/jmv.27726] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 02/24/2022] [Accepted: 03/16/2022] [Indexed: 12/15/2022]
Abstract
The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) has raised questions regarding vaccine protection against SARS-CoV-2 infection, transmission, and ongoing virus evolution. Twenty-three mildly symptomatic "vaccination breakthrough" infections were identified as early as January 2021 in Alachua County, Florida, among individuals fully vaccinated with either the BNT162b2 (Pfizer) or the Ad26 (Janssen/J&J) vaccines. SARS-CoV-2 genomes were successfully generated for 11 of the vaccine breakthroughs, and 878 individuals in the surrounding area and were included for reference-based phylogenetic investigation. These 11 individuals were characterized by infection with VOCs, but also low-frequency variants present within the surrounding population. Low-frequency mutations were observed, which have been more recently identified as mutations of interest owing to their location within targeted immune epitopes (P812L) and association with increased replicative capacity (L18F). We present these results to posit the nature of the efficacy of vaccines in reducing symptoms as both a blessing and a curse-as vaccination becomes more widespread and self-motivated testing reduced owing to the absence of severe symptoms, we face the challenge of early recognition of novel mutations of potential concern. This case study highlights the critical need for continued testing and monitoring of infection and transmission among individuals regardless of vaccination status.
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Affiliation(s)
- Brittany R. Magalis
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Department of PathologyUniversity of FloridaGainesvilleFloridaUSA
| | - Carla Mavian
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Department of PathologyUniversity of FloridaGainesvilleFloridaUSA
| | - Massimiliano Tagliamonte
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Department of PathologyUniversity of FloridaGainesvilleFloridaUSA
| | - Shannan N. Rich
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Department of Epidemiology, College of Public Health and Health Professions and College of MedicineUniversity of FloridaGainesvilleFloridaUSA
- Florida Department of HealthGainesvilleFloridaUSA
| | - Melanie Cash
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Department of PathologyUniversity of FloridaGainesvilleFloridaUSA
| | - Alberto Riva
- Interdisciplinary Center for Biotechnology ResearchUniversity of FloridaGainesvilleFloridaUSA
| | - Julia C. Loeb
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Department of Environmental and Global HealthUniversity of FloridaGainesvilleFloridaUSA
| | - Michael Norris
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Department of Environmental and Global HealthUniversity of FloridaGainesvilleFloridaUSA
| | - David M. Amador
- Interdisciplinary Center for Biotechnology ResearchUniversity of FloridaGainesvilleFloridaUSA
| | - Yanping Zhang
- Interdisciplinary Center for Biotechnology ResearchUniversity of FloridaGainesvilleFloridaUSA
| | - Jerne Shapiro
- Department of Epidemiology, College of Public Health and Health Professions and College of MedicineUniversity of FloridaGainesvilleFloridaUSA
- Florida Department of HealthGainesvilleFloridaUSA
| | - Petr Starostik
- Department of PathologyUniversity of FloridaGainesvilleFloridaUSA
| | - Simone Marini
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Department of Epidemiology, College of Public Health and Health Professions and College of MedicineUniversity of FloridaGainesvilleFloridaUSA
| | - Paul Myers
- Florida Department of HealthGainesvilleFloridaUSA
| | - David A. Ostrov
- Department of PathologyUniversity of FloridaGainesvilleFloridaUSA
| | - John A. Lednicky
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Department of Environmental and Global HealthUniversity of FloridaGainesvilleFloridaUSA
| | - J. Glenn Morris
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Division of Infectious Diseases and Global Medicine, College of MedicineUniversity of FloridaGainesvilleFloridaUSA
| | - Michael Lauzardo
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Florida Department of HealthGainesvilleFloridaUSA
- Division of Infectious Diseases and Global Medicine, College of MedicineUniversity of FloridaGainesvilleFloridaUSA
| | - Marco Salemi
- Emerging Pathogens InstituteUniversity of FloridaGainesvilleFloridaUSA
- Department of PathologyUniversity of FloridaGainesvilleFloridaUSA
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Prevention of HBV Reactivation in Hemato-Oncologic Setting during COVID-19. Pathogens 2022; 11:pathogens11050567. [PMID: 35631088 PMCID: PMC9144674 DOI: 10.3390/pathogens11050567] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/06/2022] [Accepted: 05/10/2022] [Indexed: 02/04/2023] Open
Abstract
Onco-hematologic patients are highly susceptible to SARS-CoV-2 infection and, once infected, frequently develop COVID-19 due to the immunosuppression caused by tumor growth, chemotherapy and immunosuppressive therapy. In addition, COVID-19 has also been recognized as a further cause of HBV reactivation, since its treatment includes the administration of corticosteroids and some immunosuppressive drugs. Consequently, onco-hematologic patients should undergo SARS-CoV-2 vaccination and comply with the rules imposed by lockdowns or other forms of social distancing. Furthermore, onco-hematologic facilities should be adapted to new needs and provided with numerically adequate health personnel vaccinated against SARS-CoV-2 infection. Onco-hematologic patients, both HBsAg-positive and HBsAg-negative/HBcAb-positive, may develop HBV reactivation, made possible by the support of the covalently closed circular DNA (cccDNA) persisting in the hepatocytic nuclei of patients with an ongoing or past HBV infection. This occurrence must be prevented by administering high genetic barrier HBV nucleo(t)side analogues before and throughout the antineoplastic treatment, and then during a long-term post-treatment follow up. The prevention of HBV reactivation during the SARS-CoV-2 pandemic is the topic of this narrative review.
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Li J, Huo X, Chen Y. Threshold dynamics of a viral infection model with defectively infected cells. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2022; 19:6489-6503. [PMID: 35730268 DOI: 10.3934/mbe.2022305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
In this paper, we investigate the global dynamics of a viral infection model with defectively infected cells. The explicit expression of the basic reproduction number of virus is obtained by using the next generation matrix approach, where each term has a clear biological interpretation. We show that the basic reproduction number serves as a threshold parameter. The virus dies out if the basic reproduction number is not greater than unity, otherwise the virus persists and the viral load eventually approaches a positive number. The result is established by Lyapunov's direct method. Our novel arguments for the stability of the infection equilibrium not only simplify the analysis (compared with some traditional ones in the literature) but also demonstrate some correlation between the two Lyapunov functions for the infection-free and infection equilibria.
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Affiliation(s)
- Jianquan Li
- Department of Mathematics, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Xiaoyu Huo
- Department of Mathematics, Shaanxi University of Science and Technology, Xi'an, 710021, China
| | - Yuming Chen
- Department of Mathematics, Wilfrid Laurier University, Waterloo, ON N2L 3C5, Canada
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11
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SARS-CoV-2 Pandemic Tracing in Italy Highlights Lineages with Mutational Burden in Growing Subsets. Int J Mol Sci 2022; 23:ijms23084155. [PMID: 35456974 PMCID: PMC9029933 DOI: 10.3390/ijms23084155] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 03/31/2022] [Accepted: 04/06/2022] [Indexed: 02/07/2023] Open
Abstract
Tracing the appearance and evolution of virus variants is essential in the management of the COVID-19 pandemic. Here, we focus on SARS-CoV-2 spread in Italian patients by using viral sequences deposited in public databases and a tracing procedure which is used to monitor the evolution of the pandemic and detect the spreading, within the infected population of emergent sub-clades with a potential positive selection. Analyses of a collection of monthly samples focused on Italy highlighted the appearance and evolution of all the main viral sub-trees emerging at the end of the first year of the pandemic. It also identified additional expanding subpopulations which spread during the second year (i.e., 2021). Three-dimensional (3D) modelling of the main amino acid changes in mutated viral proteins, including ORF1ab (nsp3, nsp4, 2’-o-ribose methyltransferase, nsp6, helicase, nsp12 [RdRp]), N, ORF3a, ORF8, and spike proteins, shows the potential of the analysed structural variations to result in epistatic modulation and positive/negative selection pressure. These analyzes will be of importance to the early identification of emerging clades, which can develop into new “variants of concern” (i.e., VOC). These analyses and settings will also help SARS-CoV-2 coronet genomic centers in other countries to trace emerging worldwide variants.
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12
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Cella E, Ali S, Schmedes SE, Rife Magalis B, Marini S, Salemi M, Blanton J, Azarian T. Early Emergence Phase of SARS-CoV-2 Delta Variant in Florida, US. Viruses 2022; 14:766. [PMID: 35458495 PMCID: PMC9028683 DOI: 10.3390/v14040766] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/24/2022] [Accepted: 04/04/2022] [Indexed: 12/04/2022] Open
Abstract
SARS-CoV-2, the causative agent of COVID-19, emerged in late 2019. The highly contagious B.1.617.2 (Delta) variant of concern (VOC) was first identified in October 2020 in India and subsequently disseminated worldwide, later becoming the dominant lineage in the US. Understanding the local transmission dynamics of early SARS-CoV-2 introductions may inform actionable mitigation efforts during subsequent pandemic waves. Yet, despite considerable genomic analysis of SARS-CoV-2 in the US, several gaps remain. Here, we explore the early emergence of the Delta variant in Florida, US using phylogenetic analysis of representative Florida and globally sampled genomes. We find multiple independent introductions into Florida primarily from North America and Europe, with a minority originating from Asia. These introductions led to three distinct clades that demonstrated varying relative rates of transmission and possessed five distinct substitutions that were 3-21 times more prevalent in the Florida sample as compared to the global sample. Our results underscore the benefits of routine viral genomic surveillance to monitor epidemic spread and support the need for more comprehensive genomic epidemiology studies of emerging variants. In addition, we provide a model of epidemic spread of newly emerging VOCs that can inform future public health responses.
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Affiliation(s)
- Eleonora Cella
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA; (E.C.); (S.A.)
| | - Sobur Ali
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA; (E.C.); (S.A.)
| | - Sarah E. Schmedes
- Bureau of Public Health Laboratories, Florida Department of Health, Jacksonville, FL 32202, USA; (S.E.S.); (J.B.)
| | - Brittany Rife Magalis
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32608, USA; (B.R.M.); (M.S.)
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Simone Marini
- Department of Epidemiology, University of Florida, Gainesville, FL 32608, USA;
| | - Marco Salemi
- Emerging Pathogens Institute, University of Florida, Gainesville, FL 32608, USA; (B.R.M.); (M.S.)
- Department of Pathology, Immunology, and Laboratory Medicine, University of Florida, Gainesville, FL 32608, USA
| | - Jason Blanton
- Bureau of Public Health Laboratories, Florida Department of Health, Jacksonville, FL 32202, USA; (S.E.S.); (J.B.)
| | - Taj Azarian
- Burnett School of Biomedical Sciences, University of Central Florida, Orlando, FL 32827, USA; (E.C.); (S.A.)
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13
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Lai A, Bergna A, Toppo S, Morganti M, Menzo S, Ghisetti V, Bruzzone B, Codeluppi M, Fiore V, Rullo EV, Antonelli G, Sarmati L, Brindicci G, Callegaro A, Sagnelli C, Francisci D, Vicenti I, Miola A, Tonon G, Cirillo D, Menozzi I, Caucci S, Cerutti F, Orsi A, Schiavo R, Babudieri S, Nunnari G, Mastroianni CM, Andreoni M, Monno L, Guarneri D, Coppola N, Crisanti A, Galli M, Zehender G. Phylogeography and genomic epidemiology of SARS-CoV-2 in Italy and Europe with newly characterized Italian genomes between February-June 2020. Sci Rep 2022; 12:5736. [PMID: 35388091 PMCID: PMC8986836 DOI: 10.1038/s41598-022-09738-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 03/25/2022] [Indexed: 12/29/2022] Open
Abstract
The aims of this study were to characterize new SARS-CoV-2 genomes sampled all over Italy and to reconstruct the origin and the evolutionary dynamics in Italy and Europe between February and June 2020. The cluster analysis showed only small clusters including < 80 Italian isolates, while most of the Italian strains were intermixed in the whole tree. Pure Italian clusters were observed mainly after the lockdown and distancing measures were adopted. Lineage B and B.1 spread between late January and early February 2020, from China to Veneto and Lombardy, respectively. Lineage B.1.1 (20B) most probably evolved within Italy and spread from central to south Italian regions, and to European countries. The lineage B.1.1.1 (20D) developed most probably in other European countries entering Italy only in the second half of March and remained localized in Piedmont until June 2020. In conclusion, within the limitations of phylogeographical reconstruction, the estimated ancestral scenario suggests an important role of China and Italy in the widespread diffusion of the D614G variant in Europe in the early phase of the pandemic and more dispersed exchanges involving several European countries from the second half of March 2020.
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Affiliation(s)
- Alessia Lai
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy.,Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, University of Milan, Milan, Italy
| | - Annalisa Bergna
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy
| | - Stefano Toppo
- Department of Molecular Medicine, University of Padova, Padua, Italy.,CRIBI Biotech Center, University of Padova, Padua, Italy
| | - Marina Morganti
- Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Stefano Menzo
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy
| | - Valeria Ghisetti
- Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino, Torino, Italy
| | | | - Mauro Codeluppi
- UOC of Infectious Diseases, Department of Oncology and Hematology, Guglielmo da Saliceto Hospital, AUSL Piacenza, Piacenza, Italy
| | - Vito Fiore
- Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Emmanuele Venanzi Rullo
- Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina, Messina, Italy
| | - Guido Antonelli
- Department of Molecular Medicine, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | | | | | - Annapaola Callegaro
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Caterina Sagnelli
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Daniela Francisci
- Department of Medicine and Surgery, Clinic of Infectious Diseases, "Santa Maria della Misericordia" Hospital, University of Perugia, Perugia, Italy
| | - Ilaria Vicenti
- Department of Medical Biotechnologies, University of Siena, Siena, Italy
| | - Arianna Miola
- Intesa San Paolo Innovation Center-AI LAB, Turin, Italy
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS Ospedale San Raffaele, Milan, Italy.,Division of Experimental Oncology, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Daniela Cirillo
- Division of Immunology, Transplantation and Infectious Disease, IRCCS Ospedale San Raffaele, Milan, Italy
| | - Ilaria Menozzi
- Risk Analyses and Genomic Epidemiology Unit, Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna, Parma, Italy
| | - Sara Caucci
- Department of Biomedical Sciences and Public Health, Virology Unit, Polytechnic University of Marche, Ancona, Italy
| | - Francesco Cerutti
- Laboratory of Microbiology and Virology, Amedeo di Savoia, ASL Città di Torino, Torino, Italy
| | - Andrea Orsi
- Department of Health Sciences (DISSAL), University of Genoa, Genoa, Italy
| | - Roberta Schiavo
- UOC of Microbiology, Department of Clinical Pathology, Guglielmo da Saliceto Hospital, AUSL Piacenza, Piacenza, Italy
| | - Sergio Babudieri
- Infectious and Tropical Disease Clinic, Department of Medical, Surgical and Experimental Sciences, University of Sassari, Sassari, Italy
| | - Giuseppe Nunnari
- Unit of Infectious Diseases, Department of Experimental and Clinical Medicine, University of Messina, Messina, Italy
| | - Claudio M Mastroianni
- Department of Public Health and Infectious Diseases, University Hospital Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | | | - Laura Monno
- Infectious Diseases Unit, University of Bari, Bari, Italy
| | - Davide Guarneri
- Microbiology and Virology Laboratory, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Nicola Coppola
- Department of Mental Health and Public Medicine, University of Campania "Luigi Vanvitelli", Naples, Italy
| | - Andrea Crisanti
- Microbiology and Virology Diagnostic Unit, Padua University Hospital, Padua, Italy.,Department of Life Science, Imperial College London, South Kensington Campus Imperial College Road, London, SW7 AZ, UK
| | - Massimo Galli
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy
| | - Gianguglielmo Zehender
- Department of Biomedical and Clinical Sciences Luigi Sacco, University of Milan, Milan, Italy. .,Pediatric Clinical Research Center Fondazione Romeo ed Enrica Invernizzi, University of Milan, Milan, Italy. .,CRC-Coordinated Research Center "EpiSoMI", University of Milan, Milan, Italy.
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14
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Santinelli L, Laghi L, Innocenti GP, Pinacchio C, Vassalini P, Celani L, Lazzaro A, Borrazzo C, Marazzato M, Tarsitani L, Koukopoulos AE, Mastroianni CM, d'Ettorre G, Ceccarelli G. Oral Bacteriotherapy Reduces the Occurrence of Chronic Fatigue in COVID-19 Patients. Front Nutr 2022; 8:756177. [PMID: 35096923 PMCID: PMC8790565 DOI: 10.3389/fnut.2021.756177] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/29/2021] [Indexed: 12/22/2022] Open
Abstract
Long COVID refers to patients with symptoms as fatigue, “brain fog,” pain, suggesting the chronic involvement of the central nervous system (CNS) in COVID-19. The supplementation with probiotic (OB) would have a positive effect on metabolic homeostasis, negatively impacting the occurrence of symptoms related to the CNS after hospital discharge. On a total of 58 patients hospitalized for COVID-19, 24 (41.4%) received OB during hospitalization (OB+) while 34 (58.6%) taken only the standard treatment (OB–). Serum metabolomic profiling of patients has been performed at both hospital acceptance (T0) and discharge (T1). Six months after discharge, fatigue perceived by participants was assessed by administrating the Fatigue Assessment Scale. 70.7% of participants reported fatigue while 29.3% were negative for such condition. The OB+ group showed a significantly lower proportion of subjects reporting fatigue than the OB– one (p < 0.01). Furthermore, OB+ subjects were characterized by significantly increased concentrations of serum Arginine, Asparagine, Lactate opposite to lower levels of 3-Hydroxyisobutirate than those not treated with probiotics. Our results strongly suggest that in COVID-19, the administration of probiotics during hospitalization may prevent the development of chronic fatigue by impacting key metabolites involved in the utilization of glucose as well as in energy pathways.
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Affiliation(s)
- Letizia Santinelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Luca Laghi
- Department of Agricultural and Food Sciences, University of Bologna, Bologna, Italy.,Interdepartmental Centre for Agri-Food Industrial Research, University of Bologna, Bologna, Italy
| | | | - Claudia Pinacchio
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Paolo Vassalini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Luigi Celani
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Alessandro Lazzaro
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Cristian Borrazzo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Massimiliano Marazzato
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Lorenzo Tarsitani
- Department of Human Neurosciences, Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Alexia E Koukopoulos
- Department of Human Neurosciences, Policlinico Umberto I, Sapienza University of Rome, Rome, Italy
| | - Claudio M Mastroianni
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Gabriella d'Ettorre
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
| | - Giancarlo Ceccarelli
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Rome, Italy
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15
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Maruotti A, Giovanetti M, Divino F, Broccolo F, Angeletti S, Ciccozzi M. Prisoners of variants, or free to act as prisoners of swabs? The case of Italy. J Med Virol 2022; 94:2334-2335. [PMID: 35040149 DOI: 10.1002/jmv.27597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 11/06/2022]
Abstract
To the editor, " To all evils there are two remedies: time and silence [1]." This citation from The Count of Monte Cristo by Alexandre Dumas, written in 1844, in collaboration with Auguste Maquet, appears to be timely nowadays. This showed how novels can often be able to teach us how to lead some wars. The fight against the novel coronavirus (SARS-CoV-2), that overwhelmed the planet for about two years, required and still requires silence to think and time to act, to find the right strategies for the beginning of the "new normal". This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Rio de Janeiro, Brazil.,Department of Science and Technology for Humans and the Environment, University of Campus Bio-Medico di Roma, Rome, Italy.,Federal University of Minas Gerais, Brazil
| | - Fabio Divino
- Laboratory of Biostatistics and Computational Epidemiology, Department of Biosciences, University of Molise, Italy
| | - Francesco Broccolo
- Department of Medicine and Surgery, School of Medicine, University of Milano-Bicocca, Monza, Italy.,Laboratory Cerba Healthcare, 20137, Milano, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
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16
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Munis AM, Andersson M, Mobbs A, Hyde SC, Gill DR. Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom's first national lockdown. Sci Rep 2021; 11:21484. [PMID: 34728747 PMCID: PMC8564533 DOI: 10.1038/s41598-021-01022-x] [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: 08/03/2021] [Accepted: 10/18/2021] [Indexed: 12/15/2022] Open
Abstract
Epidemiological efforts to model the spread of SARS-CoV-2, the virus that causes COVID-19, are crucial to understanding and containing current and future outbreaks and to inform public health responses. Mutations that occur in viral genomes can alter virulence during outbreaks by increasing infection rates and helping the virus evade the host immune system. To understand the changes in viral genomic diversity and molecular epidemiology in Oxford during the first wave of infections in the United Kingdom, we analyzed 563 clinical SARS-CoV-2 samples via whole-genome sequencing using Nanopore MinION sequencing. Large-scale surveillance efforts during viral epidemics are likely to be confounded by the number of independent introductions of the viral strains into a region. To avoid such issues and better understand the selection-based changes occurring in the SARS-CoV-2 genome, we utilized local isolates collected during the UK's first national lockdown whereby personal interactions, international and national travel were considerably restricted and controlled. We were able to track the short-term evolution of the virus, detect the emergence of several mutations of concern or interest, and capture the viral diversity of the region. Overall, these results demonstrate genomic pathogen surveillance efforts have considerable utility in controlling the local spread of the virus.
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Affiliation(s)
- Altar M Munis
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | | | - Alexander Mobbs
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Stephen C Hyde
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Deborah R Gill
- Gene Medicine Group, Nuffield Division of Clinical Laboratory Sciences, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.
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17
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Progress and challenges in virus genomic epidemiology. Trends Parasitol 2021; 37:1038-1049. [PMID: 34620561 DOI: 10.1016/j.pt.2021.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/24/2021] [Accepted: 08/26/2021] [Indexed: 12/18/2022]
Abstract
Genomic epidemiology, which links pathogen genomes with associated metadata to understand disease transmission, has become a key component of outbreak response. Decreasing costs of genome sequencing and increasing computational power provide opportunities to generate and analyse large viral genomic datasets that aim to uncover the spatial scales of transmission, the demographics contributing to transmission patterns, and to forecast epidemic trends. Emerging sources of genomic data and associated metadata provide new opportunities to further unravel transmission patterns. Key challenges include how to integrate genomic data with metadata from multiple sources, how to generate efficient computational algorithms to cope with large datasets, and how to establish sampling frameworks to enable robust conclusions.
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18
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Baba MM, Bitew M, Fokam J, Lelo EA, Ahidjo A, Asmamaw K, Beloumou GA, Bulimo WD, Buratti E, Chenwi C, Dadi H, D'Agaro P, De Conti L, Fainguem N, Gadzama G, Maiuri P, Majanja J, Meshack W, Ndjolo A, Nkenfou C, Oderinde BS, Opanda SM, Segat L, Stuani C, Symekher SL, Takou D, Tesfaye K, Triolo G, Tuki K, Zacchigna S, Marcello A. Diagnostic performance of a colorimetric RT -LAMP for the identification of SARS-CoV-2: A multicenter prospective clinical evaluation in sub-Saharan Africa. EClinicalMedicine 2021; 40:101101. [PMID: 34476394 PMCID: PMC8401528 DOI: 10.1016/j.eclinm.2021.101101] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/03/2021] [Accepted: 08/06/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Management and control of the COVID-19 pandemic caused by the severe acute respiratory syndrome coronavirus SARS-CoV-2 is critically dependent on quick and reliable identification of the virus in clinical specimens. Detection of viral RNA by a colorimetric reverse transcription loop-mediated isothermal amplification (RT-LAMP) is a simple, reliable and cost-effective assay, deployable in resource-limited settings (RLS). Our objective was to evaluate the intrinsic and extrinsic performances of RT-LAMP in RLS. METHODS This is a multicenter prospective observational study of diagnostic accuracy, conducted from October 2020 to February 2021 in four African Countries: Cameroon, Ethiopia, Kenya and Nigeria; and in Italy. We enroled 1657 individuals who were either COVID-19 suspect cases, or asymptomatic and presented for screening. RNA extracted from pharyngeal swabs was tested in parallel by a colorimetric RT-LAMP and by a standard real time polymerase chain reaction (RT-PCR). FINDINGS The sensitivity and specificity of index RT LAMP compared to standard RT-PCR on 1657 prospective specimens from infected individuals was determined. For a subset of 1292 specimens, which underwent exactly the same procedures in different countries, we obtained very high specificity (98%) and positive predictive value (PPV = 99%), while the sensitivity was 87%, with a negative predictive value NPV = 70%, Stratification of RT-PCR data showed superior sensitivity achieved with an RT-PCR cycle threshold (Ct) below 35 (97%), which decreased to 60% above 35. INTERPRETATION In this field trial, RT-LAMP appears to be a reliable assay, comparable to RT-PCR, particularly with medium-high viral loads (Ct < 35). Hence, RT-LAMP can be deployed in RLS for timely management and prevention of COVID-19, without compromising the quality of output.
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Affiliation(s)
- Marycelin Mandu Baba
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, Borno State P.M.B.1069, Nigeria
| | - Molalegne Bitew
- Ethiopian Biotechnology Institute (EBTI), Addis Ababa, Ethiopia
| | - Joseph Fokam
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
- Department of Medical Laboratory Science, Faculty of Health Science, University of Buea, Buea, Cameroon
| | - Eric Agola Lelo
- Center for Biotechnology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Ahmed Ahidjo
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, Borno State P.M.B.1069, Nigeria
| | | | | | | | - Emanuele Buratti
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
| | - Collins Chenwi
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
| | - Hailu Dadi
- Ethiopian Biotechnology Institute (EBTI), Addis Ababa, Ethiopia
| | - Pierlanfranco D'Agaro
- Azienda Sanitaria Universitaria Integrata di Trieste, UCO Igiene e Sanità Pubblica, Trieste, Italy
- Dipartimento di Scienze Mediche Chirurgiche e della Salute, Università di Trieste, Italy
| | - Laura De Conti
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
| | - Nadine Fainguem
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
| | - Galadima Gadzama
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, Borno State P.M.B.1069, Nigeria
| | - Paolo Maiuri
- IFOM, the FIRC Institute of Molecular Oncology, Via Adamello 16, Milano 20139, Italy
| | - Janet Majanja
- Center for Biotechnology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Wadegu Meshack
- Center for Biotechnology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Alexis Ndjolo
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
| | - Celine Nkenfou
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
| | - Bamidele Soji Oderinde
- Department of Medical Laboratory Science, College of Medical Sciences, University of Maiduguri, Borno State P.M.B.1069, Nigeria
| | | | - Ludovica Segat
- Azienda Sanitaria Universitaria Integrata di Trieste, UCO Igiene e Sanità Pubblica, Trieste, Italy
| | - Cristiana Stuani
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
| | - Samwel L. Symekher
- Center for Biotechnology Research, Kenya Medical Research Institute (KEMRI), Nairobi, Kenya
| | - Desire Takou
- The Chantal Biya International Reference Center (CIRCB), Yaounde, Cameroon
| | | | - Gianluca Triolo
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
| | - Keyru Tuki
- Ethiopian Biotechnology Institute (EBTI), Addis Ababa, Ethiopia
| | - Serena Zacchigna
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
| | - Alessandro Marcello
- International Center for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Trieste 34149, Italy
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19
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Zhu M, Shen J, Zeng Q, Tan JW, Kleepbua J, Chew I, Law JX, Chew SP, Tangathajinda A, Latthitham N, Li L. Molecular Phylogenesis and Spatiotemporal Spread of SARS-CoV-2 in Southeast Asia. Front Public Health 2021; 9:685315. [PMID: 34395364 PMCID: PMC8363229 DOI: 10.3389/fpubh.2021.685315] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 06/14/2021] [Indexed: 12/17/2022] Open
Abstract
Background: The ongoing coronavirus disease 2019 (COVID-19) pandemic has posed an unprecedented challenge to public health in Southeast Asia, a tropical region with limited resources. This study aimed to investigate the evolutionary dynamics and spatiotemporal patterns of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the region. Materials and Methods: A total of 1491 complete SARS-CoV-2 genome sequences from 10 Southeast Asian countries were downloaded from the Global Initiative on Sharing Avian Influenza Data (GISAID) database on November 17, 2020. The evolutionary relationships were assessed using maximum likelihood (ML) and time-scaled Bayesian phylogenetic analyses, and the phylogenetic clustering was tested using principal component analysis (PCA). The spatial patterns of SARS-CoV-2 spread within Southeast Asia were inferred using the Bayesian stochastic search variable selection (BSSVS) model. The effective population size (Ne) trajectory was inferred using the Bayesian Skygrid model. Results: Four major clades (including one potentially endemic) were identified based on the maximum clade credibility (MCC) tree. Similar clustering was yielded by PCA; the first three PCs explained 46.9% of the total genomic variations among the samples. The time to the most recent common ancestor (tMRCA) and the evolutionary rate of SARS-CoV-2 circulating in Southeast Asia were estimated to be November 28, 2019 (September 7, 2019 to January 4, 2020) and 1.446 × 10-3 (1.292 × 10-3 to 1.613 × 10-3) substitutions per site per year, respectively. Singapore and Thailand were the two most probable root positions, with posterior probabilities of 0.549 and 0.413, respectively. There were high-support transmission links (Bayes factors exceeding 1,000) in Singapore, Malaysia, and Indonesia; Malaysia involved the highest number (7) of inferred transmission links within the region. A twice-accelerated viral population expansion, followed by a temporary setback, was inferred during the early stages of the pandemic in Southeast Asia. Conclusions: With available genomic data, we illustrate the phylogeography and phylodynamics of SARS-CoV-2 circulating in Southeast Asia. Continuous genomic surveillance and enhanced strategic collaboration should be listed as priorities to curb the pandemic, especially for regional communities dominated by developing countries.
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Affiliation(s)
- Mingjian Zhu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jian Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qianli Zeng
- Shanghai Institute of Biological Products, Shanghai, China
| | - Joanna Weihui Tan
- Faculty of Arts and Social Sciences, National University of Singapore, Singapore, Singapore
| | | | - Ian Chew
- Zhejiang University School of Medicine, Hangzhou, China
| | | | - Sien Ping Chew
- Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | | | | | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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20
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Sagnelli C, Sica A, Gallo M, Peluso G, Varlese F, D’Alessandro V, Ciccozzi M, Crocetto F, Garofalo C, Fiorelli A, Iannuzzo G, Reginelli A, Schonauer F, Santangelo M, Sagnelli E, Creta M, Calogero A. Renal involvement in COVID-19: focus on kidney transplant sector. Infection 2021; 49:1265-1275. [PMID: 34611792 PMCID: PMC8491762 DOI: 10.1007/s15010-021-01706-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 09/22/2021] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Kidney transplant recipients and patients on the waiting list for kidney transplant who acquire SARS-CoV-2 infection are at serious risk of developing severe COVID-19, with an increased risk of mortality for the their immunosuppressive state; other risk factors for mortality have been identified in some comorbidities such as obesity, diabetes, asthma and chronic lung disease. MATERIALS AND METHODS The COVID-19 pandemic has led to a sharp reduction in kidney transplants in most countries, mainly due to the concern of patients on the waiting list for their potential increased susceptibility to acquire SARS-CoV-2 infection in healthcare facilities and for the difficulties of transplant centers to ensure full activity as hospitals have had to focus most of their attention on COVID-19 patients. Indeed, while the infection curve continued its exponential rise, there was a vertical decline in kidney donation/transplant activity. CONCLUSION This review article focuses on the damage induced by SARS-CoV-2 infection on kidney and on the adverse effect of this pandemic on the entire kidney transplant sector.
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Affiliation(s)
- Caterina Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania “Luigi Vanvitelli”, Largo Madonna delle Grazie n. 1, 80138 Naples, Italy
| | - Antonello Sica
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Naples, Italy
| | - Monica Gallo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, 80131 Naples, Italy
| | - Gaia Peluso
- Department of Advanced Biomedical Sciences, University of Naples Federico II, via Pansini, 5, 80131 Naples, Italy
| | - Filippo Varlese
- Department of Advanced Biomedical Sciences, University of Naples Federico II, via Pansini, 5, 80131 Naples, Italy
| | - Vincenzo D’Alessandro
- UOSD Centro Trapianti di rene e Chirurgia del Retroperitoneo, AOU-University of Naples Federico II, 80131 Naples, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, University Campus Bio-Medico of Rome, 80128 Rome, Italy
| | - Felice Crocetto
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy
| | - Carlo Garofalo
- Division of Nephrology, University of Campania “Luigi Vanvitelli”, 80137 Naples, Italy
| | - Alfonso Fiorelli
- Department of Thoracic Surgery, University of Campania “Luigi Vanvitelli”, 80137 Naples, Italy
| | - Gabriella Iannuzzo
- Department of Clinical Medicine and Surgery, Federico II University Naples, Naples, Italy
| | - Alfonso Reginelli
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli”, 80131 Naples, Italy
| | - Fabrizo Schonauer
- Division of Plastic, Reconstructive and Aesthetic Surgery, University of Naples Federico II, 80131 Naples, Italy
| | - Michele Santangelo
- Department of Advanced Biomedical Sciences, University of Naples Federico II, via Pansini, 5, 80131 Naples, Italy
| | - Evangelista Sagnelli
- Department of Mental Health and Public Medicine, Section of Infectious Diseases, University of Campania “Luigi Vanvitelli”, Largo Madonna delle Grazie n. 1, 80138 Naples, Italy
| | - Massimiliano Creta
- Department of Neurosciences, Reproductive Sciences and Odontostomatology, University of Naples “Federico II”, 80131 Naples, Italy
| | - Armando Calogero
- Department of Advanced Biomedical Sciences, University of Naples Federico II, via Pansini, 5, 80131 Naples, Italy
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