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Sarkar A, Ghosh TA, Bandyopadhyay B, Maiti S, Panja AS. Prediction of Prospective Mutational Landscape of SARS-CoV-2 Spike ssRNA and Evolutionary Basis of Its Host Interaction. Mol Biotechnol 2024:10.1007/s12033-024-01146-1. [PMID: 38619800 DOI: 10.1007/s12033-024-01146-1] [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: 01/23/2024] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
Booster doses are crucial against severe COVID-19, as rapid virus mutations and variant emergence prolong the pandemic crisis. The virus's quick evolution, short generation-time, and adaptive changes impact virulence and evolvability, helping predictions about variant of concerns' (VOCs') landscapes. Here, in this study, we used a new computational algorithm, to predict the mutational pattern in SARS-CoV-2 ssRNA, proteomics, structural identification, mutation stability, and functional correlation, as well as immune escape mechanisms. Interestingly, the sequence diversity of SARS Coronavirus-2 has demonstrated a predominance of G- > A and C- > U substitutions. The best validation statistics are explored here in seven homologous models of the expected mutant SARS-CoV-2 spike ssRNA and employed for hACE2 and IgG interactions. The interactome profile of SARS-CoV-2 spike with hACE2 and IgG revealed a strong correlation between phylogeny and divergence time. The systematic adaptation of SARS-CoV-2 spike ssRNA influences infectivity and immune escape. Data suggest higher propensity of Adenine rich sequence promotes MHC system avoidance, preferred by A-rich codons. Phylogenetic data revealed the evolution of SARS-CoV-2 lineages' epidemiology. Our findings may unveil processes governing the genesis of immune-resistant variants, prompting a critical reassessment of the coronavirus mutation rate and exploration of hypotheses beyond mechanical aspects.
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Affiliation(s)
- Aniket Sarkar
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Trijit Arka Ghosh
- Department of Computer Application, Burdwan Institute of Management and Computer Science, The University of Burdwan, Dewandighi, Burdwan, West Bengal, 713102, India
| | - Bidyut Bandyopadhyay
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Smarajit Maiti
- Department of Medical Laboratory Technology, Haldia Institute of Health Sciences, ICARE Complex, Haldia, West Bengal, 721657, India
| | - Anindya Sundar Panja
- Post Graduate Department of Biotechnology, Molecular Informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India.
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2
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Pushpakumara PD, Jeewandara C, Bary F, Madushanka D, Perera L, Aberathna IS, Nimasha T, Jayamali J, Ranasinghe T, Kuruppu H, Danasekara S, Wijewickrama A, Ogg GS, Malavige GN. Identification of differences in the magnitude and specificity of SARS-CoV-2 nucleocapsid antibody responses in naturally infected and vaccinated individuals. Clin Exp Immunol 2024; 215:268-278. [PMID: 37313783 PMCID: PMC10876109 DOI: 10.1093/cei/uxad066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/25/2023] [Accepted: 06/09/2023] [Indexed: 06/15/2023] Open
Abstract
As there are limited data on B-cell epitopes for the nucleocapsid protein in SARS-CoV-2, we sought to identify the immunodominant regions within the N protein, recognized by patients with varying severity of natural infection with the Wuhan strain (WT), delta, omicron, and in those who received the Sinopharm vaccines, which is an inactivated, whole virus vaccine. Using overlapping peptides representing the N protein, with an in-house ELISA, we mapped the immunodominant regions within the N protein, in seronegative (n = 30), WT infected (n = 30), delta infected (n = 30), omicron infected + vaccinated (n = 20) and Sinopharm (BBIBP-CorV) vaccinees (n = 30). We then investigated the sensitivity and specificity of these immunodominant regions and analyzed their conservation with other SARS-CoV-2 variants of concern, seasonal human coronaviruses, and bat Sarbecoviruses. We identified four immunodominant regions aa 29-52, aa 155-178, aa 274-297, and aa 365-388, which were highly conserved within SARS-CoV-2 and the bat coronaviruses. The magnitude of responses to these regions varied based on the infecting SARS-CoV-2 variants, >80% of individuals gave responses above the positive cut-off threshold to many of the four regions, with some differences with individuals who were infected with different VoCs. These regions were found to be 100% specific, as none of the seronegative individuals gave any responses. As these regions were highly specific with high sensitivity, they have a potential to be used to develop diagnostic assays and to be used in development of vaccines.
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Affiliation(s)
- Pradeep Darshana Pushpakumara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Chandima Jeewandara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Farha Bary
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Deshan Madushanka
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Lahiru Perera
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Inoka Sepali Aberathna
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Thashmi Nimasha
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Jeewantha Jayamali
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Thushali Ranasinghe
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Heshan Kuruppu
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Saubhagya Danasekara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | | | - Graham S Ogg
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Gathsaurie Neelika Malavige
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
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3
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Volz E. Fitness, growth and transmissibility of SARS-CoV-2 genetic variants. Nat Rev Genet 2023; 24:724-734. [PMID: 37328556 DOI: 10.1038/s41576-023-00610-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/25/2023] [Indexed: 06/18/2023]
Abstract
The massive scale of the global SARS-CoV-2 sequencing effort created new opportunities and challenges for understanding SARS-CoV-2 evolution. Rapid detection and assessment of new variants has become one of the principal objectives of genomic surveillance of SARS-CoV-2. Because of the pace and scale of sequencing, new strategies have been developed for characterizing fitness and transmissibility of emerging variants. In this Review, I discuss a wide range of approaches that have been rapidly developed in response to the public health threat posed by emerging variants, ranging from new applications of classic population genetics models to contemporary synthesis of epidemiological models and phylodynamic analysis. Many of these approaches can be adapted to other pathogens and will have increasing relevance as large-scale pathogen sequencing becomes a regular feature of many public health systems.
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Affiliation(s)
- Erik Volz
- Department of Infectious Disease Epidemiology, MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, UK.
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4
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Hamede R, Fountain‐Jones NM, Arce F, Jones M, Storfer A, Hohenlohe PA, McCallum H, Roche B, Ujvari B, Thomas F. The tumour is in the detail: Local phylogenetic, population and epidemiological dynamics of a transmissible cancer in Tasmanian devils. Evol Appl 2023; 16:1316-1327. [PMID: 37492149 PMCID: PMC10363845 DOI: 10.1111/eva.13569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2022] [Revised: 06/01/2023] [Accepted: 06/01/2023] [Indexed: 07/27/2023] Open
Abstract
Infectious diseases are a major threat for biodiversity conservation and can exert strong influence on wildlife population dynamics. Understanding the mechanisms driving infection rates and epidemic outcomes requires empirical data on the evolutionary trajectory of pathogens and host selective processes. Phylodynamics is a robust framework to understand the interaction of pathogen evolutionary processes with epidemiological dynamics, providing a powerful tool to evaluate disease control strategies. Tasmanian devils have been threatened by a fatal transmissible cancer, devil facial tumour disease (DFTD), for more than two decades. Here we employ a phylodynamic approach using tumour mitochondrial genomes to assess the role of tumour genetic diversity in epidemiological and population dynamics in a devil population subject to 12 years of intensive monitoring, since the beginning of the epidemic outbreak. DFTD molecular clock estimates of disease introduction mirrored observed estimates in the field, and DFTD genetic diversity was positively correlated with estimates of devil population size. However, prevalence and force of infection were the lowest when devil population size and tumour genetic diversity was the highest. This could be due to either differential virulence or transmissibility in tumour lineages or the development of host defence strategies against infection. Our results support the view that evolutionary processes and epidemiological trade-offs can drive host-pathogen coexistence, even when disease-induced mortality is extremely high. We highlight the importance of integrating pathogen and population evolutionary interactions to better understand long-term epidemic dynamics and evaluating disease control strategies.
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Affiliation(s)
- Rodrigo Hamede
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
| | | | - Fernando Arce
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Menna Jones
- School of Natural SciencesUniversity of TasmaniaHobartTasmaniaAustralia
| | - Andrew Storfer
- School of Biological SciencesWashington State UniversityPullmanWashingtonUSA
| | - Paul A. Hohenlohe
- Department of Biological Sciences, Institute for Bioinformatics and Evolutionary StudiesUniversity of IdahoMoscowIdahoUSA
| | - Hamish McCallum
- Centre for Planetary Health and Food SecurityGriffith University, Nathan CampusNathanQueenslandAustralia
| | - Benjamin Roche
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
| | - Beata Ujvari
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- Centre for Integrative Ecology, School of Life and Environmental SciencesDeakin UniversityWaurn PondsVictoriaAustralia
| | - Frédéric Thomas
- CANECEV, Centre de Recherches Ecologiques et Evolutives sur le CancerMontpellierFrance
- CREEC, MIVEGEC (CREES)University of Montpellier, CNRS, IRDMontpelierFrance
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5
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Pushpakumara PD, Jeewandara C, Bary F, Madushanka D, Perera L, Aberathna IS, Nimasha T, Jayamali J, Ranasinghe T, Kuruppu H, Danasekara S, Wijewickrama A, Ogg GS, Malavige GN. Identification of differences in the magnitude and specificity of SARS-CoV-2 nucleocapsid antibody responses in naturally infected and vaccinated individuals. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.05.23284247. [PMID: 36656781 PMCID: PMC9844014 DOI: 10.1101/2023.01.05.23284247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Background As there are limited data on B cell epitopes for the nucleocapsid protein in SARS-CoV-2, we sought to identify the immunodominant regions within the N protein, recognized by patients with varying severity of natural infection with the Wuhan strain (WT), delta, omicron and in those who received the Sinopharm vaccines, which is an inactivated, whole virus vaccine. Methods Using overlapping peptides representing the N protein, with an in-house ELISA, we mapped the immunodominant regions within the N protein, in seronegative (n=30), WT infected (n=30), delta infected (n=30), omicron infected+vaccinated (n=20) and Sinopharm (BBIBP-CorV) vaccinees (n=30). We then investigated the sensitivity and specificity of these immunodominant regions and analysed their conservation with other SARS-CoV-2 variants of concern, seasonal human coronaviruses and bat Sarbecoviruses. We then investigated the kinetics of responses to these regions in those with varying severity of acute COVID-19. Results We identified four immunodominant regions aa 29-52, aa 155-178, aa 274 to 297 and aa 365 to 388, were highly conserved within SARS-CoV-2 and the bat coronaviruses. The magnitude of responses to these regions varied based on the infecting SARS-CoV-2 variants, with WT infected individuals predominantly recognizing aa155 to 178 regions, delta infected individuals and vaccinated+omicron infected individuals predominantly recognizing regions aa 29 to 52 and aa 274 to 294 regions. Sinopharm vaccinees recognized all four regions, with the magnitude of responses significantly lower than other groups. >80% of individuals gave responses above the positive cut-off threshold to many of the four regions, with some differences with individuals who were infected with different VoCs. These regions were found to be 100% specific, as none of the seronegative individuals gave any responses. Conclusions N-protein specific responses appear to be detectable in over 90% of those who were naturally infected or vaccinated with a whole virus inactivated vaccine, with responses mainly directed against four regions of the protein, which were highly conserved. As these regions were highly specific with high sensitivity, they have a potential to be used to develop diagnostic assays and to be used in development of vaccines.
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Affiliation(s)
- Pradeep D Pushpakumara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Chandima Jeewandara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Farha Bary
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Deshan Madushanka
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Lahiru Perera
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Inoka Sepali Aberathna
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Thashmi Nimasha
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Jeewantha Jayamali
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Thushali Ranasinghe
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Heshan Kuruppu
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Saubhagya Danasekara
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | | | - Graham S Ogg
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Gathsaurie Neelika Malavige
- Allergy Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
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6
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Attwood SW, Hill SC, Aanensen DM, Connor TR, Pybus OG. Phylogenetic and phylodynamic approaches to understanding and combating the early SARS-CoV-2 pandemic. Nat Rev Genet 2022; 23:547-562. [PMID: 35459859 PMCID: PMC9028907 DOI: 10.1038/s41576-022-00483-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2022] [Indexed: 01/05/2023]
Abstract
Determining the transmissibility, prevalence and patterns of movement of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections is central to our understanding of the impact of the pandemic and to the design of effective control strategies. Phylogenies (evolutionary trees) have provided key insights into the international spread of SARS-CoV-2 and enabled investigation of individual outbreaks and transmission chains in specific settings. Phylodynamic approaches combine evolutionary, demographic and epidemiological concepts and have helped track virus genetic changes, identify emerging variants and inform public health strategy. Here, we review and synthesize studies that illustrate how phylogenetic and phylodynamic techniques were applied during the first year of the pandemic, and summarize their contributions to our understanding of SARS-CoV-2 transmission and control.
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Affiliation(s)
- Stephen W Attwood
- Department of Zoology, University of Oxford, Oxford, UK.
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK.
| | - Sarah C Hill
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Thomas R Connor
- Pathogen Genomics Unit, Public Health Wales NHS Trust, Cardiff, UK
- School of Biosciences, Cardiff University, Cardiff, UK
| | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, UK.
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, UK.
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7
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Alkhamis MA, Fountain-Jones NM, Khajah MM, Alghounaim M, Al-Sabah SK. Comparative Phylodynamics Reveals the Evolutionary History of SARS-CoV-2 Emerging Variants in the Arabian Peninsula. Virus Evol 2022; 8:veac040. [PMID: 35677574 PMCID: PMC9129158 DOI: 10.1093/ve/veac040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 11/18/2022] Open
Abstract
Emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants continue to be responsible for an unprecedented worldwide public health and economic catastrophe. Accurate understanding and comparison of global and regional evolutionary epidemiology of novel SARS-CoV-2 variants are critical to guide current and future interventions. Here, we utilized a Bayesian phylodynamic pipeline to trace and compare the evolutionary dynamics, spatiotemporal origins, and spread of five variants (Alpha, Beta, Delta, Kappa, and Eta) across the Arabian Peninsula. We found variant-specific signatures of evolution and spread that are likely linked to air travel and disease control interventions in the region. Alpha, Beta, and Delta variants went through sequential periods of growth and decline, whereas we inferred inconclusive population growth patterns for the Kappa and Eta variants due to their sporadic introductions in the region. Non-pharmaceutical interventions imposed between mid-2020 and early 2021 likely played a role in reducing the epidemic progression of the Beta and the Alpha variants. In comparison, the combination of the non-pharmaceutical interventions and the rapid rollout of vaccination might have shaped Delta variant dynamics. We found that the Alpha and Beta variants were frequently introduced into the Arab peninsula between mid-2020 and early 2021 from Europe and Africa, respectively, whereas the Delta variant was frequently introduced between early 2021 and mid-2021 from East Asia. For these three variants, we also revealed significant and intense dispersal routes between the Arab region and Africa, Europe, Asia, and Oceania. In contrast, the restricted spread and stable effective population size of the Kappa and the Eta variants suggest that they no longer need to be targeted in genomic surveillance activities in the region. In contrast, the evolutionary characteristics of the Alpha, Beta, and Delta variants confirm the dominance of these variants in the recent outbreaks. Our study highlights the urgent need to establish regional molecular surveillance programs to ensure effective decision making related to the allocation of intervention activities targeted toward the most relevant variants.
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Affiliation(s)
- Moh A Alkhamis
- Department of Epidemiology and Biostatistics, Faculty of Public Health, Health Sciences Centre, Kuwait University, Kuwait City, Kuwait
| | | | - Mohammad M Khajah
- Systems and Software development Department, Kuwait Institute for Scientific Research, Kuwait
| | - Mohammad Alghounaim
- Departement of pediatrics, Amiri Hospital, Ministry of Health, Kuwait
- Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health, Kuwait
| | - Salman K Al-Sabah
- Jaber Al-Ahmad Al-Sabah Hospital, Ministry of Health, Kuwait
- Department of Surgery, Faculty of Medicine, Health Sciences Center, Kuwait University, Kuwait
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8
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On the Origin and Propagation of the COVID-19 Outbreak in the Italian Province of Trento, a Tourist Region of Northern Italy. Viruses 2022; 14:v14030580. [PMID: 35336987 PMCID: PMC8951735 DOI: 10.3390/v14030580] [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: 10/20/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 02/05/2023] Open
Abstract
Background: Trentino is an Italian province with a tourism-based economy, bordering the regions of Lombardy and Veneto, where the two earliest and largest outbreaks of COVID-19 occurred in Italy. The earliest cases in Trentino were reported in the first week of March 2020, with most of the cases occurring in the winter sport areas in the Dolomites mountain range. The number of reported cases decreased over the summer months and was followed by a second wave in the autumn and winter of 2020. Methods: we performed high-coverage Oxford Nanopore sequencing of 253 positive SARS-CoV-2 swabs collected in Trentino between March and December 2020. Results: in this work, we analyzed genome sequences to trace the routes through which the virus entered the area, and assessed whether the autumnal resurgence could be attributed to lineages persisting undetected during summer, or as a consequence of new introductions. Conclusions: Comparing the draft genomes analyzed with a large selection of European sequences retrieved from GISAID we found that multiple introductions of the virus occurred at the early stage of the epidemics; the two epidemic waves were unrelated; the second wave was due to reintroductions of the virus in summer when traveling restrictions were uplifted.
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9
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Hunting alters viral transmission and evolution in a large carnivore. Nat Ecol Evol 2022; 6:174-182. [PMID: 35087217 PMCID: PMC10111630 DOI: 10.1038/s41559-021-01635-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 11/24/2021] [Indexed: 11/09/2022]
Abstract
Hunting can fundamentally alter wildlife population dynamics but the consequences of hunting on pathogen transmission and evolution remain poorly understood. Here, we present a study that leverages a unique landscape-scale quasi-experiment coupled with pathogen-transmission tracing, network simulation and phylodynamics to provide insights into how hunting shapes feline immunodeficiency virus (FIV) dynamics in puma (Puma concolor). We show that removing hunting pressure enhances the role of males in transmission, increases the viral population growth rate and increases the role of evolutionary forces on the pathogen compared to when hunting was reinstated. Changes in transmission observed with the removal of hunting could be linked to short-term social changes while the male puma population increased. These findings are supported through comparison with a region with stable hunting management over the same time period. This study shows that routine wildlife management can have impacts on pathogen transmission and evolution not previously considered.
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10
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Jeewandara C, Jayathilaka D, Ranasinghe D, Hsu NS, Ariyaratne D, Jayadas TT, Panambara Arachchige DM, Lindsey BB, Gomes L, Parker MD, Wijewickrama A, Karunaratne M, Ogg GS, de Silva TI, Malavige GN. Genomic and Epidemiological Analysis of SARS-CoV-2 Viruses in Sri Lanka. Front Microbiol 2021; 12:722838. [PMID: 34603246 PMCID: PMC8483294 DOI: 10.3389/fmicb.2021.722838] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/24/2021] [Indexed: 11/13/2022] Open
Abstract
Background: In order to understand the molecular epidemiology of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Sri Lanka, since March 2020, we carried out genomic sequencing overlaid on available epidemiological data until April 2021. Methods: Whole genome sequencing was carried out on diagnostic sputum or nasopharyngeal swabs from 373 patients with COVID-19. Molecular clock phylogenetic analysis was undertaken to further explore dominant lineages. Results: The B.1.411 lineage was most prevalent, which was established in Sri Lanka and caused outbreaks throughout the country until March 2021. The estimated time of the most recent common ancestor (tMRCA) of this lineage was June 1, 2020 (with 95% lower and upper bounds March 30 to July 27) suggesting cryptic transmission may have occurred, prior to a large epidemic starting in October 2020. Returning travellers were identified with infections caused by lineage B.1.258, as well as the more transmissible B.1.1.7 lineage, which has replaced B.1.411 to fuel the ongoing large outbreak in the country. Conclusions: The large outbreak that started in early October, is due to spread of a single virus lineage, B.1.411 until the end of March 2021, when B.1.1.7 emerged and became the dominant lineage.
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Affiliation(s)
- Chandima Jeewandara
- Allergy, Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Deshni Jayathilaka
- Allergy, Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Diyanath Ranasinghe
- Allergy, Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Nienyun Sharon Hsu
- Department of Infection, Immunity and Cardiovascular Diseases, Medical School, University of Sheffield, Sheffield, United Kingdom.,Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, United Kingdom
| | - Dinuka Ariyaratne
- Allergy, Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Tibutius Thanesh Jayadas
- Allergy, Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | | | - Benjamin B Lindsey
- Department of Infection, Immunity and Cardiovascular Diseases, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Laksiri Gomes
- Allergy, Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Matthew D Parker
- Sheffield Bioinformatics Core, The University of Sheffield, Sheffield, United Kingdom
| | - Ananda Wijewickrama
- MRC Weatherall Institute of Molecular Medicine, National Institute of Infectious Diseases, Angoda, Sri Lanka
| | - Malika Karunaratne
- MRC Weatherall Institute of Molecular Medicine, National Institute of Infectious Diseases, Angoda, Sri Lanka
| | - Graham S Ogg
- Allergy, Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka.,University of Oxford, Oxford, United Kingdom
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Diseases, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Gathsaurie Neelika Malavige
- Allergy, Immunology and Cell Biology Unit, Department of Immunology and Molecular Medicine, University of Sri Jayewardenepura, Nugegoda, Sri Lanka.,University of Oxford, Oxford, United Kingdom
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11
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Moustafa AM, Planet PJ. Emerging SARS-CoV-2 Diversity Revealed by Rapid Whole-Genome Sequence Typing. Genome Biol Evol 2021; 13:evab197. [PMID: 34432021 PMCID: PMC8449825 DOI: 10.1093/gbe/evab197] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/20/2021] [Indexed: 12/14/2022] Open
Abstract
Discrete classification of SARS-CoV-2 viral genotypes can identify emerging strains and detect geographic spread, viral diversity, and transmission events. We developed a tool (GNU-based Virus IDentification [GNUVID]) that integrates whole-genome multilocus sequence typing and a supervised machine learning random forest-based classifier. We used GNUVID to assign sequence type (ST) profiles to all high-quality genomes available from GISAID. STs were clustered into clonal complexes (CCs) and then used to train a machine learning classifier. We used this tool to detect potential introduction and exportation events and to estimate effective viral diversity across locations and over time in 16 US states. GNUVID is a highly scalable tool for viral genotype classification (https://github.com/ahmedmagds/GNUVID) that can quickly classify hundreds of thousands of genomes in a way that is consistent with phylogeny. Our genotyping ST/CC analysis uncovered dynamic local changes in ST/CC prevalence and diversity with multiple replacement events in different states, an average of 20.6 putative introductions and 7.5 exportations for each state over the time period analyzed. We introduce the use of effective diversity metrics (Hill numbers) that can be used to estimate the impact of interventions (e.g., travel restrictions, vaccine uptake, mask mandates) on the variation in circulating viruses. Our classification tool uncovered multiple introduction and exportation events, as well as waves of expansion and replacement of SARS-CoV-2 genotypes in different states. GNUVID classification lends itself to measures of ecological diversity, and, with systematic genomic sampling, it could be used to track circulating viral diversity and identify emerging clones and hotspots.
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Affiliation(s)
- Ahmed M Moustafa
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Pennsylvania, USA
- Division of Gastroenterology, Hepatology, and Nutrition, Children’s Hospital of Philadelphia, Pennsylvania, USA
| | - Paul J Planet
- Division of Pediatric Infectious Diseases, Children’s Hospital of Philadelphia, Pennsylvania, USA
- Department of Pediatrics, Perelman College of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Sackler Institute for Comparative Genomics, American Museum of Natural History, New York, New York, USA
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12
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Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Ongoing global and regional adaptive evolution of SARS-CoV-2. Proc Natl Acad Sci U S A 2021; 118:e2104241118. [PMID: 34292871 PMCID: PMC8307621 DOI: 10.1073/pnas.2104241118] [Citation(s) in RCA: 152] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Understanding the trends in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high-quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the region of the nucleocapsid protein associated with nuclear localization signals (NLS) are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS-associated variants across multiple partitions rose to global prominence in March to July, during a period of stasis in terms of interregional diversity. Finally, beginning in July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142;
- HHMI, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894;
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13
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Turner WC, Kamath PL, van Heerden H, Huang YH, Barandongo ZR, Bruce SA, Kausrud K. The roles of environmental variation and parasite survival in virulence-transmission relationships. ROYAL SOCIETY OPEN SCIENCE 2021; 8:210088. [PMID: 34109041 PMCID: PMC8170194 DOI: 10.1098/rsos.210088] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Disease outbreaks are a consequence of interactions among the three components of a host-parasite system: the infectious agent, the host and the environment. While virulence and transmission are widely investigated, most studies of parasite life-history trade-offs are conducted with theoretical models or tractable experimental systems where transmission is standardized and the environment controlled. Yet, biotic and abiotic environmental factors can strongly affect disease dynamics, and ultimately, host-parasite coevolution. Here, we review research on how environmental context alters virulence-transmission relationships, focusing on the off-host portion of the parasite life cycle, and how variation in parasite survival affects the evolution of virulence and transmission. We review three inter-related 'approaches' that have dominated the study of the evolution of virulence and transmission for different host-parasite systems: (i) evolutionary trade-off theory, (ii) parasite local adaptation and (iii) parasite phylodynamics. These approaches consider the role of the environment in virulence and transmission evolution from different angles, which entail different advantages and potential biases. We suggest improvements to how to investigate virulence-transmission relationships, through conceptual and methodological developments and taking environmental context into consideration. By combining developments in life-history evolution, phylogenetics, adaptive dynamics and comparative genomics, we can improve our understanding of virulence-transmission relationships across a diversity of host-parasite systems that have eluded experimental study of parasite life history.
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Affiliation(s)
- Wendy C. Turner
- US Geological Survey, Wisconsin Cooperative Wildlife Research Unit, Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Pauline L. Kamath
- School of Food and Agriculture, University of Maine, Orono, ME 04469, USA
| | - Henriette van Heerden
- Faculty of Veterinary Science, Department of Veterinary Tropical Diseases, University of Pretoria, Onderstepoort, South Africa
| | - Yen-Hua Huang
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zoe R. Barandongo
- Department of Forest and Wildlife Ecology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Spencer A. Bruce
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY 12222, USA
| | - Kyrre Kausrud
- Section for Epidemiology, Norwegian Veterinary Institute, Ullevålsveien 68, 0454 Oslo, Norway
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14
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Nel AE, Miller JF. Nano-Enabled COVID-19 Vaccines: Meeting the Challenges of Durable Antibody Plus Cellular Immunity and Immune Escape. ACS NANO 2021; 15:5793-5818. [PMID: 33793189 PMCID: PMC8029448 DOI: 10.1021/acsnano.1c01845] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
At the time of preparing this Perspective, large-scale vaccination for COVID-19 is in progress, aiming to bring the pandemic under control through vaccine-induced herd immunity. Not only does this vaccination effort represent an unprecedented scientific and technological breakthrough, moving us from the rapid analysis of viral genomes to design, manufacture, clinical trial testing, and use authorization within the time frame of less than a year, but it also highlights rapid progress in the implementation of nanotechnology to assist vaccine development. These advances enable us to deliver nucleic acid and conformation-stabilized subunit vaccines to regional lymph nodes, with the ability to trigger effective humoral and cellular immunity that prevents viral infection or controls disease severity. In addition to a brief description of the design features of unique cationic lipid and virus-mimicking nanoparticles for accomplishing spike protein delivery and presentation by the cognate immune system, we also discuss the importance of adjuvancy and design features to promote cooperative B- and T-cell interactions in lymph node germinal centers, including the use of epitope-based vaccines. Although current vaccine efforts have demonstrated short-term efficacy and vaccine safety, key issues are now vaccine durability and adaptability against viral variants. We present a forward-looking perspective of how vaccine design can be adapted to improve durability of the immune response and vaccine adaptation to overcome immune escape by viral variants. Finally, we consider the impact of nano-enabled approaches in the development of COVID-19 vaccines for improved vaccine design against other infectious agents, including pathogens that may lead to future pandemics.
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Affiliation(s)
- André E. Nel
- Division of NanoMedicine, Department of Medicine, David Geffen School of Medicine University of California, Los Angeles, Los Angeles, California, 90095, United States
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
| | - Jeff F. Miller
- California NanoSystems Institute, University of California, Los Angeles, Los Angeles, California 90095, United States
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, California, 90095, United States
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15
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Ragonnet-Cronin M, Boyd O, Geidelberg L, Jorgensen D, Nascimento FF, Siveroni I, Johnson RA, Baguelin M, Cucunubá ZM, Jauneikaite E, Mishra S, Watson OJ, Ferguson N, Cori A, Donnelly CA, Volz E. Genetic evidence for the association between COVID-19 epidemic severity and timing of non-pharmaceutical interventions. Nat Commun 2021; 12:2188. [PMID: 33846321 PMCID: PMC8041850 DOI: 10.1038/s41467-021-22366-y] [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] [Received: 11/17/2020] [Accepted: 03/10/2021] [Indexed: 01/09/2023] Open
Abstract
Unprecedented public health interventions including travel restrictions and national lockdowns have been implemented to stem the COVID-19 epidemic, but the effectiveness of non-pharmaceutical interventions is still debated. We carried out a phylogenetic analysis of more than 29,000 publicly available whole genome SARS-CoV-2 sequences from 57 locations to estimate the time that the epidemic originated in different places. These estimates were examined in relation to the dates of the most stringent interventions in each location as well as to the number of cumulative COVID-19 deaths and phylodynamic estimates of epidemic size. Here we report that the time elapsed between epidemic origin and maximum intervention is associated with different measures of epidemic severity and explains 11% of the variance in reported deaths one month after the most stringent intervention. Locations where strong non-pharmaceutical interventions were implemented earlier experienced much less severe COVID-19 morbidity and mortality during the period of study.
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Affiliation(s)
- Manon Ragonnet-Cronin
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
| | - Olivia Boyd
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Lily Geidelberg
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - David Jorgensen
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Fabricia F Nascimento
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Igor Siveroni
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Robert A Johnson
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Marc Baguelin
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Zulma M Cucunubá
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Elita Jauneikaite
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Swapnil Mishra
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Oliver J Watson
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Neil Ferguson
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Anne Cori
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
| | - Christl A Donnelly
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
- Department of Statistics, University of Oxford, Oxford, UK
| | - Erik Volz
- MRC Centre for Global Infectious Disease Analysis and the Department of Infectious Disease Epidemiology, Imperial College London, London, UK
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16
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Gutierrez B, Márquez S, Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, da Silva Candido D, Fernandez-Cadena JC, Morey-Leon G, Armas-Gonzalez R, Andrade-Molina DM, Bruno A, de Mora D, Olmedo M, Portugal D, Gonzalez M, Orlando A, Drexler JF, Moreira-Soto A, Sander AL, Brünink S, Kühne A, Patiño L, Carrazco-Montalvo A, Mestanza O, Zurita J, Sevillano G, du Plessis L, McCrone JT, Coloma J, Trueba G, Barragán V, Rojas-Silva P, Grunauer M, Kraemer MU, Faria NR, Escalera-Zamudio M, Pybus OG, Cárdenas P. Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.03.31.21254685. [PMID: 33851177 PMCID: PMC8043474 DOI: 10.1101/2021.03.31.21254685] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Characterisation of SARS-CoV-2 genetic diversity through space and time can reveal trends in virus importation and domestic circulation, and permit the exploration of questions regarding the early transmission dynamics. Here we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the COVID-19 pandemic. We generate and analyse 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylgeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions (NPIs), with differential degrees of persistence and national dissemination.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, UK
- Colegio de Ciencias Biológicas y Ambientales, Universidad San Francisco de Quito, Quito, Ecuador
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Juan Carlos Fernandez-Cadena
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón, Ecuador
| | - Gabriel Morey-Leon
- Faculty of Medical Sciences, Universidad de Guayaquil, Guayaquil, Ecuador
| | - Rubén Armas-Gonzalez
- Faculty of Sciences, Escuela Superior Politécnica del Litoral, Guayaquil, Ecuador
| | - Derly Madeleiny Andrade-Molina
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón, Ecuador
| | - Alfredo Bruno
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
- Universidad Agraria del Ecuador
| | - Domenica de Mora
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Maritza Olmedo
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Denisse Portugal
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Manuel Gonzalez
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Jan Felix Drexler
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Andres Moreira-Soto
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Anna-Lena Sander
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Sebastian Brünink
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Arne Kühne
- Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Virology, Berlin, Germany
| | - Leandro Patiño
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | | | - Orson Mestanza
- Instituto Nacional de Investigación en Salud Pública, Guayaquil, Ecuador
| | - Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito, Ecuador
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito, Ecuador
| | | | - John T. McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, UK
| | - Josefina Coloma
- School of Public Health, University of California, Berkeley, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito, Quito, Ecuador
| | | | - Nuno R. Faria
- Department of Zoology, University of Oxford, Oxford, UK
- MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, London, UK
| | | | - Oliver G. Pybus
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, Royal Veterinary College London, London, UK
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito, Ecuador
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17
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Rochman ND, Wolf YI, Faure G, Mutz P, Zhang F, Koonin EV. Ongoing Global and Regional Adaptive Evolution of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2020.10.12.336644. [PMID: 33083804 PMCID: PMC7574262 DOI: 10.1101/2020.10.12.336644] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Understanding the trends in SARS-CoV-2 evolution is paramount to control the COVID-19 pandemic. We analyzed more than 300,000 high quality genome sequences of SARS-CoV-2 variants available as of January 2021. The results show that the ongoing evolution of SARS-CoV-2 during the pandemic is characterized primarily by purifying selection, but a small set of sites appear to evolve under positive selection. The receptor-binding domain of the spike protein and the nuclear localization signal (NLS) associated region of the nucleocapsid protein are enriched with positively selected amino acid replacements. These replacements form a strongly connected network of apparent epistatic interactions and are signatures of major partitions in the SARS-CoV-2 phylogeny. Virus diversity within each geographic region has been steadily growing for the entirety of the pandemic, but analysis of the phylogenetic distances between pairs of regions reveals four distinct periods based on global partitioning of the tree and the emergence of key mutations. The initial period of rapid diversification into region-specific phylogenies that ended in February 2020 was followed by a major extinction event and global homogenization concomitant with the spread of D614G in the spike protein, ending in March 2020. The NLS associated variants across multiple partitions rose to global prominence in March-July, during a period of stasis in terms of inter-regional diversity. Finally, beginning July 2020, multiple mutations, some of which have since been demonstrated to enable antibody evasion, began to emerge associated with ongoing regional diversification, which might be indicative of speciation.
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Affiliation(s)
- Nash D Rochman
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Guilhem Faure
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
| | - Pascal Mutz
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA 02142
- Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894
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18
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Trevisan M, Riccetti S, Sinigaglia A, Barzon L. SARS-CoV-2 Infection and Disease Modelling Using Stem Cell Technology and Organoids. Int J Mol Sci 2021; 22:ijms22052356. [PMID: 33652988 PMCID: PMC7956599 DOI: 10.3390/ijms22052356] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/08/2021] [Accepted: 02/23/2021] [Indexed: 02/07/2023] Open
Abstract
In this Review, we briefly describe the basic virology and pathogenesis of SARS-CoV-2, highlighting how stem cell technology and organoids can contribute to the understanding of SARS-CoV-2 cell tropisms and the mechanism of disease in the human host, supporting and clarifying findings from clinical studies in infected individuals. We summarize here the results of studies, which used these technologies to investigate SARS-CoV-2 pathogenesis in different organs. Studies with in vitro models of lung epithelia showed that alveolar epithelial type II cells, but not differentiated lung alveolar epithelial type I cells, are key targets of SARS-CoV-2, which triggers cell apoptosis and inflammation, while impairing surfactant production. Experiments with human small intestinal organoids and colonic organoids showed that the gastrointestinal tract is another relevant target for SARS-CoV-2. The virus can infect and replicate in enterocytes and cholangiocytes, inducing cell damage and inflammation. Direct viral damage was also demonstrated in in vitro models of human cardiomyocytes and choroid plexus epithelial cells. At variance, endothelial cells and neurons are poorly susceptible to viral infection, thus supporting the hypothesis that neurological symptoms and vascular damage result from the indirect effects of systemic inflammatory and immunological hyper-responses to SARS-CoV-2 infection.
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19
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Gutierrez B, Márquez S, Prado-Vivar B, Becerra-Wong M, Guadalupe JJ, Candido DDS, Fernandez-Cadena JC, Morey-Leon G, Armas-Gonzalez R, Andrade-Molina DM, Bruno A, De Mora D, Olmedo M, Portugal D, Gonzalez M, Orlando A, Drexler JF, Moreira-Soto A, Sander AL, Brünink S, Kühne A, Patiño L, Carrazco-Montalvo A, Mestanza O, Zurita J, Sevillano G, Du Plessis L, McCrone JT, Coloma J, Trueba G, Barragán V, Rojas-Silva P, Grunauer M, Kraemer MUG, Faria NR, Escalera-Zamudio M, Pybus OG, Cárdenas P. Genomic epidemiology of SARS-CoV-2 transmission lineages in Ecuador. Virus Evol 2021; 7:veab051. [PMID: 34527281 PMCID: PMC8244811 DOI: 10.1093/ve/veab051] [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] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/12/2021] [Accepted: 06/03/2021] [Indexed: 12/23/2022] Open
Abstract
Characterisation of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic diversity through space and time can reveal trends in virus importation and domestic circulation and permit the exploration of questions regarding the early transmission dynamics. Here, we present a detailed description of SARS-CoV-2 genomic epidemiology in Ecuador, one of the hardest hit countries during the early stages of the coronavirus-19 pandemic. We generated and analysed 160 whole genome sequences sampled from all provinces of Ecuador in 2020. Molecular clock and phylogeographic analysis of these sequences in the context of global SARS-CoV-2 diversity enable us to identify and characterise individual transmission lineages within Ecuador, explore their spatiotemporal distributions, and consider their introduction and domestic circulation. Our results reveal a pattern of multiple international importations across the country, with apparent differences between key provinces. Transmission lineages were mostly introduced before the implementation of non-pharmaceutical interventions, with differential degrees of persistence and national dissemination.
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Affiliation(s)
- Bernardo Gutierrez
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Sully Márquez
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Belén Prado-Vivar
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Mónica Becerra-Wong
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Juan José Guadalupe
- Laboratorio de Biotecnología Vegetal, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | | | - Juan Carlos Fernandez-Cadena
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón 092301, Ecuador
| | - Gabriel Morey-Leon
- Faculty of Medical Sciences, Universidad de Guayaquil, Guayaquil 090613, Ecuador
| | - Rubén Armas-Gonzalez
- Faculty of Sciences, Escuela Superior Politécnica del Litoral, Guayaquil 090112, Ecuador
| | - Derly Madeleiny Andrade-Molina
- Omics Sciences Laboratory, Faculty of Medical Sciences, Universidad de Especialidades Espíritu Santo, Samborondón 092301, Ecuador
| | - Alfredo Bruno
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Domenica De Mora
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Maritza Olmedo
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Denisse Portugal
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Manuel Gonzalez
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Alberto Orlando
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | - Jan Felix Drexler
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Andres Moreira-Soto
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Anna-Lena Sander
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Sebastian Brünink
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Arne Kühne
- Institute of Virology, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin 10117, Germany
| | - Leandro Patiño
- Instituto Nacional de Investigación en Salud Pública, Guayaquil 3961, Ecuador
| | | | - Orson Mestanza
- Servicio de Genética, Instituto Nacional de Salud del Niño San Borja, Lima 15037, Perú
| | - Jeannete Zurita
- Facultad de Medicina, Pontificia Universidad Católica del Ecuador, Quito 170143, Ecuador
| | - Gabriela Sevillano
- Unidad de Investigaciones en Biomedicina, Zurita & Zurita Laboratorios, Quito 170104, Ecuador
| | - Louis Du Plessis
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - John T McCrone
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JW, UK
| | - Josefina Coloma
- School of Public Health, University of California, Berkeley CA 94704, USA
| | - Gabriel Trueba
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Verónica Barragán
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Patricio Rojas-Silva
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Michelle Grunauer
- Escuela de Medicina, Universidad San Francisco de Quito, Quito 170901, Ecuador
| | - Moritz U G Kraemer
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Nuno R Faria
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | | | - Oliver G Pybus
- Department of Zoology, University of Oxford, Oxford, Oxfordshire OX1 3SY, UK
| | - Paúl Cárdenas
- Instituto de Microbiología, Universidad San Francisco de Quito, Quito 170901, Ecuador
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20
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van Dorp L, Richard D, Tan CCS, Shaw LP, Acman M, Balloux F. No evidence for increased transmissibility from recurrent mutations in SARS-CoV-2. Nat Commun 2020; 11:5986. [PMID: 33239633 PMCID: PMC7688939 DOI: 10.1038/s41467-020-19818-2] [Citation(s) in RCA: 190] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 10/30/2020] [Indexed: 02/07/2023] Open
Abstract
COVID-19 is caused by the coronavirus SARS-CoV-2, which jumped into the human population in late 2019 from a currently uncharacterised animal reservoir. Due to this recent association with humans, SARS-CoV-2 may not yet be fully adapted to its human host. This has led to speculations that SARS-CoV-2 may be evolving towards higher transmissibility. The most plausible mutations under putative natural selection are those which have emerged repeatedly and independently (homoplasies). Here, we formally test whether any homoplasies observed in SARS-CoV-2 to date are significantly associated with increased viral transmission. To do so, we develop a phylogenetic index to quantify the relative number of descendants in sister clades with and without a specific allele. We apply this index to a curated set of recurrent mutations identified within a dataset of 46,723 SARS-CoV-2 genomes isolated from patients worldwide. We do not identify a single recurrent mutation in this set convincingly associated with increased viral transmission. Instead, recurrent mutations currently in circulation appear to be evolutionary neutral and primarily induced by the human immune system via RNA editing, rather than being signatures of adaptation. At this stage we find no evidence for significantly more transmissible lineages of SARS-CoV-2 due to recurrent mutations.
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Affiliation(s)
- Lucy van Dorp
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
| | - Damien Richard
- Cirad, UMR PVBMT, F-97410 St Pierre, Réunion, France
- Université de la Réunion, UMR PVBMT, F-97490 St Denis, Réunion, France
| | - Cedric C S Tan
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - Liam P Shaw
- Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DU, UK
| | - Mislav Acman
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
| | - François Balloux
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.
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