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Cheng HCR, Belman S, Salje H, Dagan R, Bentley SD. Estimating geographical spread of Streptococcus pneumoniae within Israel using genomic data. Microb Genom 2024; 10:001262. [PMID: 38913413 PMCID: PMC11261897 DOI: 10.1099/mgen.0.001262] [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: 02/22/2024] [Accepted: 05/30/2024] [Indexed: 06/25/2024] Open
Abstract
Understanding how pathogens spread across geographical space is fundamental for control measures such as vaccination. Streptococcus pneumoniae (the pneumococcus) is a respiratory bacterium responsible for a large proportion of infectious disease morbidity and mortality globally. Even in the post-vaccination era, the rates of invasive pneumococcal disease (IPD) remain stable in most countries, including Israel. To understand the geographical spread of the pneumococcus in Israel, we analysed 1174 pneumococcal genomes from patients with IPD across multiple regions. We included the evolutionary distance between pairs of isolates inferred using whole-genome data within a relative risk (RR) ratio framework to capture the geographical structure of S. pneumoniae. While we could not find geographical structure at the overall lineage level, the extra granularity provided by whole-genome sequence data showed that it takes approximately 5 years for invasive pneumococcal isolates to become fully mixed across the country.This article contains data hosted by Microreact.
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Affiliation(s)
| | - Sophie Belman
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
- Global Health Resilience, Earth Sciences Department, Barcelona Supercomputing Center, Barcelona, Spain
| | - Henrik Salje
- Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK
| | - Ron Dagan
- Gunzburger Chair for Study of Infectious Diseases, The Shraga Segal Department of Microbiology, Immunology and Genetics, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Stephen D. Bentley
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK
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Maduranga S, Valencia BM, Sigera C, Adikari T, Weeratunga P, Fernando D, Rajapakse S, Lloyd AR, Bull RA, Rodrigo C. Genomic Surveillance of Recent Dengue Outbreaks in Colombo, Sri Lanka. Viruses 2023; 15:1408. [PMID: 37515097 PMCID: PMC10384240 DOI: 10.3390/v15071408] [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: 05/23/2023] [Revised: 06/19/2023] [Accepted: 06/19/2023] [Indexed: 07/30/2023] Open
Abstract
All four serotypes of the dengue virus (DENV1-4) cause a phenotypically similar illness, but serial infections from different serotypes increase the risk of severe disease. Thus, genomic surveillance of circulating viruses is important to detect serotype switches that precede community outbreaks of disproportionate magnitude. A phylogenetic analysis was conducted on near full length DENV genomes sequenced from serum collected from a prospective cohort study from the Colombo district, Sri Lanka during a 28-month period using Oxford nanopore technology, and the consensus sequences were analyzed using maximum likelihood and Bayesian evolutionary analysis. From 523 patients, 328 DENV sequences were successfully generated (DENV1: 43, DENV2: 219, DENV3:66). Most circulating sequences originated from a common ancestor that was estimated to have existed from around 2010 for DENV2 and around 2015/2016 for DENV1 and DENV3. Four distinct outbreaks coinciding with monsoon rain seasons were identified during the observation period mostly driven by DENV2 cosmopolitan genotype, except for a large outbreak in 2019 contributed by DENV3 genotype I. This serotype switch did not result in a more clinically severe illness. Phylogeographic analyses showed that all outbreaks started within Colombo city and then spread to the rest of the district. In 2019, DENV3 genotype I, previously, rarely reported in Sri Lanka, is likely to have contributed to a disease outbreak. However, this did not result in more severe disease in those infected, probably due to pre-existing DENV3 immunity in the community. Targeted vector control within Colombo city before anticipated seasonal outbreaks may help to limit the geographic spread of outbreaks.
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Affiliation(s)
- Sachith Maduranga
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | | | - Chathurani Sigera
- Faculty of Medicine, University of Colombo, Colombo 00800, Sri Lanka
| | - Thiruni Adikari
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
| | | | - Deepika Fernando
- Faculty of Medicine, University of Colombo, Colombo 00800, Sri Lanka
| | - Senaka Rajapakse
- Faculty of Medicine, University of Colombo, Colombo 00800, Sri Lanka
| | - Andrew R Lloyd
- Kirby Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Rowena A Bull
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW 2052, Australia
| | - Chaturaka Rodrigo
- School of Biomedical Sciences, UNSW Sydney, Sydney, NSW 2052, Australia
- Kirby Institute, UNSW Sydney, Sydney, NSW 2052, Australia
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3
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Orf GS, Pérez LJ, Ciuoderis K, Cardona A, Villegas S, Hernández-Ortiz JP, Baele G, Mohaimani A, Osorio JE, Berg MG, Cloherty GA. The Principles of SARS-CoV-2 Intervariant Competition Are Exemplified in the Pre-Omicron Era of the Colombian Epidemic. Microbiol Spectr 2023; 11:e0534622. [PMID: 37191534 PMCID: PMC10269686 DOI: 10.1128/spectrum.05346-22] [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: 12/28/2022] [Accepted: 04/25/2023] [Indexed: 05/17/2023] Open
Abstract
The first 18 months of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in Colombia were characterized by three epidemic waves. During the third wave, from March through August 2021, intervariant competition resulted in Mu replacing Alpha and Gamma. We employed Bayesian phylodynamic inference and epidemiological modeling to characterize the variants in the country during this period of competition. Phylogeographic analysis indicated that Mu did not emerge in Colombia but acquired increased fitness there through local transmission and diversification, contributing to its export to North America and Europe. Despite not having the highest transmissibility, Mu's genetic composition and ability to evade preexisting immunity facilitated its domination of the Colombian epidemic landscape. Our results support previous modeling studies demonstrating that both intrinsic factors (transmissibility and genetic diversity) and extrinsic factors (time of introduction and acquired immunity) influence the outcome of intervariant competition. This analysis will help set practical expectations about the inevitable emergences of new variants and their trajectories. IMPORTANCE Before the appearance of the Omicron variant in late 2021, numerous SARS-CoV-2 variants emerged, were established, and declined, often with different outcomes in different geographic areas. In this study, we considered the trajectory of the Mu variant, which only successfully dominated the epidemic landscape of a single country: Colombia. We demonstrate that Mu competed successfully there due to its early and opportune introduction time in late 2020, combined with its ability to evade immunity granted by prior infection or the first generation of vaccines. Mu likely did not effectively spread outside of Colombia because other immune-evading variants, such as Delta, had arrived in those locales and established themselves first. On the other hand, Mu's early spread within Colombia may have prevented the successful establishment of Delta there. Our analysis highlights the geographic heterogeneity of early SARS-CoV-2 variant spread and helps to reframe the expectations for the competition behaviors of future variants.
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Affiliation(s)
- Gregory S. Orf
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Lester J. Pérez
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Karl Ciuoderis
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Andrés Cardona
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Simón Villegas
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Juan P. Hernández-Ortiz
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Laboratory of Clinical and Evolutionary Virology, Rega Institute, KU Leuven, Leuven, Belgium
| | - Aurash Mohaimani
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Jorge E. Osorio
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
- UW-GHI One Health Colombia, Universidad Nacional de Colombia Sede en Medellín, Medellín, Colombia
- UW-GHI One Health Colombia, University of Wisconsin—Madison, Madison, Wisconsin, USA
| | - Michael G. Berg
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
| | - Gavin A. Cloherty
- Infectious Disease Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, Illinois, USA
- Abbott Pandemic Defense Coalition (APDC), Abbott Park, Illinois, USA
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Layan M, Müller NF, Dellicour S, De Maio N, Bourhy H, Cauchemez S, Baele G. Impact and mitigation of sampling bias to determine viral spread: Evaluating discrete phylogeography through CTMC modeling and structured coalescent model approximations. Virus Evol 2023; 9:vead010. [PMID: 36860641 PMCID: PMC9969415 DOI: 10.1093/ve/vead010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 01/06/2023] [Accepted: 02/02/2023] [Indexed: 02/08/2023] Open
Abstract
Bayesian phylogeographic inference is a powerful tool in molecular epidemiological studies, which enables reconstruction of the origin and subsequent geographic spread of pathogens. Such inference is, however, potentially affected by geographic sampling bias. Here, we investigated the impact of sampling bias on the spatiotemporal reconstruction of viral epidemics using Bayesian discrete phylogeographic models and explored different operational strategies to mitigate this impact. We considered the continuous-time Markov chain (CTMC) model and two structured coalescent approximations (Bayesian structured coalescent approximation [BASTA] and marginal approximation of the structured coalescent [MASCOT]). For each approach, we compared the estimated and simulated spatiotemporal histories in biased and unbiased conditions based on the simulated epidemics of rabies virus (RABV) in dogs in Morocco. While the reconstructed spatiotemporal histories were impacted by sampling bias for the three approaches, BASTA and MASCOT reconstructions were also biased when employing unbiased samples. Increasing the number of analyzed genomes led to more robust estimates at low sampling bias for the CTMC model. Alternative sampling strategies that maximize the spatiotemporal coverage greatly improved the inference at intermediate sampling bias for the CTMC model, and to a lesser extent, for BASTA and MASCOT. In contrast, allowing for time-varying population sizes in MASCOT resulted in robust inference. We further applied these approaches to two empirical datasets: a RABV dataset from the Philippines and a SARS-CoV-2 dataset describing its early spread across the world. In conclusion, sampling biases are ubiquitous in phylogeographic analyses but may be accommodated by increasing the sample size, balancing spatial and temporal composition in the samples, and informing structured coalescent models with reliable case count data.
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Affiliation(s)
| | | | | | | | - Hervé Bourhy
- Lyssavirus Epidemiology and Neuropathology Unit, Institut Pasteur, Université Paris Cité, 25-28 rue du Docteur Roux, Paris 75014, France,WHO Collaborating Centre for Reference and Research on Rabies, Institut Pasteur, Université Paris Cité, 28 rue du Docteur Roux, Paris 75724, France
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5
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Gass JD, Dusek RJ, Hall JS, Hallgrimsson GT, Halldórsson HP, Vignisson SR, Ragnarsdottir SB, Jónsson JE, Krauss S, Wong SS, Wan XF, Akter S, Sreevatsan S, Trovão NS, Nutter FB, Runstadler JA, Hill NJ. Global dissemination of influenza A virus is driven by wild bird migration through arctic and subarctic zones. Mol Ecol 2023; 32:198-213. [PMID: 36239465 PMCID: PMC9797457 DOI: 10.1111/mec.16738] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/03/2022] [Accepted: 10/07/2022] [Indexed: 12/31/2022]
Abstract
Influenza A viruses (IAV) circulate endemically among many wild aquatic bird populations that seasonally migrate between wintering grounds in southern latitudes to breeding ranges along the perimeter of the circumpolar arctic. Arctic and subarctic zones are hypothesized to serve as ecologic drivers of the intercontinental movement and reassortment of IAVs due to high densities of disparate populations of long distance migratory and native bird species present during breeding seasons. Iceland is a staging ground that connects the East Atlantic and North Atlantic American flyways, providing a unique study system for characterizing viral flow between eastern and western hemispheres. Using Bayesian phylodynamic analyses, we sought to evaluate the viral connectivity of Iceland to proximal regions and how inter-species transmission and reassortment dynamics in this region influence the geographic spread of low and highly pathogenic IAVs. Findings demonstrate that IAV movement in the arctic and subarctic reflects wild bird migration around the perimeter of the circumpolar north, favouring short-distance flights between proximal regions rather than long distance flights over the polar interior. Iceland connects virus movement between mainland Europe and North America, consistent with the westward migration of wild birds from mainland Europe to Northeastern Canada and Greenland. Though virus diffusion rates were similar among avian taxonomic groups in Iceland, gulls play an outsized role as sinks of IAVs from other avian hosts prior to onward migration. These data identify patterns of virus movement in northern latitudes and inform future surveillance strategies related to seasonal and emergent IAVs with potential public health concern.
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Affiliation(s)
- Jonathon D. Gass
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | | | | | | | | | - Solvi Runar Vignisson
- University of Iceland’s Research Centre in Suðurnes
- Suðurnes Science and Learning Center
| | | | | | - Scott Krauss
- Department of Infectious Diseases, St. Jude Children’s Research Hospital
| | - Sook-San Wong
- Department of Infectious Diseases, St. Jude Children’s Research Hospital
| | - Xiu-Feng Wan
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia
- Bond Life Sciences Center, University of Missouri, Columbia
- Department of Electronic Engineering and Computer Science, University of Missouri, Columbia
| | - Sadia Akter
- Center for Influenza and Emerging Infectious Diseases (CIEID), University of Missouri, Columbia
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia
- Bond Life Sciences Center, University of Missouri, Columbia
- Department of Electronic Engineering and Computer Science, University of Missouri, Columbia
| | | | - Nídia S. Trovão
- Division of International Epidemiology and Population Studies, Fogarty International Center, National Institutes of Health
| | - Felicia B. Nutter
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | - Jonathan A. Runstadler
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
| | - Nichola J. Hill
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University
- Department of Biology, University of Massachusetts, Boston
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6
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Nahata KD, Bielejec F, Monetta J, Dellicour S, Rambaut A, Suchard MA, Baele G, Lemey P. SPREAD 4: online visualisation of pathogen phylogeographic reconstructions. Virus Evol 2022; 8:veac088. [PMID: 36325034 PMCID: PMC9615431 DOI: 10.1093/ve/veac088] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/16/2022] [Indexed: 01/27/2023] Open
Abstract
Phylogeographic analyses aim to extract information about pathogen spread from genomic data, and visualising spatio-temporal reconstructions is a key aspect of this process. Here we present SPREAD 4, a feature-rich web-based application that visualises estimates of pathogen dispersal resulting from Bayesian phylogeographic inference using BEAST on a geographic map, offering zoom-and-filter functionality and smooth animation over time. SPREAD 4 takes as input phylogenies with both discrete and continuous location annotation and offers customised visualisation as well as generation of publication-ready figures. SPREAD 4 now features account-based storage and easy sharing of visualisations by means of unique web addresses. SPREAD 4 is intuitive to use and is available online at https://spreadviz.org, with an accompanying web page containing answers to frequently asked questions at https://beast.community/spread4.
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Affiliation(s)
- Kanika D Nahata
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven 3000, Belgium
| | - Filip Bielejec
- Nonce Filip Bielejec, Łódź Voivodeship, 90-245 Lodz, Poland
| | - Juan Monetta
- Departamento de Montevideo, Guayabos 1924, Montevideo 11200,Uruguay
| | | | | | | | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Herestraat 49, Leuven 3000, Belgium
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7
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McLaughlin A, Montoya V, Miller RL, Mordecai GJ, Worobey M, Poon AFY, Joy JB. Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada. eLife 2022; 11:e73896. [PMID: 35916373 PMCID: PMC9345601 DOI: 10.7554/elife.73896] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 07/12/2022] [Indexed: 12/15/2022] Open
Abstract
Tracking the emergence and spread of SARS-CoV-2 lineages using phylogenetics has proven critical to inform the timing and stringency of COVID-19 public health interventions. We investigated the effectiveness of international travel restrictions at reducing SARS-CoV-2 importations and transmission in Canada in the first two waves of 2020 and early 2021. Maximum likelihood phylogenetic trees were used to infer viruses' geographic origins, enabling identification of 2263 (95% confidence interval: 2159-2366) introductions, including 680 (658-703) Canadian sublineages, which are international introductions resulting in sampled Canadian descendants, and 1582 (1501-1663) singletons, introductions with no sampled descendants. Of the sublineages seeded during the first wave, 49% (46-52%) originated from the USA and were primarily introduced into Quebec (39%) and Ontario (36%), while in the second wave, the USA was still the predominant source (43%), alongside a larger contribution from India (16%) and the UK (7%). Following implementation of restrictions on the entry of foreign nationals on 21 March 2020, importations declined from 58.5 (50.4-66.5) sublineages per week to 10.3-fold (8.3-15.0) lower within 4 weeks. Despite the drastic reduction in viral importations following travel restrictions, newly seeded sublineages in summer and fall 2020 contributed to the persistence of COVID-19 cases in the second wave, highlighting the importance of sustained interventions to reduce transmission. Importations rebounded further in November, bringing newly emergent variants of concern (VOCs). By the end of February 2021, there had been an estimated 30 (19-41) B.1.1.7 sublineages imported into Canada, which increasingly displaced previously circulating sublineages by the end of the second wave.Although viral importations are nearly inevitable when global prevalence is high, with fewer importations there are fewer opportunities for novel variants to spark outbreaks or outcompete previously circulating lineages.
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Affiliation(s)
- Angela McLaughlin
- British Columbia Centre for Excellence in HIV/AIDSVancouverCanada
- Bioinformatics, University of British ColumbiaVancouverCanada
| | - Vincent Montoya
- British Columbia Centre for Excellence in HIV/AIDSVancouverCanada
| | - Rachel L Miller
- British Columbia Centre for Excellence in HIV/AIDSVancouverCanada
- Bioinformatics, University of British ColumbiaVancouverCanada
| | - Gideon J Mordecai
- Department of Medicine, University of British ColumbiaVancouverCanada
| | | | - Michael Worobey
- Department of Ecology and Evolution, University of ArizonaTucsonUnited States
| | - Art FY Poon
- Department of Pathology and Laboratory Medicine, Western UniversityLondonCanada
| | - Jeffrey B Joy
- British Columbia Centre for Excellence in HIV/AIDSVancouverCanada
- Bioinformatics, University of British ColumbiaVancouverCanada
- Department of Medicine, University of British ColumbiaVancouverCanada
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8
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Truong Nguyen P, Kant R, Van den Broeck F, Suvanto MT, Alburkat H, Virtanen J, Ahvenainen E, Castren R, Hong SL, Baele G, Ahava MJ, Jarva H, Jokiranta ST, Kallio-Kokko H, Kekäläinen E, Kirjavainen V, Kortela E, Kurkela S, Lappalainen M, Liimatainen H, Suchard MA, Hannula S, Ellonen P, Sironen T, Lemey P, Vapalahti O, Smura T. The phylodynamics of SARS-CoV-2 during 2020 in Finland. COMMUNICATIONS MEDICINE 2022; 2:65. [PMID: 35698660 PMCID: PMC9187640 DOI: 10.1038/s43856-022-00130-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 05/23/2022] [Indexed: 02/01/2023] Open
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of infections and fatalities globally since its emergence in late 2019. The virus was first detected in Finland in January 2020, after which it rapidly spread among the populace in spring. However, compared to other European nations, Finland has had a low incidence of SARS-CoV-2. To gain insight into the origins and turnover of SARS-CoV-2 lineages circulating in Finland in 2020, we investigated the phylogeographic and -dynamic history of the virus. Methods The origins of SARS-CoV-2 introductions were inferred via Travel-aware Bayesian time-measured phylogeographic analyses. Sequences for the analyses included virus genomes belonging to the B.1 lineage and with the D614G mutation from countries of likely origin, which were determined utilizing Google mobility data. We collected all available sequences from spring and fall peaks to study lineage dynamics. Results We observed rapid turnover among Finnish lineages during this period. Clade 20C became the most prevalent among sequenced cases and was replaced by other strains in fall 2020. Bayesian phylogeographic reconstructions suggested 42 independent introductions into Finland during spring 2020, mainly from Italy, Austria, and Spain. Conclusions A single introduction from Spain might have seeded one-third of cases in Finland during spring in 2020. The investigations of the original introductions of SARS-CoV-2 to Finland during the early stages of the pandemic and of the subsequent lineage dynamics could be utilized to assess the role of transboundary movements and the effects of early intervention and public health measures.
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Affiliation(s)
- Phuoc Truong Nguyen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Ravi Kant
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Frederik Van den Broeck
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Maija T. Suvanto
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Hussein Alburkat
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Jenni Virtanen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Ella Ahvenainen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Robert Castren
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Samuel L. Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Maarit J. Ahava
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hanna Jarva
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Suvi Tuulia Jokiranta
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
- Department of Bacteriology and Immunology, University of Helsinki, Helsinki, Finland
| | - Hannimari Kallio-Kokko
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Eliisa Kekäläinen
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Translational Immunology Research Program, University of Helsinki, Helsinki, Finland
| | - Vesa Kirjavainen
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Elisa Kortela
- Infectious Diseases, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Satu Kurkela
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Maija Lappalainen
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Hanna Liimatainen
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Marc A. Suchard
- Departments of Biomathematics, Biostatistics and Human Genetics, University of California, Los Angeles (UCLA), Los Angeles, CA USA
| | - Sari Hannula
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
| | - Tarja Sironen
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Philippe Lemey
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Olli Vapalahti
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Teemu Smura
- Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- HUS Diagnostic Center, HUSLAB, Clinical Microbiology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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9
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Perez LJ, Orf GS, Berg MG, Rodgers MA, Meyer TV, Mohaimani A, Olivo A, Harris B, Mowerman I, Padane A, Dela-del Lawson AT, Mboup A, Mbow M, Leye N, Touré-Kane NC, Ahouidi AD, Cloherty GA, Mboup S. The Early SARS-CoV-2 Epidemic in Senegal was Driven by the Local Emergence of B.1.416 and the Introduction of B.1.1.420 from Europe. Virus Evol 2022; 8:veac025. [PMID: 35371561 PMCID: PMC8971539 DOI: 10.1093/ve/veac025] [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: 12/20/2021] [Revised: 02/13/2022] [Accepted: 03/18/2022] [Indexed: 11/22/2022] Open
Abstract
Molecular surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is growing in west Africa, especially in the Republic of Senegal. Here, we present a molecular epidemiology study of the early waves of SARS-CoV-2 infections in this country based on Bayesian phylogeographic approaches. Whereas the first wave in mid-2020 was characterized by a significant diversification of lineages and predominance of B.1.416, the second wave in late 2020 was composed primarily of B.1.1.420. Our results indicate that B.1.416 originated in Senegal and was exported mainly to Europe. In contrast, B.1.1.420 was introduced from Italy, gained fitness in Senegal, and then spread worldwide. Since both B.1.416 and B.1.1.420 lineages carry several positive selected mutations in the spike and nucleocapsid genes, each of which may explain their local dominance, their mutation profiles should be carefully monitored. As the pandemic continues to evolve, molecular surveillance in all regions of Africa will play a key role in stemming its spread.
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Affiliation(s)
- Lester J Perez
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064, USA
| | - Gregory S Orf
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064, USA
| | - Michael G Berg
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064, USA
| | - Mary A Rodgers
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064, USA
| | - Todd V Meyer
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064, USA
| | - Aurash Mohaimani
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064, USA
| | - Ana Olivo
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064, USA
| | - Barbara Harris
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064, USA
| | - Illya Mowerman
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064, USA
| | - Abdou Padane
- Institut de Recherche en Santé de Surveillance Épidémiologique et de Formation, Diamniadio, Dakar, Senegal
| | | | - Aminata Mboup
- Institut de Recherche en Santé de Surveillance Épidémiologique et de Formation, Diamniadio, Dakar, Senegal
| | - Moustapha Mbow
- Institut de Recherche en Santé de Surveillance Épidémiologique et de Formation, Diamniadio, Dakar, Senegal
| | - Nafissatou Leye
- Institut de Recherche en Santé de Surveillance Épidémiologique et de Formation, Diamniadio, Dakar, Senegal
| | - Ndeye Coumba Touré-Kane
- Institut de Recherche en Santé de Surveillance Épidémiologique et de Formation, Diamniadio, Dakar, Senegal
| | - Ambroise D Ahouidi
- Institut de Recherche en Santé de Surveillance Épidémiologique et de Formation, Diamniadio, Dakar, Senegal
| | - Gavin A Cloherty
- Infectious Disease Core Research, Abbott Diagnostics Division, Abbott Laboratories, Abbott Park, IL 60064, USA
| | - Souleymane Mboup
- Institut de Recherche en Santé de Surveillance Épidémiologique et de Formation, Diamniadio, Dakar, Senegal
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10
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Orf GS, Forberg K, Meyer TV, Mowerman I, Mohaimani A, Faron ML, Jennings C, Landay AL, Goldstein DY, Fox AS, Berg MG, Cloherty GA. SNP and Phylogenetic Characterization of Low Viral Load SARS-CoV-2 Specimens by Target Enrichment. FRONTIERS IN VIROLOGY 2021. [DOI: 10.3389/fviro.2021.765974] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Background: Surveillance of SARS-CoV-2 across the globe has enabled detection of new variants and informed the public health response. With highly sensitive methods like qPCR widely adopted for diagnosis, the ability to sequence and characterize specimens with low titers needs to keep pace.Methods: Nucleic acids extracted from nasopharyngeal swabs collected from four sites in the United States in early 2020 were converted to NGS libraries to sequence SARS-CoV-2 genomes using metagenomic and xGen target enrichment approaches. Single nucleotide polymorphism (SNP) analysis and phylogeny were used to determine clade assignments and geographic origins of strains.Results: SARS-CoV-2-specific xGen enrichment enabled full genome coverage for 87 specimens with Ct values <29, corresponding to viral loads of >10,000 cp/ml. For samples with viral loads between 103 and 106 cp/ml, the median genome coverage for xGen was 99.1%, sequence depth was 605X, and the “on-target” rate was 57 ± 21%, compared to 13%, 2X and 0.001 ± 0.016%, respectively, for metagenomic sequencing alone. Phylogenetic analysis revealed the presence of most clades that existed at the time of the study, though clade GH dominated in the Midwest.Conclusions: Even as vaccines are being widely distributed, a high case load of SARS-CoV-2 infection persists around the world. Viral genetic surveillance has succeeded in warning the public of new variants in circulation and ensured that diagnostic tools remain resilient to a steadily increasing number of mutations. Target capture offers a means of characterizing low viral load samples which would normally pose a challenge for metagenomic sequencing.
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11
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Dudas G, Hong SL, Potter BI, Calvignac-Spencer S, Niatou-Singa FS, Tombolomako TB, Fuh-Neba T, Vickos U, Ulrich M, Leendertz FH, Khan K, Huber C, Watts A, Olendraitė I, Snijder J, Wijnant KN, Bonvin AMJJ, Martres P, Behillil S, Ayouba A, Maidadi MF, Djomsi DM, Godwe C, Butel C, Šimaitis A, Gabrielaitė M, Katėnaitė M, Norvilas R, Raugaitė L, Koyaweda GW, Kandou JK, Jonikas R, Nasvytienė I, Žemeckienė Ž, Gečys D, Tamušauskaitė K, Norkienė M, Vasiliūnaitė E, Žiogienė D, Timinskas A, Šukys M, Šarauskas M, Alzbutas G, Aziza AA, Lusamaki EK, Cigolo JCM, Mawete FM, Lofiko EL, Kingebeni PM, Tamfum JJM, Belizaire MRD, Essomba RG, Assoumou MCO, Mboringong AB, Dieng AB, Juozapaitė D, Hosch S, Obama J, Ayekaba MO, Naumovas D, Pautienius A, Rafaï CD, Vitkauskienė A, Ugenskienė R, Gedvilaitė A, Čereškevičius D, Lesauskaitė V, Žemaitis L, Griškevičius L, Baele G. Emergence and spread of SARS-CoV-2 lineage B.1.620 with variant of concern-like mutations and deletions. Nat Commun 2021; 12:5769. [PMID: 34599175 PMCID: PMC8486757 DOI: 10.1038/s41467-021-26055-8] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/15/2021] [Indexed: 12/12/2022] Open
Abstract
Distinct SARS-CoV-2 lineages, discovered through various genomic surveillance initiatives, have emerged during the pandemic following unprecedented reductions in worldwide human mobility. We here describe a SARS-CoV-2 lineage - designated B.1.620 - discovered in Lithuania and carrying many mutations and deletions in the spike protein shared with widespread variants of concern (VOCs), including E484K, S477N and deletions HV69Δ, Y144Δ, and LLA241/243Δ. As well as documenting the suite of mutations this lineage carries, we also describe its potential to be resistant to neutralising antibodies, accompanying travel histories for a subset of European cases, evidence of local B.1.620 transmission in Europe with a focus on Lithuania, and significance of its prevalence in Central Africa owing to recent genome sequencing efforts there. We make a case for its likely Central African origin using advanced phylogeographic inference methodologies incorporating recorded travel histories of infected travellers.
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Affiliation(s)
- Gytis Dudas
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden.
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania.
| | - Samuel L Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Barney I Potter
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Sébastien Calvignac-Spencer
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
- Viral Evolution, Robert Koch Institute, 13353, Berlin, Germany
| | - Frédéric S Niatou-Singa
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Thais B Tombolomako
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Terence Fuh-Neba
- WWF Central African Republic Programme Office, Dzanga Sangha Protected Areas, BP 1053, Bangui, Central African Republic
| | - Ulrich Vickos
- Infectious and Tropical Diseases Unit, Department of medicine, Amitié Hospital, Bangui, Central African Republic
- Academic Department of Pediatrics, Clinical immunology and vaccinology, Children's Hospital Bambino Gesù, IRCCS, Rome, Italy
| | - Markus Ulrich
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
| | - Fabian H Leendertz
- Epidemiology of Highly Pathogenic Organisms, Robert Koch Institute, 13353, Berlin, Germany
| | - Kamran Khan
- BlueDot, Toronto, ON, M5J 1A7, Canada
- Li Ka Shing Knowledge Institute, St. Michael's Hospital, Toronto, ON, M5B 1A6, Canada
- Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, ON, M5S 3H2, Canada
| | | | | | - Ingrida Olendraitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital Lab, CB2 2QQ, Cambridge, UK
| | - Joost Snijder
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Kim N Wijnant
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute of Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Alexandre M J J Bonvin
- Bijvoet Centre for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Pascale Martres
- Microbiology, Centre Hospitalier René Dubos, Cergy Pontoise, France
| | - Sylvie Behillil
- Molecular Genetics of RNA viruses, CNRS UMR 3569, Université de Paris, Institut Pasteur, Paris, France
- National Reference Center for Respiratory Viruses, Institut Pasteur, Paris, France
| | - Ahidjo Ayouba
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, 34394, Montpellier cedex, France
| | - Martin Foudi Maidadi
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Dowbiss Meta Djomsi
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Celestin Godwe
- Centre de Recherches sur les Maladies Émergentes, Ré-émergentes et la Médecine Nucléaire, Institut de Recherches Médicales et D'études des Plantes Médicinales, Yaoundé, Cameroon
| | - Christelle Butel
- TransVIHMI, Université de Montpellier, IRD, INSERM, 911 Avenue Agropolis, 34394, Montpellier cedex, France
| | - Aistis Šimaitis
- The Office of the Government of the Republic of Lithuania, Vilnius, Lithuania
| | | | - Monika Katėnaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Rimvydas Norvilas
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
- Department of Experimental, Preventive and Clinical Medicine, State Research Institute Centre for Innovative Medicine, Vilnius, Lithuania
| | - Ligita Raugaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Giscard Wilfried Koyaweda
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Jephté Kaleb Kandou
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Rimvydas Jonikas
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Inga Nasvytienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Živilė Žemeckienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Dovydas Gečys
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Kamilė Tamušauskaitė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Milda Norkienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Emilija Vasiliūnaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Danguolė Žiogienė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Albertas Timinskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Marius Šukys
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Mantas Šarauskas
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
| | - Gediminas Alzbutas
- Institute for Digestive Research, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Adrienne Amuri Aziza
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Eddy Kinganda Lusamaki
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Jean-Claude Makangara Cigolo
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Francisca Muyembe Mawete
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Emmanuel Lokilo Lofiko
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
| | - Placide Mbala Kingebeni
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | - Jean-Jacques Muyembe Tamfum
- National Institute for Biomedical Research (INRB), Avenue De la Democratie (Ex Huileries), BP 1197, Kinshasa-Gombe, Democratic Republic of the Congo
- University of Kinshasa (UNIKIN), BP 127, Kinshasa XI, Democratic Republic of the Congo
| | | | - René Ghislain Essomba
- National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | - Marie Claire Okomo Assoumou
- National Public Health Laboratory, Ministry of Public Health, Yaoundé, Cameroon
- Faculty of Medicine and Biomedical Sciences, University of Yaoundé I, Yaoundé, Cameroon
| | | | - Alle Baba Dieng
- World Health Organization, Cameroon Office, Yaoundé, Cameroon
| | - Dovilė Juozapaitė
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Salome Hosch
- Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Justino Obama
- Ministry of Health and Social Welfare, Malabo, Equatorial Guinea
| | | | - Daniel Naumovas
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Arnoldas Pautienius
- Institute of Microbiology and Virology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Clotaire Donatien Rafaï
- Le Laboratoire National de Biologie Clinique et de Santé Publique (LNBCSP), Bangui, Central African Republic
| | - Astra Vitkauskienė
- Department of Laboratory Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Rasa Ugenskienė
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Department of Genetics and Molecular Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Alma Gedvilaitė
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Darius Čereškevičius
- Department of Genetics and Molecular Medicine, Hospital of Lithuanian University of Health Sciences Kauno Klinikos, Kaunas, Lithuania
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vaiva Lesauskaitė
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Lukas Žemaitis
- Institute of Cardiology, Lithuanian University of Health Sciences, Kaunas, Lithuania
- National Public Health Surveillance Laboratory, Vilnius, Lithuania
| | - Laimonas Griškevičius
- Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santaros Klinikos, Vilnius, Lithuania
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium.
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12
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Butera Y, Mukantwari E, Artesi M, Umuringa JD, O'Toole ÁN, Hill V, Rooke S, Hong SL, Dellicour S, Majyambere O, Bontems S, Boujemla B, Quick J, Resende PC, Loman N, Umumararungu E, Kabanda A, Murindahabi MM, Tuyisenge P, Gashegu M, Rwabihama JP, Sindayiheba R, Gikic D, Souopgui J, Ndifon W, Rutayisire R, Gatare S, Mpunga T, Ngamije D, Bours V, Rambaut A, Nsanzimana S, Baele G, Durkin K, Mutesa L, Rujeni N. Genomic sequencing of SARS-CoV-2 in Rwanda reveals the importance of incoming travelers on lineage diversity. Nat Commun 2021; 12:5705. [PMID: 34588460 PMCID: PMC8481346 DOI: 10.1038/s41467-021-25985-7] [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: 04/14/2021] [Accepted: 09/10/2021] [Indexed: 01/24/2023] Open
Abstract
COVID-19 transmission rates are often linked to locally circulating strains of SARS-CoV-2. Here we describe 203 SARS-CoV-2 whole genome sequences analyzed from strains circulating in Rwanda from May 2020 to February 2021. In particular, we report a shift in variant distribution towards the emerging sub-lineage A.23.1 that is currently dominating. Furthermore, we report the detection of the first Rwandan cases of the B.1.1.7 and B.1.351 variants of concern among incoming travelers tested at Kigali International Airport. To assess the importance of viral introductions from neighboring countries and local transmission, we exploit available individual travel history metadata to inform spatio-temporal phylogeographic inference, enabling us to take into account infections from unsampled locations. We uncover an important role of neighboring countries in seeding introductions into Rwanda, including those from which no genomic sequences were available. Our results highlight the importance of systematic genomic surveillance and regional collaborations for a durable response towards combating COVID-19.
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Affiliation(s)
- Yvan Butera
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | - Enatha Mukantwari
- National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda
| | - Maria Artesi
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | | | - Áine Niamh O'Toole
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland
| | - Verity Hill
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland
| | - Stefan Rooke
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland
| | - Samuel Leandro Hong
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, Leuven, Belgium
| | - Simon Dellicour
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, Leuven, Belgium
- Spatial Epidemiology Laboratory, Université Libre de Bruxelles, Brussels, Belgium
| | | | - Sebastien Bontems
- Department of Clinical Microbiology, University Hospital of Liège, Liège, Belgium
| | - Bouchra Boujemla
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
| | - Josh Quick
- University of Birmingham, Birmingham, England
| | - Paola Cristina Resende
- University College London, London, England
- Laboratory of Respiratory Viruses and Measles, Oswaldo Cruz Institute, FIOCRUZ, Rio de Janeiro, Brazil
| | - Nick Loman
- University of Birmingham, Birmingham, England
| | | | - Alice Kabanda
- National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda
| | - Marylin Milumbu Murindahabi
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- School of Science, College of Science and Technology, University of Rwanda, Kigali, Rwanda
| | - Patrick Tuyisenge
- National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda
| | - Misbah Gashegu
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
| | - Jean Paul Rwabihama
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
| | | | - Djordje Gikic
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
| | - Jacob Souopgui
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda
- Department of Molecular Biology, Institute of Biology and Molecular Medicine, IBMM, Université Libre de, Bruxelles, Gosselies, Belgium
| | - Wilfred Ndifon
- African Institute for Mathematical Sciences, Kigali, Rwanda
| | - Robert Rutayisire
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda
| | - Swaibu Gatare
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
- National Reference Laboratory, Rwanda Biomedical Center, Kigali, Rwanda
| | - Tharcisse Mpunga
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
| | - Daniel Ngamije
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
| | - Vincent Bours
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium
- Department of Human Genetics, University Hospital of Liège, Liège, Belgium
| | - Andrew Rambaut
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh, Scotland
| | - Sabin Nsanzimana
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda
| | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute KU Leuven, Leuven, Belgium.
| | - Keith Durkin
- Laboratory of Human Genetics, GIGA Research Institute, Liège, Belgium.
| | - Leon Mutesa
- Center for Human Genetics, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda.
| | - Nadine Rujeni
- Rwanda National Joint Task Force COVID-19, Rwanda Biomedical Centre, Ministry of Health, Kigali, Rwanda.
- School of Health Sciences, College of Medicine and Health Sciences, University of Rwanda, Kigali, Rwanda.
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13
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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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