1
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Bukhari AR, Ashraf J, Kanji A, Rahman YA, Trovão NS, Thielen PM, Yameen M, Kanwar S, Khan W, Kabir F, Nisar MI, Merritt B, Hasan R, Spiro D, Rasmussen Z, Aamir UB, Hasan Z. Sequential viral introductions and spread of BA.1 across Pakistan provinces during the Omicron wave. BMC Genomics 2023; 24:432. [PMID: 37532989 PMCID: PMC10399012 DOI: 10.1186/s12864-023-09539-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/27/2023] [Indexed: 08/04/2023] Open
Abstract
BACKGROUND COVID-19 waves caused by specific SARS-CoV-2 variants have occurred globally at different times. We focused on Omicron variants to understand the genomic diversity and phylogenetic relatedness of SARS-CoV-2 strains in various regions of Pakistan. METHODS We studied 276,525 COVID-19 cases and 1,031 genomes sequenced from December 2021 to August 2022. Sequences were analyzed and visualized using phylogenetic trees. RESULTS The highest case numbers and deaths were recorded in Sindh and Punjab, the most populous provinces in Pakistan. Omicron variants comprised 93% of all genomes, with BA.2 (32.6%) and BA.5 (38.4%) predominating. The first Omicron wave was associated with the sequential identification of BA.1 in Sindh, then Islamabad Capital Territory, Punjab, Khyber Pakhtunkhwa (KP), Azad Jammu Kashmir (AJK), Gilgit-Baltistan (GB) and Balochistan. Phylogenetic analysis revealed Sindh to be the source of BA.1 and BA.2 introductions into Punjab and Balochistan during early 2022. BA.4 was first introduced in AJK and BA.5 in Punjab. Most recent common ancestor (MRCA) analysis revealed relatedness between the earliest BA.1 genome from Sindh with Balochistan, AJK, Punjab and ICT, and that of first BA.1 from Punjab with strains from KPK and GB. CONCLUSIONS Phylogenetic analysis provides insights into the introduction and transmission dynamics of the Omicron variant in Pakistan, identifying Sindh as a hotspot for viral dissemination. Such data linked with public health efforts can help limit surges of new infections.
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Affiliation(s)
- Ali Raza Bukhari
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Javaria Ashraf
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Yusra Abdul Rahman
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Nídia S Trovão
- Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD, 20892, USA
| | - Peter M Thielen
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD, 20723, USA
| | - Maliha Yameen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - Samiah Kanwar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Waqasuddin Khan
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Furqan Kabir
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Muhammad Imran Nisar
- Department of Pediatrics and Child Health, Aga Khan University, Karachi, 74800, Pakistan
| | - Brian Merritt
- Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD, 20723, USA
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan
| | - David Spiro
- Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD, 20892, USA
| | - Zeba Rasmussen
- Fogarty International Center, U.S. National Institutes of Health, 16 Center Drive, Bethesda, MD, 20892, USA
| | - Uzma Bashir Aamir
- World Health Organization Country Office, Park Road, Chak Shahzad, Islamabad, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, 74800, Pakistan.
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2
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Nasir A, Bukhari AR, Trovão NS, Thielen PM, Kanji A, Mahmood SF, Ghanchi NK, Ansar Z, Merritt B, Mehoke T, Razzak SA, Syed MA, Shaikh SR, Wassan M, Bashir Aamir U, Baele G, Rasmussen Z, Spiro D, Hasan R, Hasan Z. Evolutionary History and Introduction of SARS-CoV-2 Alpha VOC/B.1.1.7 in Pakistan Through International Travelers. Virus Evol 2022; 8:veac020. [PMID: 35462736 PMCID: PMC9021734 DOI: 10.1093/ve/veac020] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/18/2022] [Accepted: 03/14/2022] [Indexed: 11/12/2022] Open
Abstract
Abstract
SARS-CoV-2 variants continue to emerge, and their identification is important for the public health response to COVID-19. Genomic sequencing provides robust information but may not always be accessible and therefore rapid mutation-based PCR approaches can be used to identify known variants. International travelers arriving in Karachi between December 2020 and February 2021 were tested for SARS-CoV-2 by PCR. A subset of positive samples was tested for S-Gene Target Failure (SGTF) on TaqPathTM COVID-19 (Thermo Fisher Scientific) and for mutations using the GSD NovaType SARS-CoV-2 (Eurofins Technologies) assays. Sequencing was conducted on the MinION platform (Oxford Nanopore Technologies (ONT). Bayesian phylogeographic inference was performed integrating the patients’ travel history information. Of the thirty-five COVID-19 cases screened, thirteen had isolates with SGTF. The travelers transmitted infection to sixty-eight contact cases. The B.1.1.7 lineage was confirmed through sequencing and PCR. Phylogenetic analysis of sequence data available for six cases included four B.1.1.7 strains and one B.1.36 and B.1.1.212 lineage isolate, respectively. Phylogeographic modeling estimated at least three independent B.1.1.7 introductions into Karachi, Pakistan, originating from the UK. B.1.1.212 and B.1.36 were inferred to be introduced either from the UK or the travelers’ layover location. We report the introduction of SARS-CoV-2 B.1.1.7 and other lineages in Pakistan by international travelers arriving via different flight routes. This highlights SARS-CoV-2 transmission through travel, importance of testing and quarantine post-travel to prevent transmission of new strains, as well as recording detailed patients’ metadata. Such results help inform policies on restricting travel from destinations where new highly transmissible variants have emerged.
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Affiliation(s)
- Asghar Nasir
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Ali Raza Bukhari
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Nídia S Trovão
- Fogarty International Center, National Institute of Health, Bethesda, Maryland, USA
| | - Peter M Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Akbar Kanji
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | | | - Najia Karim Ghanchi
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Zeeshan Ansar
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Brian Merritt
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Thomas Mehoke
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Safina Abdul Razzak
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | | | | | - Mansoor Wassan
- Department of Medicine, The Aga Khan University, Karachi, Pakistan
| | | | - Guy Baele
- Department of Microbiology, Immunology and Transplantation, Rega Institute, KU Leuven, Leuven, Belgium
| | - Zeba Rasmussen
- Fogarty International Center, National Institute of Health, Bethesda, Maryland, USA
| | - David Spiro
- Fogarty International Center, National Institute of Health, Bethesda, Maryland, USA
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, The Aga Khan University, Karachi, Pakistan
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3
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Thielen PM, Wohl S, Mehoke T, Ramakrishnan S, Kirsche M, Falade-Nwulia O, Trovão NS, Ernlund A, Howser C, Sadowski N, Morris CP, Hopkins M, Schwartz M, Fan Y, Gniazdowski V, Lessler J, Sauer L, Schatz MC, Evans JD, Ray SC, Timp W, Mostafa HH. Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area. JCI Insight 2021; 6:144350. [PMID: 33749660 PMCID: PMC8026189 DOI: 10.1172/jci.insight.144350] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 02/10/2021] [Indexed: 01/19/2023] Open
Abstract
The early COVID-19 pandemic was characterized by rapid global spread. In Maryland and Washington, DC, United States, more than 2500 cases were reported within 3 weeks of the first COVID-19 detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2 — the virus that causes COVID-19 — in the region. We analyzed 620 samples collected from the Johns Hopkins Health System during March 11–31, 2020, comprising 28.6% of the total cases in Maryland and Washington, DC. From these samples, we generated 114 complete viral genomes. Analysis of these genomes alongside a subsampling of over 1000 previously published sequences showed that the diversity in this region rivaled global SARS-CoV-2 genetic diversity at that time and that the sequences belong to all of the major globally circulating lineages, suggesting multiple introductions into the region. We also analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and found that clinically severe cases had viral genomes belonging to all major viral lineages. We conclude that efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and the interconnectedness of the region as a whole.
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Affiliation(s)
- Peter M Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Shirlee Wohl
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Thomas Mehoke
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | | | - Melanie Kirsche
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
| | - Oluwaseun Falade-Nwulia
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Nídia S Trovão
- NIH, Fogarty International Center, Bethesda, Maryland, USA
| | - Amanda Ernlund
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Craig Howser
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Norah Sadowski
- Department of Emergency Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - C Paul Morris
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Hopkins
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew Schwartz
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Yunfan Fan
- Departments of Biomedical Engineering and Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Victoria Gniazdowski
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Justin Lessler
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Lauren Sauer
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Emergency Medicine, Johns Hopkins University, Baltimore, Maryland, USA
| | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA
| | - Jared D Evans
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland, USA
| | - Stuart C Ray
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Winston Timp
- Department of Medicine, Division of Infectious Disease, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Departments of Biomedical Engineering and Molecular Biology and Genetics, Johns Hopkins University, Baltimore, Maryland, USA
| | - Heba H Mostafa
- Department of Pathology, Division of Medical Microbiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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4
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Thielen PM, Pendleton AL, Player RA, Bowden KV, Lawton TJ, Wisecaver JH. Reference Genome for the Highly Transformable Setaria viridis ME034V. G3 (Bethesda) 2020; 10:3467-3478. [PMID: 32694197 PMCID: PMC7534418 DOI: 10.1534/g3.120.401345] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 07/16/2020] [Indexed: 12/22/2022]
Abstract
Setaria viridis (green foxtail) is an important model system for improving cereal crops due to its diploid genome, ease of cultivation, and use of C4 photosynthesis. The S. viridis accession ME034V is exceptionally transformable, but the lack of a sequenced genome for this accession has limited its utility. We present a 397 Mb highly contiguous de novo assembly of ME034V using ultra-long nanopore sequencing technology (read N50 = 41kb). We estimate that this genome is largely complete based on our updated k-mer based genome size estimate of 401 Mb for S. viridis Genome annotation identified 37,908 protein-coding genes and >300k repetitive elements comprising 46% of the genome. We compared the ME034V assembly with two other previously sequenced Setaria genomes as well as to a diversity panel of 235 S. viridis accessions. We found the genome assemblies to be largely syntenic, but numerous unique polymorphic structural variants were discovered. Several ME034V deletions may be associated with recent retrotransposition of copia and gypsy LTR repeat families, as evidenced by their low genotype frequencies in the sampled population. Lastly, we performed a phylogenomic analysis to identify gene families that have expanded in Setaria, including those involved in specialized metabolism and plant defense response. The high continuity of the ME034V genome assembly validates the utility of ultra-long DNA sequencing to improve genetic resources for emerging model organisms. Structural variation present in Setaria illustrates the importance of obtaining the proper genome reference for genetic experiments. Thus, we anticipate that the ME034V genome will be of significant utility for the Setaria research community.
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Affiliation(s)
- Peter M Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Amanda L Pendleton
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Robert A Player
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Kenneth V Bowden
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Thomas J Lawton
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Jennifer H Wisecaver
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
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5
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Thielen PM, Wohl S, Mehoke T, Ramakrishnan S, Kirsche M, Falade-Nwulia O, Trovão NS, Ernlund A, Howser C, Sadowski N, Morris P, Hopkins M, Schwartz M, Fan Y, Gniazdowski V, Lessler J, Sauer L, Schatz MC, Evans JD, Ray SC, Timp W, Mostafa HH. Genomic Diversity of SARS-CoV-2 During Early Introduction into the United States National Capital Region. medRxiv 2020:2020.08.13.20174136. [PMID: 32817965 PMCID: PMC7430609 DOI: 10.1101/2020.08.13.20174136] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
BACKGROUND The early COVID-19 pandemic has been characterized by rapid global spread. In the United States National Capital Region, over 2,000 cases were reported within three weeks of its first detection in March 2020. We aimed to use genomic sequencing to understand the initial spread of SARS-CoV-2, the virus that causes COVID-19, in the region. By correlating genetic information to disease phenotype, we also aimed to gain insight into any correlation between viral genotype and case severity or transmissibility. METHODS We performed whole genome sequencing of clinical SARS-CoV-2 samples collected in March 2020 by the Johns Hopkins Health System. We analyzed these regional SARS-CoV-2 genomes alongside detailed clinical metadata and the global phylogeny to understand early establishment of the virus within the region. RESULTS We analyzed 620 samples from the Johns Hopkins Health System collected between March 11-31, 2020, comprising 37.3% of the total cases in Maryland during this period. We selected 143 of these samples for sequencing, generating 114 complete viral genomes. These genomes belong to all five major Nextstrain-defined clades, suggesting multiple introductions into the region and underscoring the diversity of the regional epidemic. We also found that clinically severe cases had genomes belonging to all of these clades. CONCLUSIONS We established a pipeline for SARS-CoV-2 sequencing within the Johns Hopkins Health system, which enabled us to capture the significant viral diversity present in the region as early as March 2020. Efforts to control local spread of the virus were likely confounded by the number of introductions into the region early in the epidemic and interconnectedness of the region as a whole.
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Affiliation(s)
- Peter M. Thielen
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Shirlee Wohl
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Thomas Mehoke
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | | | - Melanie Kirsche
- Johns Hopkins University Department of Computer Science, Baltimore, Maryland 21218
| | - Oluwaseun Falade-Nwulia
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
| | - Nídia S. Trovão
- National Institutes of Health, Fogarty International Center, Bethesda, Maryland 20892
| | - Amanda Ernlund
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Craig Howser
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Norah Sadowski
- Johns Hopkins University Department of Emergency Medicine, Baltimore, Maryland 21205
| | - Paul Morris
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Mark Hopkins
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Matthew Schwartz
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Yunfan Fan
- Johns Hopkins University Departments of Biomedical Engineering and Molecular Biology and Genetics, Baltimore, Maryland 21205
| | - Victoria Gniazdowski
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
| | - Justin Lessler
- Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205
| | - Lauren Sauer
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
- Johns Hopkins University Department of Emergency Medicine, Baltimore, Maryland 21205
| | - Michael C. Schatz
- Johns Hopkins University Department of Computer Science, Baltimore, Maryland 21218
| | - Jared D. Evans
- Johns Hopkins University Applied Physics Laboratory, Laurel, Maryland 20723
| | - Stuart C. Ray
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
| | - Winston Timp
- Johns Hopkins University School of Medicine, Department of Medicine, Division of Infectious Disease, Baltimore, Maryland 21205
- Johns Hopkins University Departments of Biomedical Engineering and Molecular Biology and Genetics, Baltimore, Maryland 21205
| | - Heba H. Mostafa
- Johns Hopkins University School of Medicine, Department of Pathology, Division of Medical Microbiology, Baltimore, Maryland 21205
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6
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Saeedi H, Reimer JD, Brandt MI, Dumais PO, Jażdżewska AM, Jeffery NW, Thielen PM, Costello MJ. Global marine biodiversity in the context of achieving the Aichi Targets: ways forward and addressing data gaps. PeerJ 2019; 7:e7221. [PMID: 31681508 PMCID: PMC6824330 DOI: 10.7717/peerj.7221] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 05/31/2019] [Indexed: 01/13/2023] Open
Abstract
In 2010, the Conference of the Parties of the Convention on Biological Diversity agreed on the Strategic Plan for Biodiversity 2011–2020 in Aichi Prefecture, Japan. As this plan approaches its end, we discussed whether marine biodiversity and prediction studies were nearing the Aichi Targets during the 4th World Conference on Marine Biodiversity held in Montreal, Canada in June 2018. This article summarises the outcome of a five-day group discussion on how global marine biodiversity studies should be focused further to better understand the patterns of biodiversity. We discussed and reviewed seven fundamental biodiversity priorities related to nine Aichi Targets focusing on global biodiversity discovery and predictions to improve and enhance biodiversity data standards (quantity and quality), tools and techniques, spatial and temporal scale framing, and stewardship and dissemination. We discuss how identifying biodiversity knowledge gaps and promoting efforts have and will reduce such gaps, including via the use of new databases, tools and technology, and how these resources could be improved in the future. The group recognised significant progress toward Target 19 in relation to scientific knowledge, but negligible progress with regard to Targets 6 to 13 which aimed to safeguard and reduce human impacts on biodiversity.
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Affiliation(s)
- Hanieh Saeedi
- Senckenberg Research Institute and Natural History Museum, Frankfurt am Main, Germany.,FB 15 Biological Sciences Institute for Ecology, Diversity and Evolution Biologicum, Goethe University of Frankfurt, Frankfurt am Main, Germany.,Senckenberg Research Institute and Natural History Museum, OBIS Data Manager, Deep-sea Node, Frankfurt am Main, Germany
| | - James Davis Reimer
- Marine Invertebrate Systematics & Ecology Laboratory, Faculty of Science, University of the Ryukyus, Nishihara, Okinawa, Japan
| | | | | | - Anna Maria Jażdżewska
- Laboratory of Polar Biology and Oceanobiology, Department of Invertebrate Zoology and Hydrobiology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Nicholas W Jeffery
- Fisheries and Oceans Canada, Bedford Institute of Oceanography, Dartmouth, Nova Scotia, Canada
| | - Peter M Thielen
- Research and Exploratory Development Department, Johns Hopkins Applied Physics Laboratory, Laurel, MD, United States of America
| | - Mark John Costello
- Institute of Marine Science, University of Auckland, Auckland, New Zealand
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7
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Rotem A, Serohijos AWR, Chang CB, Wolfe JT, Fischer AE, Mehoke TS, Zhang H, Tao Y, Lloyd Ung W, Choi JM, Rodrigues JV, Kolawole AO, Koehler SA, Wu S, Thielen PM, Cui N, Demirev PA, Giacobbi NS, Julian TR, Schwab K, Lin JS, Smith TJ, Pipas JM, Wobus CE, Feldman AB, Weitz DA, Shakhnovich EI. Evolution on the Biophysical Fitness Landscape of an RNA Virus. Mol Biol Evol 2019; 35:2390-2400. [PMID: 29955873 PMCID: PMC6188569 DOI: 10.1093/molbev/msy131] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Viral evolutionary pathways are determined by the fitness landscape, which maps viral genotype to fitness. However, a quantitative description of the landscape and the evolutionary forces on it remain elusive. Here, we apply a biophysical fitness model based on capsid folding stability and antibody binding affinity to predict the evolutionary pathway of norovirus escaping a neutralizing antibody. The model is validated by experimental evolution in bulk culture and in a drop-based microfluidics that propagates millions of independent small viral subpopulations. We demonstrate that along the axis of binding affinity, selection for escape variants and drift due to random mutations have the same direction, an atypical case in evolution. However, along folding stability, selection and drift are opposing forces whose balance is tuned by viral population size. Our results demonstrate that predictable epistatic tradeoffs between molecular traits of viral proteins shape viral evolution.
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Affiliation(s)
- Assaf Rotem
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Adrian W R Serohijos
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA.,Département de Biochimie et Centre Robert-Cedergren en Bioinformatique et Génomique, Université de Montréal, Montréal, QC, Canada
| | - Connie B Chang
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA.,Department of Chemical and Biological Engineering, Montana State University, Bozeman, MT
| | - Joshua T Wolfe
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD
| | - Audrey E Fischer
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD
| | - Thomas S Mehoke
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD
| | - Huidan Zhang
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA.,Key Laboratory of Cell Biology, Department of Cell Biology, Ministry of Public Health, China Medical University, Shenyang, China.,Key Laboratory of Medical Cell Biology, Ministry of Education, China Medical University, Shenyang, China
| | - Ye Tao
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - W Lloyd Ung
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Jeong-Mo Choi
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | - João V Rodrigues
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
| | - Abimbola O Kolawole
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
| | - Stephan A Koehler
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Susan Wu
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD
| | - Peter M Thielen
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD
| | - Naiwen Cui
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
| | - Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD
| | | | - Timothy R Julian
- Environmental Health Sciences and the Hopkins Water Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD.,Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag), Dübendorf, Switzerland
| | - Kellogg Schwab
- Environmental Health Sciences and the Hopkins Water Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Jeffrey S Lin
- Applied Physics Laboratory, Johns Hopkins University, Laurel, MD
| | - Thomas J Smith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, TX
| | - James M Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI
| | - Andrew B Feldman
- Department of Emergency Medicine, Johns Hopkins Medicine, Baltimore, MD
| | - David A Weitz
- Department of Physics, School of Engineering and Applied Sciences, Harvard University, Cambridge, MA
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8
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Fischer AE, Wu SK, Proescher JBG, Rotem A, Chang CB, Zhang H, Tao Y, Mehoke TS, Thielen PM, Kolawole AO, Smith TJ, Wobus CE, Weitz DA, Lin JS, Feldman AB, Wolfe JT. A high-throughput drop microfluidic system for virus culture and analysis. J Virol Methods 2014; 213:111-7. [PMID: 25522923 DOI: 10.1016/j.jviromet.2014.12.003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 02/05/2023]
Abstract
High mutation rates and short replication times lead to rapid evolution in RNA viruses. New tools for high-throughput culture and analysis of viral phenotypes will enable more effective studies of viral evolutionary processes. A water-in-oil drop microfluidic system to study virus-cell interactions at the single event level on a massively parallel scale is described here. Murine norovirus (MNV-1) particles were co-encapsulated with individual RAW 264.7 cells in 65 pL aqueous drops formed by flow focusing in 50 μm microchannels. At low multiplicity of infection (MOI), viral titers increased greatly, reaching a maximum 18 h post-encapsulation. This system was employed to evaluate MNV-1 escape from a neutralizing monoclonal antibody (clone A6.2). Further, the system was validated as a means for testing escape from antibody neutralization using a series of viral point mutants. Finally, the replicative capacity of single viral particles in drops under antibody stress was tested. Under standard conditions, many RNA virus stocks harbor minority populations of genotypic and phenotypic variants, resulting in quasispecies. These data show that when single cells are encapsulated with single viral particles under antibody stress without competition from other virions, the number of resulting infectious particles is nearly equivalent to the number of viral genomes present. These findings suggest that lower fitness virions can infect cells successfully and replicate, indicating that the microfluidics system may serve as an effective tool for isolating mutants that escape evolutionary stressors.
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Affiliation(s)
- Audrey E Fischer
- The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
| | - Susan K Wu
- The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
| | - Jody B G Proescher
- The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
| | - Assaf Rotem
- Harvard School of Engineering and Applied Sciences, 9 Oxford Street, Cambridge, MA 02138, USA
| | - Connie B Chang
- Harvard School of Engineering and Applied Sciences, 9 Oxford Street, Cambridge, MA 02138, USA
| | - Huidan Zhang
- Harvard School of Engineering and Applied Sciences, 9 Oxford Street, Cambridge, MA 02138, USA
| | - Ye Tao
- Harvard School of Engineering and Applied Sciences, 9 Oxford Street, Cambridge, MA 02138, USA
| | - Thomas S Mehoke
- The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
| | - Peter M Thielen
- The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
| | - Abimbola O Kolawole
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Thomas J Smith
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, 301 University Boulevard, Galveston, TX 77555, USA
| | - Christiane E Wobus
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
| | - David A Weitz
- Harvard School of Engineering and Applied Sciences, 9 Oxford Street, Cambridge, MA 02138, USA
| | - Jeffrey S Lin
- The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
| | - Andrew B Feldman
- The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA
| | - Joshua T Wolfe
- The Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD 20723, USA.
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