11 results on '"Pond, Sergei L. K."'
Search Results
2. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
- Author
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Faria, Nuno R., primary, Mellan, Thomas A., additional, Whittaker, Charles, additional, Claro, Ingra M., additional, Candido, Darlan da S., additional, Mishra, Swapnil, additional, Crispim, Myuki A. E., additional, Sales, Flavia C. S., additional, Hawryluk, Iwona, additional, McCrone, John T., additional, Hulswit, Ruben J. G., additional, Franco, Lucas A. M., additional, Ramundo, Mariana S., additional, de Jesus, Jaqueline G., additional, Andrade, Pamela S., additional, Coletti, Thais M., additional, Ferreira, Giulia M., additional, Silva, Camila A. M., additional, Manuli, Erika R., additional, Pereira, Rafael H. M., additional, Peixoto, Pedro S., additional, Kraemer, Moritz U. G., additional, Gaburo, Nelson, additional, Camilo, Cecilia da C., additional, Hoeltgebaum, Henrique, additional, Souza, William M., additional, Rocha, Esmenia C., additional, de Souza, Leandro M., additional, de Pinho, Mariana C., additional, Araujo, Leonardo J. T., additional, Malta, Frederico S. V., additional, de Lima, Aline B., additional, Silva, Joice do P., additional, Zauli, Danielle A. G., additional, Ferreira, Alessandro C. de S., additional, Schnekenberg, Ricardo P., additional, Laydon, Daniel J., additional, Walker, Patrick G. T., additional, Schlüter, Hannah M., additional, dos Santos, Ana L. P., additional, Vidal, Maria S., additional, Del Caro, Valentina S., additional, Filho, Rosinaldo M. F., additional, dos Santos, Helem M., additional, Aguiar, Renato S., additional, Proença-Modena, José L., additional, Nelson, Bruce, additional, Hay, James A., additional, Monod, Mélodie, additional, Miscouridou, Xenia, additional, Coupland, Helen, additional, Sonabend, Raphael, additional, Vollmer, Michaela, additional, Gandy, Axel, additional, Prete, Carlos A., additional, Nascimento, Vitor H., additional, Suchard, Marc A., additional, Bowden, Thomas A., additional, Pond, Sergei L. K., additional, Wu, Chieh-Hsi, additional, Ratmann, Oliver, additional, Ferguson, Neil M., additional, Dye, Christopher, additional, Loman, Nick J., additional, Lemey, Philippe, additional, Rambaut, Andrew, additional, Fraiji, Nelson A., additional, Carvalho, Maria do P. S. S., additional, Pybus, Oliver G., additional, Flaxman, Seth, additional, Bhatt, Samir, additional, and Sabino, Ester C., additional
- Published
- 2021
- Full Text
- View/download PDF
3. An Evolutionary Portrait of the Progenitor SARS-CoV-2 and Its Dominant Offshoots in COVID-19 Pandemic
- Author
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Kumar, Sudhir, primary, Tao, Qiqing, additional, Weaver, Steven, additional, Sanderford, Maxwell, additional, Caraballo-Ortiz, Marcos A, additional, Sharma, Sudip, additional, Pond, Sergei L K, additional, and Miura, Sayaka, additional
- Published
- 2021
- Full Text
- View/download PDF
4. Genomics and epidemiology of the P.1 SARS-CoV-2 lineage in Manaus, Brazil
- Author
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Faria, Nuno R., Mellan, Thomas A., Whittaker, Charles, Claro, Ingra M., Candido, Darlan da S., Mishra, Swapnil, Crispim, Myuki A. E., Sales, Flavia C., Hawryluk, Iwona, McCrone, John T., Hulswit, Ruben J. G., Franco, Lucas A. M., Ramundo, Mariana S., de Jesus, Jaqueline G., Andrade, Pamela S., Coletti, Thais M., Ferreira, Giulia M., Silva, Camila A. M., Manuli, Erika R., Pereira, Rafael H. M., Peixoto, Pedro S., Kraemer, Moritz U., Gaburo, Nelson, Camilo, Cecilia da C., Hoeltgebaum, Henrique, Souza, William M., Rocha, Esmenia C., de Souza, Leandro M., de Pinho, Mariana C., Araujo, Leonardo J. T., Malta, Frederico S., de Lima, Aline B., Silva, Joice do P., Zauli, Danielle A. G., Ferreira, Alessandro C. de S., Schnekenberg, Ricardo P., Laydon, Daniel J., Walker, Patrick G. T., Schlueter, Hannah M., dos Santos, Ana L. P., Vidal, Maria S., Del Caro, Valentina S., Filho, Rosinaldo M. F., dos Santos, Helem M., Aguiar, Renato S., Proenca-Modena, Jose L. P., Nelson, Bruce, Hay, James A., Monod, Melodie, Miscouridou, Xenia, Coupland, Helen, Sonabend, Raphael, Vollmer, Michaela, Gandy, Axel, Prete, Carlos A., Nascimento, Vitor H., Suchard, Marc A., Bowden, Thomas A., Pond, Sergei L. K., Wu, Chieh-Hsi, Ratmann, Oliver, Ferguson, Neil M., Dye, Christopher, Loman, Nick J., Lemey, Philippe, Rambaut, Andrew, Fraiji, Nelson A., Carvalho, Maria do P. S. S., Pybus, Oliver G., Flaxman, Seth, Bhatt, Samir, Sabino, Ester C., Faria, Nuno R., Mellan, Thomas A., Whittaker, Charles, Claro, Ingra M., Candido, Darlan da S., Mishra, Swapnil, Crispim, Myuki A. E., Sales, Flavia C., Hawryluk, Iwona, McCrone, John T., Hulswit, Ruben J. G., Franco, Lucas A. M., Ramundo, Mariana S., de Jesus, Jaqueline G., Andrade, Pamela S., Coletti, Thais M., Ferreira, Giulia M., Silva, Camila A. M., Manuli, Erika R., Pereira, Rafael H. M., Peixoto, Pedro S., Kraemer, Moritz U., Gaburo, Nelson, Camilo, Cecilia da C., Hoeltgebaum, Henrique, Souza, William M., Rocha, Esmenia C., de Souza, Leandro M., de Pinho, Mariana C., Araujo, Leonardo J. T., Malta, Frederico S., de Lima, Aline B., Silva, Joice do P., Zauli, Danielle A. G., Ferreira, Alessandro C. de S., Schnekenberg, Ricardo P., Laydon, Daniel J., Walker, Patrick G. T., Schlueter, Hannah M., dos Santos, Ana L. P., Vidal, Maria S., Del Caro, Valentina S., Filho, Rosinaldo M. F., dos Santos, Helem M., Aguiar, Renato S., Proenca-Modena, Jose L. P., Nelson, Bruce, Hay, James A., Monod, Melodie, Miscouridou, Xenia, Coupland, Helen, Sonabend, Raphael, Vollmer, Michaela, Gandy, Axel, Prete, Carlos A., Nascimento, Vitor H., Suchard, Marc A., Bowden, Thomas A., Pond, Sergei L. K., Wu, Chieh-Hsi, Ratmann, Oliver, Ferguson, Neil M., Dye, Christopher, Loman, Nick J., Lemey, Philippe, Rambaut, Andrew, Fraiji, Nelson A., Carvalho, Maria do P. S. S., Pybus, Oliver G., Flaxman, Seth, Bhatt, Samir, and Sabino, Ester C.
- Abstract
Cases of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in Manaus, Brazil, resurged in late 2020 despite previously high levels of infection. Genome sequencing of viruses sampled in Manaus between November 2020 and January 2021 revealed the emergence and circulation of a novel SARS-CoV-2 variant of concern. Lineage P.1 acquired 17 mutations, including a trio in the spike protein (K417T, E484K, and N501Y) associated with increased binding to the human ACE2 (angiotensin-converting enzyme 2) receptor. Molecular clock analysis shows that P.1 emergence occurred around mid-November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.7- to 2.4-fold more transmissible and that previous (non-P.1) infection provides 54 to 79% of the protection against infection with P.1 that it provides against non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness.
- Published
- 2021
5. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil
- Author
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Faria, Nuno R., primary, Mellan, Thomas A., additional, Whittaker, Charles, additional, Claro, Ingra M., additional, Candido, Darlan da S., additional, Mishra, Swapnil, additional, Crispim, Myuki A. E., additional, Sales, Flavia C., additional, Hawryluk, Iwona, additional, McCrone, John T., additional, Hulswit, Ruben J. G., additional, Franco, Lucas A. M., additional, Ramundo, Mariana S., additional, de Jesus, Jaqueline G., additional, Andrade, Pamela S., additional, Coletti, Thais M., additional, Ferreira, Giulia M., additional, Silva, Camila A. M., additional, Manuli, Erika R., additional, Pereira, Rafael H. M., additional, Peixoto, Pedro S., additional, Kraemer, Moritz U., additional, Gaburo, Nelson, additional, Camilo, Cecilia da C., additional, Hoeltgebaum, Henrique, additional, Souza, William M., additional, Rocha, Esmenia C., additional, de Souza, Leandro M., additional, de Pinho, Mariana C., additional, Araujo, Leonardo J. T, additional, Malta, Frederico S. V., additional, de Lima, Aline B., additional, Silva, Joice do P., additional, Zauli, Danielle A. G., additional, Ferreira, Alessandro C. de S., additional, Schnekenberg, Ricardo P, additional, Laydon, Daniel J., additional, Walker, Patrick G. T., additional, Schlüter, Hannah M., additional, dos Santos, Ana L. P., additional, Vidal, Maria S., additional, Del Caro, Valentina S., additional, Filho, Rosinaldo M. F., additional, dos Santos, Helem M., additional, Aguiar, Renato S., additional, Modena, José L. P., additional, Nelson, Bruce, additional, Hay, James A., additional, Monod, Melodie, additional, Miscouridou, Xenia, additional, Coupland, Helen, additional, Sonabend, Raphael, additional, Vollmer, Michaela, additional, Gandy, Axel, additional, Suchard, Marc A., additional, Bowden, Thomas A., additional, Pond, Sergei L. K., additional, Wu, Chieh-Hsi, additional, Ratmann, Oliver, additional, Ferguson, Neil M., additional, Dye, Christopher, additional, Loman, Nick J., additional, Lemey, Philippe, additional, Rambaut, Andrew, additional, Fraiji, Nelson A., additional, Carvalho, Maria do P. S. S., additional, Pybus, Oliver G., additional, Flaxman, Seth, additional, Bhatt, Samir, additional, and Sabino, Ester C., additional
- Published
- 2021
- Full Text
- View/download PDF
6. An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic
- Author
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Kumar, Sudhir, primary, Tao, Qiqing, additional, Weaver, Steven, additional, Sanderford, Maxwell, additional, Caraballo-Ortiz, Marcos A., additional, Sharma, Sudip, additional, Pond, Sergei L. K., additional, and Miura, Sayaka, additional
- Published
- 2020
- Full Text
- View/download PDF
7. The phylogenomics and evolutionary dynamics of the organellar genomes in carnivorous Utricularia and Genlisea species (Lentibulariaceae).
- Author
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Silva SR, Miranda VFO, Michael TP, Płachno BJ, Matos RG, Adamec L, Pond SLK, Lucaci AG, Pinheiro DG, and Varani AM
- Subjects
- Phylogeny, Biological Evolution, Magnoliopsida genetics, Lamiales
- Abstract
Utricularia and Genlisea are highly specialized carnivorous plants whose phylogenetic history has been poorly explored using phylogenomic methods. Additional sampling and genomic data are needed to advance our phylogenetic and taxonomic knowledge of this group of plants. Within a comparative framework, we present a characterization of plastome (PT) and mitochondrial (MT) genes of 26 Utricularia and six Genlisea species, with representatives of all subgenera and growth habits. All PT genomes maintain similar gene content, showing minor variation across the genes located between the PT junctions. One exception is a major variation related to different patterns in the presence and absence of ndh genes in the small single copy region, which appears to follow the phylogenetic history of the species rather than their lifestyle. All MT genomes exhibit similar gene content, with most differences related to a lineage-specific pseudogenes. We find evidence for episodic positive diversifying selection in PT and for most of the Utricularia MT genes that may be related to the current hypothesis that bladderworts' nuclear DNA is under constant ROS oxidative DNA damage and unusual DNA repair mechanisms, or even low fidelity polymerase that bypass lesions which could also be affecting the organellar genomes. Finally, both PT and MT phylogenetic trees were well resolved and highly supported, providing a congruent phylogenomic hypothesis for Utricularia and Genlisea clade given the study sampling., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier Inc. All rights reserved.)
- Published
- 2023
- Full Text
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8. TopHap: Rapid inference of key phylogenetic structures from common haplotypes in large genome collections with limited diversity.
- Author
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Caraballo-Ortiz MA, Miura S, Sanderford M, Dolker T, Tao Q, Weaver S, Pond SLK, and Kumar S
- Abstract
Motivation: Building reliable phylogenies from very large collections of sequences with a limited number of phylogenetically informative sites is challenging because sequencing errors and recurrent/backward mutations interfere with the phylogenetic signal, confounding true evolutionary relationships. Massive global efforts of sequencing genomes and reconstructing the phylogeny of SARS-CoV-2 strains exemplify these difficulties since there are only hundreds of phylogenetically informative sites and millions of genomes. For such datasets, we set out to develop a method for building the phylogenetic tree of genomic haplotypes consisting of positions harboring common variants to improve the signal-to-noise ratio for more accurate phylogenetic inference of resolvable phylogenetic features., Results: We present the TopHap approach that determines spatiotemporally common haplotypes of common variants and builds their phylogeny at a fraction of the computational time of traditional methods. To assess topological robustness, we develop a bootstrap resampling strategy that resamples genomes spatiotemporally. The application of TopHap to build a phylogeny of 68,057 genomes (68KG) produced an evolutionary tree of major SARS-CoV-2 haplotypes. This phylogeny is concordant with the mutation tree inferred using the co-occurrence pattern of mutations and recovers key phylogenetic relationships from more traditional analyses. We also evaluated alternative roots of the SARS-CoV-2 phylogeny and found that the earliest sampled genomes in 2019 likely evolved by four mutations of the most recent common ancestor of all SARS-CoV-2 genomes. An application of TopHap to more than 1 million genomes reconstructed the most comprehensive evolutionary relationships of major variants, which confirmed the 68KG phylogeny and provided evolutionary origins of major variants of concern., Availability: TopHap is available on the web at https://github.com/SayakaMiura/TopHap ., Contact: s.kumar@temple.edu.
- Published
- 2021
- Full Text
- View/download PDF
9. Genomics and epidemiology of a novel SARS-CoV-2 lineage in Manaus, Brazil.
- Author
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Faria NR, Mellan TA, Whittaker C, Claro IM, Candido DDS, Mishra S, Crispim MAE, Sales FC, Hawryluk I, McCrone JT, Hulswit RJG, Franco LAM, Ramundo MS, de Jesus JG, Andrade PS, Coletti TM, Ferreira GM, Silva CAM, Manuli ER, Pereira RHM, Peixoto PS, Kraemer MU, Gaburo N Jr, Camilo CDC, Hoeltgebaum H, Souza WM, Rocha EC, de Souza LM, de Pinho MC, Araujo LJT, Malta FSV, de Lima AB, Silva JDP, Zauli DAG, de S Ferreira AC, Schnekenberg RP, Laydon DJ, Walker PGT, Schlüter HM, Dos Santos ALP, Vidal MS, Del Caro VS, Filho RMF, Dos Santos HM, Aguiar RS, Modena JLP, Nelson B, Hay JA, Monod M, Miscouridou X, Coupland H, Sonabend R, Vollmer M, Gandy A, Suchard MA, Bowden TA, Pond SLK, Wu CH, Ratmann O, Ferguson NM, Dye C, Loman NJ, Lemey P, Rambaut A, Fraiji NA, Carvalho MDPSS, Pybus OG, Flaxman S, Bhatt S, and Sabino EC
- Abstract
Cases of SARS-CoV-2 infection in Manaus, Brazil, resurged in late 2020, despite high levels of previous infection there. Through genome sequencing of viruses sampled in Manaus between November 2020 and January 2021, we identified the emergence and circulation of a novel SARS-CoV-2 variant of concern, lineage P.1, that acquired 17 mutations, including a trio in the spike protein (K417T, E484K and N501Y) associated with increased binding to the human ACE2 receptor. Molecular clock analysis shows that P.1 emergence occurred around early November 2020 and was preceded by a period of faster molecular evolution. Using a two-category dynamical model that integrates genomic and mortality data, we estimate that P.1 may be 1.4-2.2 times more transmissible and 25-61% more likely to evade protective immunity elicited by previous infection with non-P.1 lineages. Enhanced global genomic surveillance of variants of concern, which may exhibit increased transmissibility and/or immune evasion, is critical to accelerate pandemic responsiveness., Competing Interests: Competing interests: Authors declare that they have no competing interests.
- Published
- 2021
- Full Text
- View/download PDF
10. An evolutionary portrait of the progenitor SARS-CoV-2 and its dominant offshoots in COVID-19 pandemic.
- Author
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Kumar S, Tao Q, Weaver S, Sanderford M, Caraballo-Ortiz MA, Sharma S, Pond SLK, and Miura S
- Abstract
We report the likely most recent common ancestor of SARS-CoV-2 - the coronavirus that causes COVID-19. This progenitor SARS-CoV-2 genome was recovered through a novel application and advancement of computational methods initially developed to reconstruct the mutational history of tumor cells in a patient. The progenitor differs from the earliest coronaviruses sampled in China by three variants, implying that none of the earliest patients represent the index case or gave rise to all the human infections. However, multiple coronavirus infections in China and the USA harbored the progenitor genetic fingerprint in January 2020 and later, suggesting that the progenitor was spreading worldwide as soon as weeks after the first reported cases of COVID-19. Mutations of the progenitor and its offshoots have produced many dominant coronavirus strains, which have spread episodically over time. Fingerprinting based on common mutations reveals that the same coronavirus lineage has dominated North America for most of the pandemic. There have been multiple replacements of predominant coronavirus strains in Europe and Asia and the continued presence of multiple high-frequency strains in Asia and North America. We provide a continually updating dashboard of global evolution and spatiotemporal trends of SARS-CoV-2 spread (http://sars2evo.datamonkey.org/)., Competing Interests: Competing Interests The authors declare that they have no competing interests.
- Published
- 2021
- Full Text
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11. Transmitted HIV type 1 drug resistance among individuals with recent HIV infection in East and Southern Africa.
- Author
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Price MA, Wallis CL, Lakhi S, Karita E, Kamali A, Anzala O, Sanders EJ, Bekker LG, Twesigye R, Hunter E, Kaleebu P, Kayitenkore K, Allen S, Ruzagira E, Mwangome M, Mutua G, Amornkul PN, Stevens G, Pond SL, Schaefer M, Papathanasopoulos MA, Stevens W, and Gilmour J
- Subjects
- Adolescent, Adult, Africa, Eastern epidemiology, Africa, Southern epidemiology, Female, Genotype, Geography, HIV Infections virology, HIV-1 genetics, HIV-1 isolation & purification, Humans, Male, Middle Aged, Molecular Epidemiology, Mutation, Missense, Prevalence, RNA, Viral genetics, Sequence Analysis, DNA, Young Adult, pol Gene Products, Human Immunodeficiency Virus genetics, Anti-HIV Agents pharmacology, Drug Resistance, Viral, HIV Infections epidemiology, HIV Infections transmission, HIV-1 drug effects
- Abstract
To characterize WHO-defined transmitted HIV drug resistance mutation (TDRM) data from recently HIV-infected African volunteers, we sequenced HIV (pol) and evaluated for TDRM the earliest available specimens from ARV-naive volunteers diagnosed within 1 year of their estimated date of infection at eight research centers in sub-Saharan Africa. TDRMs were detected in 19/408 (5%) volunteers. The prevalence of TDRMs varied by research center, from 5/26 (19%) in Entebbe, 6/78 (8%) in Kigali, 2/49 (4%) in Kilifi, to 3/106 (3%) in Lusaka. One of five volunteers from Cape Town (20%) had TDRMs. Despite small numbers, our data suggest an increase in DRMs by year of infection in Zambia (p = 0.004). The prevalence observed in Entebbe was high across the entire study. ARV history data from 12 (63%) HIV-infected sexual partners were available; 3 reported ARV use prior to transmission. Among four partners with sequence data available, transmission linkage was confirmed and two had the same TDRMs as the newly infected volunteer (both K103N). As ARV therapy continues to increase in availability throughout Africa, monitoring incident virus strains for the presence of TDRMs should be a priority. Early HIV infection cohorts provide an excellent and important platform to monitor the development of TDRMs to inform treatment guidelines, drug choices, and strategies for secondary prevention of TDRM transmission.
- Published
- 2011
- Full Text
- View/download PDF
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