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Featured researches published by Lark L. Coffey.


PLOS ONE | 2007

Human Muscle Satellite Cells as Targets of Chikungunya Virus Infection

Simona Ozden; Michel Huerre; Jean Pierre Riviere; Lark L. Coffey; Philippe V. Afonso; Vincent Mouly; Jean de Monredon; Jean Christophe Roger; Mohamed El Amrani; Jean Luc Yvin; Marie Christine Jaffar; Marie Pascale Frenkiel; Marion Sourisseau; Olivier Schwartz; Gillian Butler-Browne; Philippe Desprès; Antoine Gessain; Pierre Emmanuel Ceccaldi

Background Chikungunya (CHIK) virus is a mosquito-transmitted alphavirus that causes in humans an acute infection characterised by fever, polyarthralgia, head-ache, and myalgia. Since 2005, the emergence of CHIK virus was associated with an unprecedented magnitude outbreak of CHIK disease in the Indian Ocean. Clinically, this outbreak was characterized by invalidating poly-arthralgia, with myalgia being reported in 97.7% of cases. Since the cellular targets of CHIK virus in humans are unknown, we studied the pathogenic events and targets of CHIK infection in skeletal muscle. Methodology/Principal Findings Immunohistology on muscle biopsies from two CHIK virus-infected patients with myositic syndrome showed that viral antigens were found exclusively inside skeletal muscle progenitor cells (designed as satelllite cells), and not in muscle fibers. To evaluate the ability of CHIK virus to replicate in human satellite cells, we assessed virus infection on primary human muscle cells; viral growth was observed in CHIK virus-infected satellite cells with a cytopathic effect, whereas myotubes were essentially refractory to infection. Conclusions/Significance This report provides new insights into CHIK virus pathogenesis, since it is the first to identify a cellular target of CHIK virus in humans and to report a selective infection of muscle satellite cells by a viral agent in humans.


Proceedings of the National Academy of Sciences of the United States of America | 2011

Arbovirus high fidelity variant loses fitness in mosquitoes and mice

Lark L. Coffey; Yasnee Beeharry; Antonio V. Bordería; Hervé Blanc; Marco Vignuzzi

The error rate of RNA-dependent RNA polymerases (RdRp) affects the mutation frequency in a population of viral RNAs. Using chikungunya virus (CHIKV), we describe a unique arbovirus fidelity variant with a single C483Y amino acid change in the nsP4 RdRp that increases replication fidelity and generates populations with reduced genetic diversity. In mosquitoes, high fidelity CHIKV presents lower infection and dissemination titers than wild type. In newborn mice, high fidelity CHIKV produces truncated viremias and lower organ titers. These results indicate that increased replication fidelity and reduced genetic diversity negatively impact arbovirus fitness in invertebrate and vertebrate hosts.


Emerging Infectious Diseases | 2003

West Nile virus in Mexico: evidence of widespread circulation since July 2002.

Jose G. Estrada-Franco; Roberto Navarro-Lopez; David W. C. Beasley; Lark L. Coffey; Anne-Sophie Carrara; Amelia Travassos da Rosa; Tamara Clements; Eryu Wang; George V. Ludwig; Arturo Campomanes Cortes; Pedro Paz Ramirez; Robert B. Tesh; Alan D. T. Barrett; Scott C. Weaver

West Nile virus (WNV) antibodies were detected in horses from five Mexican states, and WNV was isolated from a Common Raven in the state of Tabasco. Phylogenetic studies indicate that this isolate, the first from Mexico, is related to strains from the central United States but has a relatively high degree of sequence divergence.


Proceedings of the National Academy of Sciences of the United States of America | 2008

Arbovirus evolution in vivo is constrained by host alternation

Lark L. Coffey; Nikos Vasilakis; Aaron C. Brault; Ann M. Powers; Frédéric Tripet; Scott C. Weaver

The intrinsic plasticity of RNA viruses can facilitate host range changes that lead to epidemics. However, evolutionary processes promoting cross-species transfers are poorly defined, especially for arthropod-borne viruses (arboviruses). In theory, cross species transfers by arboviruses may be constrained by their alternating infection of disparate hosts, where optimal replication in one host involves a fitness tradeoff for the other. Accordingly, freeing arboviruses from alternate replication via specialization in a single host should accelerate adaptation. This hypothesis has been tested by using cell culture model systems with inconclusive results. Therefore, we tested it using an in vivo system with Venezuelan equine encephalitis virus (VEEV), an emerging alphavirus of the Americas. VEEV serially passaged in mosquitoes exhibited increased mosquito infectivity and vertebrate-specialized strains produced higher viremias. Conversely, alternately passaged VEEV experienced no detectable fitness gains in either host. These results suggest that arbovirus adaptation and evolution is limited by obligate host alternation and predict that arboviral emergence via host range changes may be less frequent than that of single host animal RNA viruses.


Journal of Virology | 2013

The Perils of Pathogen Discovery: Origin of a Novel Parvovirus-Like Hybrid Genome Traced to Nucleic Acid Extraction Spin Columns

Samia N. Naccache; Alexander L. Greninger; Deanna Lee; Lark L. Coffey; Tung Phan; Annie Rein-Weston; Andrew Aronsohn; John Hackett; Eric Delwart; Charles Y. Chiu

ABSTRACT Next-generation sequencing was used for discovery and de novo assembly of a novel, highly divergent DNA virus at the interface between the Parvoviridae and Circoviridae. The virus, provisionally named parvovirus-like hybrid virus (PHV), is nearly identical by sequence to another DNA virus, NIH-CQV, previously detected in Chinese patients with seronegative (non-A-E) hepatitis. Although we initially detected PHV in a wide range of clinical samples, with all strains sharing ∼99% nucleotide and amino acid identity with each other and with NIH-CQV, the exact origin of the virus was eventually traced to contaminated silica-binding spin columns used for nucleic acid extraction. Definitive confirmation of the origin of PHV, and presumably NIH-CQV, was obtained by in-depth analyses of water eluted through contaminated spin columns. Analysis of environmental metagenome libraries detected PHV sequences in coastal marine waters of North America, suggesting that a potential association between PHV and diatoms (algae) that generate the silica matrix used in the spin columns may have resulted in inadvertent viral contamination during manufacture. The confirmation of PHV/NIH-CQV as laboratory reagent contaminants and not bona fide infectious agents of humans underscores the rigorous approach needed to establish the validity of new viral genomes discovered by next-generation sequencing.


Journal of Virology | 2011

Host Alternation of Chikungunya Virus Increases Fitness while Restricting Population Diversity and Adaptability to Novel Selective Pressures

Lark L. Coffey; Marco Vignuzzi

ABSTRACT The mechanisms by which RNA arboviruses, including chikungunya virus (CHIKV), evolve and maintain the ability to infect vertebrate and invertebrate hosts are poorly understood. To understand how host specificity shapes arbovirus populations, we studied CHIKV populations passaged alternately between invertebrate and vertebrate cells (invertebrate ↔ vertebrate) to simulate natural alternation and contrasted the results with those for populations that were artificially released from cycling by passage in single cell types. These CHIKV populations were characterized by measuring genetic diversity, changes in fitness, and adaptability to novel selective pressures. The greatest fitness increases were observed in alternately passaged CHIKV, without drastic changes in population diversity. The greatest increases in genetic diversity were observed after serial passage and correlated with greater adaptability. These results suggest an evolutionary trade-off between maintaining fitness for invertebrate ↔ vertebrate cell cycling, where maximum adaptability is possible only via enhanced population diversity and extensive exploration of sequence space.


Microbes and Infection | 2009

Human genetic determinants of dengue virus susceptibility

Lark L. Coffey; Eva Mertens; Anne Claire Brehin; Maria Dolores Fernandez-Garcia; Ali Amara; Philippe Desprès; Anavaj Sakuntabhai

Dengue virus (DENV) is an emerging mosquito-borne pathogen that produces significant morbidity worldwide resulting in an estimated 50-100 million infections annually. DENV causes a spectrum of illness ranging from inapparent infection to life-threatening hemorrhagic fever and shock. The varied DENV disease outcome is determined by complex interactions between immunopathologic, viral, and human genetic factors. This review summarizes these interactions with a focus on human genetic determinants of DENV susceptibility, including human leukocyte antigens, blood type, and single nucleotide polymorphisms in immune response genes that have been associated with DENV disease. We also discuss other factors related to DENV outcome including viral genetic determinants, age, ethnicity, and nutritional status as they relate to DENV susceptibility. We emphasize the need for functional genetics studies to complement association-based data and we call for controlled study designs and standard clinical DENV disease definitions that will strengthen conclusions based on human genetic DENV studies.


Emerging Infectious Diseases | 2004

Dengue Emergence and Adaptation to Peridomestic Mosquitoes

Abelardo C. Moncayo; Zoraida Fernandez; Diana Ortiz; Mawlouth Diallo; Amadou A. Sall; Sammie Hartman; C. Todd Davis; Lark L. Coffey; Christian Mathiot; Robert B. Tesh; Scott C. Weaver

Endemic dengue virus (DENV) type 2 strains infect Aedes aegypti and Ae. albopictus more efficiently than ancestral sylvatic strains, which suggests that adaptation to these vectors mediated DENV emergence.


Future Microbiology | 2013

Factors shaping the adaptive landscape for arboviruses: implications for the emergence of disease

Lark L. Coffey; Naomi L. Forrester; Konstantin A. Tsetsarkin; Nikos Vasilakis; Scott C. Weaver

Many examples of the emergence or re-emergence of infectious diseases involve the adaptation of zoonotic viruses to new amplification hosts or to humans themselves. These include several instances of simple mutational adaptations, often to hosts closely related to the natural reservoirs. However, based on theoretical grounds, arthropod-borne viruses, or arboviruses, may face several challenges for adaptation to new hosts. Here, we review recent findings regarding adaptive evolution of arboviruses and its impact on disease emergence. We focus on the zoonotic alphaviruses Venezuelan equine encephalitis and chikungunya viruses, which have undergone adaptive evolution that mediated recent outbreaks of disease, as well as the flaviviruses dengue and West Nile viruses, which have emerged via less dramatic adaptive mechanisms.


Viruses | 2014

Chikungunya Virus–Vector Interactions

Lark L. Coffey; Anna Bella Failloux; Scott C. Weaver

Chikungunya virus (CHIKV) is a mosquito-borne alphavirus that causes chikungunya fever, a severe, debilitating disease that often produces chronic arthralgia. Since 2004, CHIKV has emerged in Africa, Indian Ocean islands, Asia, Europe, and the Americas, causing millions of human infections. Central to understanding CHIKV emergence is knowledge of the natural ecology of transmission and vector infection dynamics. This review presents current understanding of CHIKV infection dynamics in mosquito vectors and its relationship to human disease emergence. The following topics are reviewed: CHIKV infection and vector life history traits including transmission cycles, genetic origins, distribution, emergence and spread, dispersal, vector competence, vector immunity and microbial interactions, and co-infection by CHIKV and other arboviruses. The genetics of vector susceptibility and host range changes, population heterogeneity and selection for the fittest viral genomes, dual host cycling and its impact on CHIKV adaptation, viral bottlenecks and intrahost diversity, and adaptive constraints on CHIKV evolution are also discussed. The potential for CHIKV re-emergence and expansion into new areas and prospects for prevention via vector control are also briefly reviewed.

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Scott C. Weaver

University of Texas Medical Branch

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Robert B. Tesh

University of Texas Medical Branch

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Eric Delwart

Systems Research Institute

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Abelardo C. Moncayo

University of Texas Medical Branch

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Amelia Travassos da Rosa

University of Texas Medical Branch

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Cameron Scott Ball

Sandia National Laboratories

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Eryu Wang

University of Texas Medical Branch

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Patricia V. Aguilar

University of Texas Medical Branch

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Robert J. Meagher

Sandia National Laboratories

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