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Papers by Alexander Ciota

Virus Evolution, 2019

Following its introduction into New York State (NYS) in 1999, West Nile virus (WNV; Flavivirus, F... more Following its introduction into New York State (NYS) in 1999, West Nile virus (WNV; Flavivirus, Flaviviridae) underwent a rapid expansion throughout the USA and into Canada and Latin America. WNV has been characterized as being evolutionarily stable, with weak geographic structure, a dominance of purifying selection and limited adaptive change. We analyzed all available full-genome WNV sequences, focusing on the 543 available sequences from NYS, which included 495 newly sequenced 2000–15 isolates. In addition, we analyzed deep-sequencing data from 317 of these isolates. While our data are generally in agreement with the limited pace of evolutionary change and broad geographic and temporal mixing identified in other studies, we have identified some important exceptions. Most notably, there are 14 codons which demonstrated evidence of positive selection as determined by multiple models, including some positions with evidence of selection in NYS exclusively. Coincident with increased W...

Viruses

Flaviviruses include several emerging and re-emerging arboviruses which cause millions of infecti... more Flaviviruses include several emerging and re-emerging arboviruses which cause millions of infections each year. Although relatively well-studied, much remains unknown regarding the mechanisms and means by which these viruses readily alternate and adapt to different hosts and environments. Here, we review a subset of the different aspects of flaviviral biology which impact host switching and viral fitness. These include the mechanism of replication and structural biology of the NS3 and NS5 proteins, which reproduce the viral genome; rates of mutation resulting from this replication and the role of mutational frequency in viral fitness; and the theory of quasispecies evolution and how it contributes to our understanding of genetic and phenotypic plasticity.

Microorganisms

Bourbon virus (BRBV, family Orthomyxoviridae) is a tickborne virus recently detected in the Unite... more Bourbon virus (BRBV, family Orthomyxoviridae) is a tickborne virus recently detected in the United States (US). BRBV was first identified from a fatal human case in 2014 in Bourbon County, Kansas. Enhanced surveillance in Kansas and Missouri implicated Amblyomma americanum as the primary vector for BRBV. Historically, BRBV was only detected in the lower midwestern US, but since 2020 it has been reported in North Carolina, Virginia, New Jersey, and New York State (NYS). This study aimed to elucidate genetic and phenotypic characteristics of BRBV strains from NYS through whole genome sequencing and the assessment of replication kinetics in mammalian cultures and A. americanum nymphs. Sequence analysis revealed the existence of two divergent BRBV clades circulating in NYS. BRBV NY21-2143 is closely related to the midwestern BRBV strains but has unique substitutions in the glycoprotein. Two other NYS BRBV strains, BRBV NY21-1814 and BRBV NY21-2666, form a distinct clade unique from prev...

Virology, 2019

Rabensburg virus (RBGV; Flaviviridae, Flavivirus) has been classified as both a novel flavivirus ... more Rabensburg virus (RBGV; Flaviviridae, Flavivirus) has been classified as both a novel flavivirus and a unique lineage of West Nile virus (WNV). RBGV and WNV share approximately 76% sequence homology, yet RBGV does not replicate to high viral titers within vertebrate cell lines at physiological temperatures and has not been naturally isolated from a vertebrate host. These unique genetic and biological characteristics make RBGV a viable tool to identify the genetic determinants of flavivirus infectivity and fitness in vertebrate hosts. Using experimental evolution, we characterized mutated variants of RBGV that have altered capacity for infection and replication in various cell lines. Shared genetic differences within these variants were identified throughout the genome, with a large majority found in the NS3 and NS5 genes. Our results support a role for the replication complex in host utilization and suggest that epistatic interactions likely contribute to host-specific fitness and emergence.

Frontiers in Virology, 2021

Viral diversity and evolution play a central role in processes such as disease emergence, vaccine... more Viral diversity and evolution play a central role in processes such as disease emergence, vaccine failure, drug resistance, and virulence. However, significant challenges remain to better understand and manage these processes. Here, we discuss five of these challenges. These include improving our ability to predict viral evolution, developing more relevant experimental evolutionary systems, integrating viral dynamics and evolution at different scales, systematic appraisal of the virosphere, and deepening our understanding of virus-virus interactions. Intensifying future research on these areas should improve our ability to combat viral diseases, as well as to exploit viral diversity and evolution for biotechnological purposes.

The American Journal of Tropical Medicine and Hygiene, 2020

The Asian tiger mosquito (Aedes albopictus) is an important vector of a number of arboviruses, in... more The Asian tiger mosquito (Aedes albopictus) is an important vector of a number of arboviruses, including Zika (ZIKV), dengue (DENV), and chikungunya (CHIKV) viruses, and has recently expanded its range in the eastern United States to southern New England and New York. Given the recent establishment and proliferation of Ae. albopictus in this region and the increasing amount of international travel between the United States and endemic countries, there is a need to elucidate the public health risk posed by this mosquito species in the Northeast. Accordingly, we evaluated the competence of four Ae. albopictus populations from Connecticut and New York, for two strains each of ZIKV, DENV serotype 2 (DENV-2), and CHIKV, currently circulating in the Americas, to evaluate the local transmission risk by this vector. We found that local Ae. albopictus populations are susceptible to infection by all three viruses but are most capable of transmitting CHIKV. Variation in competence was observed for ZIKV and CHIKV, driven by the virus strains and mosquito population, whereas competence was more homogeneous for the DENV-2 strains under evaluation. These results suggest that under optimal circumstances, Ae. albopictus could support localized transmission of these viruses and emphasize the importance of maintaining mosquito surveillance and control programs to suppress Ae. albopictus populations and limit further range expansion of this species.

Parasites & Vectors, 2021

Background Vector-borne pathogens must survive and replicate in the hostile environment of an ins... more Background Vector-borne pathogens must survive and replicate in the hostile environment of an insect’s midgut before successful dissemination. Midgut microbiota interfere with pathogen infection by activating the basal immunity of the mosquito and by synthesizing pathogen-inhibitory metabolites. Methods The goal of this study was to assess the influence of Zika virus (ZIKV) infection and increased temperature on Aedes albopictus midgut microbiota. Aedes albopictus were reared at diurnal temperatures of day 28 °C/night 24 °C (L) or day 30 °C/night 26 °C (M). The mosquitoes were given infectious blood meals with 2.0 × 108 PFU/ml ZIKV, and 16S rRNA sequencing was performed on midguts at 7 days post-infectious blood meal exposure. Results Our findings demonstrate that Elizabethkingia anophelis albopictus was associated with Ae. albopictus midguts exposed to ZIKV infectious blood meal. We observed a negative correlation between ZIKV and E. anophelis albopictus in the midguts of Ae. albop...

Journal of Medical Entomology, 2021

Eastern equine encephalitis virus (EEEV; Togaviridae, Alphavirus) is an arthropod-borne virus (ar... more Eastern equine encephalitis virus (EEEV; Togaviridae, Alphavirus) is an arthropod-borne virus (arbovirus) primarily maintained in an enzootic cycle between Culiseta melanura (Coquillett) and passerine birds. EEEV, which has the highest reported case- fatality rate among arbovirus in the Americas, is responsible for sporadic outbreaks in the Eastern and Midwest United States. Infection is associated with severe neurologic disease and mortality in horses, humans, and other vertebrate hosts. Here, we review what is known about EEEV taxonomy, functional genomics, and evolution, and identify gaps in knowledge regarding the role of EEEV genetic diversity in transmission and disease.

Journal of Medicinal Chemistry, 2021

The naturally occurring nucleotide 3'-deoxy-3',4'-didehydro-cytidine-5'-triphosph... more The naturally occurring nucleotide 3'-deoxy-3',4'-didehydro-cytidine-5'-triphosphate (ddhCTP) was recently found to exert potent and broad-spectrum antiviral activity. However, nucleoside 5'-triphosphates in general are not cell-permeable, which precludes the direct use of ddhCTP as a therapeutic. To harness the therapeutic potential of this endogenous antiviral nucleotide, we synthesized phosphoramidate prodrug HLB-0532247 (1) and found it to result in dramatically elevated levels of ddhCTP in cells. We compared 1 and 3'-deoxy-3',4'-didehydro-cytidine (ddhC) and found that 1 more effectively reduces titers of Zika and West Nile viruses in cell culture with minimal nonspecific toxicity to host cells. We conclude that 1 is a promising antiviral agent based on a novel strategy of facilitating elevated levels of the endogenous ddhCTP antiviral nucleotide.

Analytical Chemistry, 2021

We propose a novel approach for building a classification/identification framework based on the f... more We propose a novel approach for building a classification/identification framework based on the full complement of RNA post-transcriptional modifications (rPTMs) expressed by an organism at basal conditions. The approach relies on advanced mass spectrometry techniques to characterize the products of exonuclease digestion of total RNA extracts. Sample profiles comprising identities and relative abundances of all detected rPTM were used to train and test the capabilities of different machine learning (ML) algorithms. Each algorithm proved capable of identifying rigorous decision rules for differentiating closely related classes and correctly assigning unlabeled samples. The ML classifiers resolved different members of the Enterobacteriaceae family, alternative Escherichia coli serotypes, a series of Saccharomyces cerevisiae knockout mutants, and primary cells of the Homo sapiens central nervous system, which shared very similar genetic backgrounds. The excellent levels of accuracy and resolving power achieved by training on a limited number of classes were successfully replicated when the number of classes was significantly increased to escalate complexity. A dendrogram generated from ML-curated data exhibited a hierarchical organization that closely resembled those afforded by established taxonomic systems. Finer clustering patterns revealed the extensive effects induced by the deletion of a single pivotal gene. This information provided a putative roadmap for exploring the roles of rPTMs in their respective regulatory networks, which will be essential to decipher the epitranscriptomics code. The ubiquitous presence of RNA in virtually all living organisms promises to enable the broadest possible range of applications, with significant implications in the diagnosis of RNA-related diseases.

Frontiers in Microbiology, 2020

Rapid and significant range expansion of both the Zika virus (ZIKV) and its Aedes vector species ... more Rapid and significant range expansion of both the Zika virus (ZIKV) and its Aedes vector species has resulted in the declaration of ZIKV as a global health threat. Successful transmission of ZIKV by its vector requires a complex series of interactions between these entities including the establishment, replication and dissemination of the virus within the mosquito. The metabolic conditions within the mosquito tissues play a critical role in mediating the crucial processes of viral infection and replication and represent targets for prevention of virus transmission. In this study, we carried out a comprehensive metabolomic phenotyping of ZIKV infected and uninfected Ae. albopictus by untargeted analysis of primary metabolites, lipids and biogenic amines. We performed a comparative metabolomic study of infection state with the aim of understanding the biochemical changes resulting from the interaction between the ZIKV and its vector. We have demonstrated that ZIKV infection results in...

The American Journal of Tropical Medicine and Hygiene, 2018

Aedes aegypti (L.) (Diptera: Culicidae) have a global distribution and are the primary vector of ... more Aedes aegypti (L.) (Diptera: Culicidae) have a global distribution and are the primary vector of a number of mosquito-borne viruses responsible for epidemics throughout the Americas. As in much of South America, the threat from pathogens including dengue virus (DENV; Flaviviridae, Flavivirus) and chikungunya virus (CHIKV; Togaviridae, Alphavirus) has increased in Argentina in recent years. The complexity of transmission cycles makes predicting the occurrence and intensity of arbovirus outbreaks difficult. To gain a better understanding of the risk of DENV and CHIKV in Argentina and the factors influencing this risk, we evaluated the role of population and temperature in the vector competence and vectorial capacity (VC) of Ae. aegypti from geographically and ecologically distinct locations. Our results demonstrate that intrinsic and extrinsic factors including mosquito population, viral species, and temperature significantly influence both vector competence and overall VC of Ae. aegypti in Argentina, yet also that the magnitude of these influences is highly variable. Specifically, results suggest that CHIKV competence is more dependent on mosquito genetics than is DENV competence, whereas temperature has a greater effect on DENV transmission. In addition, although there is an overall positive correlation between temperature and competence for both viruses, there are exceptions to this for individual virus-population combinations. Together, these data establish large variability in VC for these pathogens among distinct Ae. aegypti populations in Argentina and demonstrate that accurate assessment of arbovirus risk will require nuanced models that fully consider the complexity of interactions between virus, temperature, mosquito genetics, and hosts.

Emerging infectious diseases, Jul 1, 2017

In the Western Hemisphere, Zika virus is thought to be transmitted primarily by Aedes aegypti mos... more In the Western Hemisphere, Zika virus is thought to be transmitted primarily by Aedes aegypti mosquitoes. To determine the extent to which Ae. albopictus mosquitoes from the United States are capable of transmitting Zika virus and the influence of virus dose, virus strain, and mosquito species on vector competence, we evaluated multiple doses of representative Zika virus strains in Ae. aegypti and Ae. albopictus mosquitoes. Virus preparation (fresh vs. frozen) significantly affected virus infectivity in mosquitoes. We calculated 50% infectious doses to be 6.1-7.5 log 10 PFU/mL; minimum infective dose was 4.2 log 10 PFU/mL. Ae. albopictus mosquitoes were more susceptible to infection than Ae. aegypti mosquitoes, but transmission efficiency was higher for Ae. aegypti mosquitoes, indicating a transmission barrier in Ae. albopictus mosquitoes. Results suggest that, although Zika virus transmission is relatively inefficient overall and dependent on virus strain and mosquito species, Ae. ...

Virology, Jan 7, 2015

West Nile virus (WNV; Flaviviridae, Flavivirus) is the most geographically widespread arthropod-b... more West Nile virus (WNV; Flaviviridae, Flavivirus) is the most geographically widespread arthropod-borne virus (arbovirus) in the world and is found in multiple ecologically distinct settings. Despite the likelihood of frequent exposure to novel hosts, studies evaluating the capacity and correlates of host range expansions or shifts of WNV and other arboviruses are generally lacking. We utilized experimental evolution of WNV in an Amblyomma americanum tick cell line to model an invertebrate host shift and evaluate the adaptive potential of WNV outside of its primary transmission cycle. Our results demonstrate that highly significant gains in replicative ability in ixodid tick cells are attainable for WNV but are also associated with widespread genetic change and significant phenotypic costs in vitro. Decreased fitness in primary hosts could represent a barrier to frequent exploitation of hard ticks by WNV in nature.

Viruses, 2013

West Nile virus (WNV; Flavivirus; Flaviviridae) is the cause of the most widespread arthropod-bor... more West Nile virus (WNV; Flavivirus; Flaviviridae) is the cause of the most widespread arthropod-borne viral disease in the world and the largest outbreak of neuroinvasive disease ever observed. Mosquito-borne outbreaks are influenced by intrinsic (e.g., vector and viral genetics, vector and host competence, vector life-history traits) and extrinsic (e.g., temperature, rainfall, human land use) factors that affect virus activity and mosquito biology in complex ways. The concept of vectorial capacity integrates these factors to address interactions of the virus with the arthropod host, leading to a clearer understanding of their complex interrelationships, how they affect transmission of vector-borne disease, and how they impact human health. Vertebrate factors including host competence, population dynamics, and immune status also affect transmission dynamics. The complexity of these interactions are further exacerbated by the fact that not only can divergent hosts differentially alter the virus, but the virus also can affect both vertebrate and invertebrate hosts in ways that significantly alter patterns of virus transmission. This chapter concentrates on selected components of the virus-vector-vertebrate interrelationship, focusing specifically on how interactions between vector, virus, and environment shape the patterns and intensity of WNV transmission.

PLoS ONE, 2012

Rabensburg virus (RABV), a Flavivirus with ,76% nucleotide and 90% amino acid identity with repre... more Rabensburg virus (RABV), a Flavivirus with ,76% nucleotide and 90% amino acid identity with representative members of lineage one and two West Nile virus (WNV), previously was isolated from Culex pipiens and Aedes rossicus mosquitoes in the Czech Republic, and phylogenetic and serologic analyses demonstrated that it was likely a new lineage of WNV. However, no direct link between RABV and human disease has been definitively established and the extent to which RABV utilizes the typical WNV transmission cycle is unknown. Herein, we evaluated vector competence and capacity for vertical transmission (VT) in Cx. pipiens; in vitro growth on avian, mammalian, and mosquito cells; and infectivity and viremia production in birds. RABV infection and replication only were detected on mosquito cells. Experimentally inoculated birds did not become infected. Cx. pipiens had poor peroral vector competence and a higher VT rate as compared to US-WNV in Cx. pipiens. As a result, we postulate that RABV is an intermediate between the mosquito-specific and horizontally transmitted flaviviruses.

Journal of General Virology, 2014

Understanding the potential for host range shifts and expansions of RNA viruses is critical to pr... more Understanding the potential for host range shifts and expansions of RNA viruses is critical to predicting the evolutionary and epidemiological paths of these pathogens. As arthropod-borne viruses (arboviruses) experience frequent spillover from their amplification cycles and are generalists by nature, they are likely to experience a relatively high frequency of success in a range of host environments. Despite this, the potential for host expansion, the genetic correlates of adaptation to novel environments and the costs of such adaptations in originally competent hosts are still not characterized fully for arboviruses. In the studies presented here, we utilized experimental evolution of St. Louis encephalitis virus (SLEV; family Flaviviridae, genus Flavivirus) in vitro in the Dermacentor andersoni line of tick cells to model adaptation to a novel invertebrate host. Our results demonstrated that levels of adaptation and costs in alternate hosts are highly variable among lineages, but...

Current opinion in virology, 2015

The inter-relationship between mosquitoes and the viruses they transmit is complex. While previou... more The inter-relationship between mosquitoes and the viruses they transmit is complex. While previously understood barriers to infection and transmission remain valid, additional factors have been uncovered that suggest an 'arms race' between mosquito and virus. These include the mosquito microbiota and interplay between mosquito and viral genetics. Following an infectious blood meal, the mosquito mounts an immune and transcriptional response, leading to altered expression of multiple genes. These complex interactions, specific to vector and virus genotypes, combine with external influences, particularly temperature, to determine vector competence. The mosquito's response to the infecting agent may have consequences in terms of longevity, feeding behavior and/or fecundity. These factors, together with population density and the frequency of host contact determine vectorial capacity.

Scientific Reports

Insect midgut microbial symbionts have been considered as an integral component in thermal adapta... more Insect midgut microbial symbionts have been considered as an integral component in thermal adaptation due to their differential thermal sensitivity. Altered midgut microbial communities can influence both insect physiology and competence for important vector-borne pathogens. This study sought to gain insights into how Aedes aegypti midgut microbes and life history traits are affected by increase in baseline diurnal temperature. Increase in temperature resulted in the enrichment of specific taxa with Bacillus being the most enriched. Bacillus is known to be heat tolerant. It also resulted in a dissimilar microbial assemblage (Bray–Curtis Index, PERMANOVA, F = 2.2063; R2 = 0.16706; P = 0.002) and reduced survivorship (Log-rank [Mantel-Cox] test, Chi-square = 35.66 df = 5, P