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Article ; Online: The Ecology of New Constituents of the Tick Virome and Their Relevance to Public Health.

Vandegrift, Kurt J / Kapoor, Amit

2019 Volume 11, Issue 6

Abstract: Ticks are vectors of several pathogens that can be transmitted to humans and their geographic ranges are expanding. The exposure of ticks to new hosts in a rapidly changing environment is likely to further increase the prevalence and diversity of tick- ... ...

Abstract	Ticks are vectors of several pathogens that can be transmitted to humans and their geographic ranges are expanding. The exposure of ticks to new hosts in a rapidly changing environment is likely to further increase the prevalence and diversity of tick-borne diseases. Although ticks are known to transmit bacteria and viruses, most studies of tick-borne disease have focused upon Lyme disease, which is caused by infection with
MeSH term(s)	Animals ; Arachnid Vectors/virology ; Biodiversity ; Borrelia burgdorferi ; Climate Change ; Communicable Diseases, Emerging/virology ; Ecology ; Encephalitis, Tick-Borne ; Flavivirus ; Humans ; Ixodes/virology ; Lyme Disease ; Phlebovirus ; Phylogeny ; Public Health ; Tick-Borne Diseases/transmission ; Tick-Borne Diseases/virology ; Ticks/virology
Language	English
Publishing date	2019-06-07
Publishing country	Switzerland
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Review
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v11060529
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: The Ecology of New Constituents of the Tick Virome and Their Relevance to Public Health

Vandegrift, Kurt J / Kapoor, Amit

Viruses. 2019 June 07, v. 11, no. 6

2019

Abstract	Ticks are vectors of several pathogens that can be transmitted to humans and their geographic ranges are expanding. The exposure of ticks to new hosts in a rapidly changing environment is likely to further increase the prevalence and diversity of tick-borne diseases. Although ticks are known to transmit bacteria and viruses, most studies of tick-borne disease have focused upon Lyme disease, which is caused by infection with Borrelia burgdorferi. Until recently, ticks were considered as the vectors of a few viruses that can infect humans and animals, such as Powassan, Tick-Borne Encephalitis and Crimean–Congo hemorrhagic fever viruses. Interestingly, however, several new studies undertaken to reveal the etiology of unknown human febrile illnesses, or to describe the virome of ticks collected in different countries, have uncovered a plethora of novel viruses in ticks. Here, we compared the virome compositions of ticks from different countries and our analysis indicates that the global tick virome is dominated by RNA viruses. Comparative phylogenetic analyses of tick viruses from these different countries reveals distinct geographical clustering of the new tick viruses. Some of these new tick RNA viruses (notably severe fever with thrombocytopenia syndrome virus and Heartland virus) were found to be associated with serious human diseases. Their relevance to public health remains unknown. It is plausible that most of these newly identified tick viruses are of endogenous origin or are restricted in their transmission potential, but the efforts to identify new tick viruses should continue. Indeed, future research aimed at defining the origin, the ecology and the spillover potential of this novel viral biodiversity will be critical to understand the relevance to public health.
Keywords	Borrelia burgdorferi ; Lyme disease ; RNA viruses ; bacteria ; biodiversity ; fever ; geographical distribution ; hosts ; human diseases ; humans ; pathogens ; phylogeny ; public health ; thrombocytopenia ; tick-borne encephalitis ; ticks ; viruses
Language	English
Dates of publication	2019-0607
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2516098-9
ISSN	1999-4915
ISSN	1999-4915
DOI	10.3390/v11060529
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A molecular reconstruction of holarctic Heligmosomidae reveals a new species of Heligmosomoides (Nematoda: Heligmosomidae) in Peromyscus maniculatus (Neotominae) from Canada

Alnaqeb, Haitham / Greiman, Stephen E. / Vandegrift, Kurt J. / Campbell, Mariel L. / Meagher, Shawn / Jiménez-Ruiz, F. Agustín

Systematics and Biodiversity. 2022 Dec. 31, v. 20, no. 1 p.1-19

2022

Abstract: A new species of Heligmosomoides Hall, 1916 is proposed for nematodes collected from deer mice, Peromyscus maniculatus, in western Canada. The unequivocal diagnostic character for this species is the presence of two internal bursal membranes. Only four ... ...

Abstract	A new species of Heligmosomoides Hall, 1916 is proposed for nematodes collected from deer mice, Peromyscus maniculatus, in western Canada. The unequivocal diagnostic character for this species is the presence of two internal bursal membranes. Only four species, Heligmosomoides bullosus, Heligmosomoides douglasi, Heligmosomoides montanus and Heligmosomoides vandegrifti, are characterized as possessing a single internal bursal membrane. The genetic distance between Heligmosomoides bibullosus sp. nov., and its putative sister clade Heligmosomoides vandegrifti is congruent with their geographic separation by the mountain range of the Rockies and 4000 km; both morphological difference as well as geography and genetic distance suggest isolation among the two species. Further, H. bibullosus sp. nov. infects deer mice (P. maniculatus) whereas H. vandegrifti is frequently collected in white-footed mice (P. leucopus). Finally, this study supports the taxonomic importance of the monodelphic/didelphic condition as a diagnostic trait within the family, the paraphyly of Heligmosomoides, and reveals undocumented diversity of Heligmosomoides in Nearctic rodents of the Neotominae. The present taxon is the third species in members of this subfamily of rodents. http://www.zoobank.org/urn:lsid:zoobank.org:pub:DE78368D-2CDE-4F9D-AB85-A3CE20D957F4
Keywords	Heligmosomoides ; Nearctic region ; Peromyscus maniculatus ; biodiversity ; deer ; genetic distance ; geography ; mountains ; new species ; paraphyly ; Canada ; Rocky Mountain region ; Heligmosomoides, Heligmosomoides bibullosus ; Nematoda ; Heligmosomoidea ; museum research ; Yukon Territory ; British Columbia
Language	English
Dates of publication	2022-1231
Size	p. 1-19.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	2110629-0
ISSN	1478-0933 ; 1477-2000
ISSN (online)	1478-0933
ISSN	1477-2000
DOI	10.1080/14772000.2022.2046199
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Article: A CNN model for predicting binding affinity changes between SARS-CoV-2 spike RBD variants and ACE2 homologues.

Chen, Chen / Boorla, Veda Sheersh / Chowdhury, Ratul / Nissly, Ruth H / Gontu, Abhinay / Chothe, Shubhada K / LaBella, Lindsey / Jakka, Padmaja / Ramasamy, Santhamani / Vandegrift, Kurt J / Nair, Meera Surendran / Kuchipudi, Suresh V / Maranas, Costas D

bioRxiv : the preprint server for biology

2022

Abstract: The cellular entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involves the association of its receptor binding domain (RBD) with human angiotensin converting enzyme 2 (hACE2) as the first crucial step. Efficient and reliable ... ...

Abstract	The cellular entry of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) involves the association of its receptor binding domain (RBD) with human angiotensin converting enzyme 2 (hACE2) as the first crucial step. Efficient and reliable prediction of RBD-hACE2 binding affinity changes upon amino acid substitutions can be valuable for public health surveillance and monitoring potential spillover and adaptation into non-human species. Here, we introduce a convolutional neural network (CNN) model trained on protein sequence and structural features to predict experimental RBD-hACE2 binding affinities of 8,440 variants upon single and multiple amino acid substitutions in the RBD or ACE2. The model achieves a classification accuracy of 83.28% and a Pearson correlation coefficient of 0.85 between predicted and experimentally calculated binding affinities in five-fold cross-validation tests and predicts improved binding affinity for most circulating variants. We pro-actively used the CNN model to exhaustively screen for novel RBD variants with combinations of up to four single amino acid substitutions and suggested candidates with the highest improvements in RBD-ACE2 binding affinity for human and animal ACE2 receptors. We found that the binding affinity of RBD variants against animal ACE2s follows similar trends as those against human ACE2. White-tailed deer ACE2 binds to RBD almost as tightly as human ACE2 while cattle, pig, and chicken ACE2s bind weakly. The model allows testing whether adaptation of the virus for increased binding with other animals would cause concomitant increases in binding with hACE2 or decreased fitness due to adaptation to other hosts.
Language	English
Publishing date	2022-03-23
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.03.22.485413
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Article ; Online: Presence of Segmented Flavivirus Infections in North America

Vandegrift, Kurt J / Kumar, Arvind / Sharma, Himanshu / Murthy, Satyapramod / Kramer, Laura D / Ostfeld, Richard / Hudson, Peter J / Kapoor, Amit

Emerging infectious diseases

2020 Volume 26, Issue 8, Page(s) 1810–1817

Abstract: Identifying viruses in synanthropic animals is necessary for understanding the origin of many viruses that can infect humans and developing strategies to prevent new zoonotic infections. The white-footed mouse, Peromyscus leucopus, is one of the most ... ...

Abstract	Identifying viruses in synanthropic animals is necessary for understanding the origin of many viruses that can infect humans and developing strategies to prevent new zoonotic infections. The white-footed mouse, Peromyscus leucopus, is one of the most abundant rodent species in the northeastern United States. We characterized the serum virome of 978 free-ranging P. leucopus mice caught in Pennsylvania. We identified many new viruses belonging to 26 different virus families. Among these viruses was a highly divergent segmented flavivirus whose genetic relatives were recently identified in ticks, mosquitoes, and vertebrates, including febrile humans. This novel flavi-like segmented virus was found in rodents and shares ≤70% aa identity with known viruses in the highly conserved region of the viral polymerase. Our data will enable researchers to develop molecular reagents to further characterize this virus and its relatives infecting other hosts and to curtail their spread, if necessary.
MeSH term(s)	Animals ; Flavivirus/genetics ; Flavivirus Infections/epidemiology ; Flavivirus Infections/veterinary ; Mice ; New England ; North America/epidemiology ; Pennsylvania/epidemiology
Keywords	covid19
Language	English
Publishing date	2020-07-20
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	1380686-5
ISSN	1080-6059 ; 1080-6040
ISSN (online)	1080-6059
ISSN	1080-6040
DOI	10.3201/eid2608.190986
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Article ; Online: Motivations, barriers, and communication recommendations for promoting face coverings during the COVID-19 pandemic: Survey findings from a diverse sample.

Vereen, Rhyan N / Lazard, Allison J / Frank, Simone C / Pulido, Marlyn / Richter, Ana Paula C / Higgins, Isabella C A / Shelus, Victoria S / Vandegrift, Sara M / Hall, Marissa G / Ribisl, Kurt M

PloS one

2021 Volume 16, Issue 5, Page(s) e0251169

Abstract: State and local health departments have been tasked with promoting the use of face coverings to decrease the spread of COVID-19 in their respective communities. However, little is known about motivations and barriers to wearing face coverings in the ... ...

Abstract	State and local health departments have been tasked with promoting the use of face coverings to decrease the spread of COVID-19 in their respective communities. However, little is known about motivations and barriers to wearing face coverings in the context of COVID-19 prevention, particularly among communities of color who are at an increased risk of serious illness from the disease. The purpose of this study was to identify common motivations and barriers to face covering use, as well as explore perceptions of messages encouraging the use of face coverings among a racially and ethnically diverse sample. A survey was distributed electronically to North Carolina (NC) residents through NC Department of Health and Human Services listservs in July 2020. Participants self-categorized as Latino/a (33.5%), Black (39.1%), or white or another race (27.5%). The most commonly endorsed motivations for wearing face coverings were to avoid spreading COVID-19 (77%), as well as to protect people who are vulnerable (76%) and one's community (72%). Being uncomfortable (40%) was the most commonly endorsed barrier. Messages that included a clear request (ex. please wear a face covering) and a direct benefit (ex. keep community safe) were more commonly endorsed than those that did not. Commonly endorsed motivations, behaviors, and messages differed by race and ethnicity. Increased attention to message content, message structure, and access to information and resources may aid local officials in increasing consistent use of face coverings.
MeSH term(s)	Adolescent ; Adult ; COVID-19/epidemiology ; COVID-19/prevention & control ; COVID-19/virology ; Communication ; Ethnicity ; Female ; Humans ; Male ; Masks ; Motivation ; North Carolina/epidemiology ; Pandemics ; SARS-CoV-2/isolation & purification ; Surveys and Questionnaires ; Young Adult
Language	English
Publishing date	2021-05-07
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0251169
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Peromyscus as a model system for human hepatitis C: An opportunity to advance our understanding of a complex host parasite system.

Vandegrift, Kurt J / Critchlow, Justin T / Kapoor, Amit / Friedman, David A / Hudson, Peter J

Seminars in cell & developmental biology

2017 Volume 61, Page(s) 123–130

Abstract: Worldwide, there are 185 million people infected with hepatitis C virus and approximately 350,000 people die each year from hepatitis C associated liver diseases. Human hepatitis C research has been hampered by the lack of an appropriate in vivo model ... ...

Abstract	Worldwide, there are 185 million people infected with hepatitis C virus and approximately 350,000 people die each year from hepatitis C associated liver diseases. Human hepatitis C research has been hampered by the lack of an appropriate in vivo model system. Most of the in vivo research has been conducted on chimpanzees, which is complicated by ethical concerns, small sample sizes, high costs, and genetic heterogeneity. The house mouse system has led to greater understanding of a wide variety of human pathogens, but it is unreasonable to expect Mus musculus to be a good model system for every human pathogen. Alternative animal models can be developed in these cases. Ferrets (influenza), cotton rats (human respiratory virus), and woodchucks (hepatitis B) are all alternative models that have led to a greater understanding of human pathogens. Rodent models are tractable, genetically amenable and inbred and outbred strains can provide homogeneity in results. Recently, a rodent homolog of hepatitis C was discovered and isolated from the liver of a Peromyscus maniculatus. This represents the first small mammal (mouse) model system for human hepatitis C and it offers great potential to contribute to our understanding and ultimately aid in our efforts to combat this serious public health concern. Peromyscus are available commercially and can be used to inform questions about the origin, transmission, persistence, pathology, and rational treatment of hepatitis C. Here, we provide a disease ecologist's overview of this new virus and some suggestions for useful future experiments.
Language	English
Publishing date	2017-01
Publishing country	England
Document type	Review ; Journal Article
ZDB-ID	1312473-0
ISSN	1096-3634 ; 1084-9521
ISSN (online)	1096-3634
ISSN	1084-9521
DOI	10.1016/j.semcdb.2016.07.031
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Article ; Online: Presence of Segmented Flaviviruses in Wild Rodents, Pennsylvania, USA

Arvind Kumar / Kurt J. Vandegrift / Himanshu Sharma / Satyapramod Murthy / Laura D. Kramer / Richard Ostfeld / Peter Hudson / Amit Kapoor

Emerging Infectious Diseases, Vol 26, Iss 8, Pp 1810-

2020 Volume 1817

Abstract: Identifying viruses in synanthropic animals is necessary for understanding the origin of many viruses that can infect human hosts and developing strategies to prevent new zoonotic infections. The white-footed mouse, Peromyscus leucopus, is one of the ... ...

Abstract	Identifying viruses in synanthropic animals is necessary for understanding the origin of many viruses that can infect human hosts and developing strategies to prevent new zoonotic infections. The white-footed mouse, Peromyscus leucopus, is one of the most abundant rodent species in the northeastern United States. We characterized the serum virome of 978 free-ranging P. leucopus mice caught in Pennsylvania. We identified many new viruses from 26 different virus families. Among these viruses was a highly divergent segmented flavivirus whose genetic relatives were recently identified in ticks, mosquitos, and vertebrates, including febrile patients. The novel flavi-like segmented virus, isolated from ticks in Pennsylvania, shares ˂70% aa identity with known viruses in the highly conserved region of the viral polymerase. Our data will enable researchers to develop molecular reagents to further characterize this virus and its relatives infecting other hosts and to curtail their spread, if necessary.
Keywords	arbovirus ; Alongshan ; deer mice virome ; flaviviruses ; Jingmen ; northeastern United States ; Medicine ; R ; Infectious and parasitic diseases ; RC109-216
Language	English
Publishing date	2020-08-01T00:00:00Z
Publisher	Centers for Disease Control and Prevention
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Detection of SARS-CoV-2 Omicron variant (B.1.1.529) infection of white-tailed deer.

bioRxiv : the preprint server for biology

2022

Abstract: White-tailed deer ( : Key findings: These studies provide strong evidence of infection of free-living white-tailed deer with the SARS-CoV-2 B.1.1.529 Omicron variant of concern on Staten Island, New York, and highlight an urgent need for ... ...

Abstract	White-tailed deer ( Key findings: These studies provide strong evidence of infection of free-living white-tailed deer with the SARS-CoV-2 B.1.1.529 Omicron variant of concern on Staten Island, New York, and highlight an urgent need for investigations on human-to-animal-to-human spillovers/spillbacks as well as on better defining the expanding host-range of SARS-CoV-2 in non-human animals and the environment.
Language	English
Publishing date	2022-02-07
Publishing country	United States
Document type	Preprint
DOI	10.1101/2022.02.04.479189
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Article ; Online: Response to enrichment, type and timing: small mammals vary in their response to a springtime cicada but not a carbohydrate pulse.

Vandegrift, Kurt J / Hudson, Peter J

The Journal of animal ecology

2009 Volume 78, Issue 1, Page(s) 202–209

Abstract: 1. Masting events in the autumn provide a carbohydrate-rich pulse of resources that can influence the dynamics of small mammals and their natural enemies. Similar patterns are observed with the periodical cicada emergence which provides a protein-rich ... ...

Abstract	1. Masting events in the autumn provide a carbohydrate-rich pulse of resources that can influence the dynamics of small mammals and their natural enemies. Similar patterns are observed with the periodical cicada emergence which provides a protein-rich pulse in the spring, but comparisons are confounded by timing and food type. 2. We compared the influence of a naturally occurring spring pulse of cicadas with an experimental spring pulse of carbohydrate-rich seeds. We used a replicated population level field experiment and capture-mark-recapture techniques to record the vital rates, demographics, and abundance of Peromyscus leucopus (the white-footed mouse), as well as other small mammals and their parasites. 3. The density of P. leucopus on grids where cicadas emerged was 55% higher than controls as a consequence of early breeding. This was followed by an increase in the prevalence of the nematode Pterygodermatities peromysci, reduced breeding and decreased recruitment rates. Other small mammals including Tamias striatus (eastern chipmunk) and Blarina brevicauda (short-tailed shrew), increased in density, but there was no affect on Sorex cinereus (masked shrew). 4. In contrast to the presence of cicadas, there was no influence of sunflower seed supplementation on small mammal density, vital rates, or reproduction with the exception of an increase in B. brevicauda density. The response of small mammals to seasonal pulses depends on timing, food type, and species.
MeSH term(s)	Animals ; Dietary Carbohydrates/metabolism ; Female ; Hemiptera/physiology ; Intestines/parasitology ; Male ; Mice ; Nematoda/physiology ; Nematode Infections/parasitology ; Nematode Infections/veterinary ; Peromyscus/parasitology ; Peromyscus/physiology ; Population Density ; Reproduction/physiology ; Rodent Diseases/parasitology ; Sciuridae/physiology ; Seasons ; Shrews/physiology ; Survival Analysis ; Time Factors
Chemical Substances	Dietary Carbohydrates
Language	English
Publishing date	2009-01
Publishing country	England
Document type	Journal Article ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	3024-7
ISSN	1365-2656 ; 0021-8790
ISSN (online)	1365-2656
ISSN	0021-8790
DOI	10.1111/j.1365-2656.2008.01456.x
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