2024

Embracing Complexity: What Novel Sequencing Methods are Teaching Us About Herpesvirus Genomic Diversity.
Ortigas-Vásquez A, Szpara ML. Invited & under review, Annual Review of Virology.

2023

Comparative Analysis of Multiple Consensus Genomes of the Same Strain of Marek’s Disease Virus Reveals Intrastrain Variation.
Ortigas-Vásquez A, Pandey U, Renner D, Bowen CD, Baigent SJ, Dunn JR, Cheng H, Yao Y, Read A, Nair VK, Kennedy DA, Szpara ML. bioRxiv; 2023.  [DOI: https://doi.org/10.1101/2023.09.04.556264]

Shared sequence characteristics identified in non-canonical rearrangements of HSV-1 genomes.
Shitrit A, Nisnevich V, Rozenshtein N, Kobo H, Phan HV, Tay S, Szpara M, Weitzman MD, Drayman N, Kobiler O. J Virol. 2023 Nov 22;e00955-23. [DOI: https://doi.org/10.1128/jvi.00955-23][PDF]

2022

Viral Shedding 1 Year Following First-Episode Genital HSV-1 Infection.
Johnston C, Magaret A, Son H, Stern M, Rathbun M, Renner D, Szpara M, Gunby S, Ott M, Jing L, Campbell VL, Huang M li, Selke S, Jerome KR, Koelle DM, Wald A – JAMA, 2022. 328(17):1730–1739. [DOI: https://doi.org/10.1001/jama.2022.19061][PDF]

Multi-Phenotype Analysis for Enhanced Classification of 11 Herpes Simplex Virus 1 Strains.
Dweikat SN, Renner DW, Bowen CD, Szpara ML – Journal of General Virology, 2022. 103(10). [DOI: https://doi.org/10.1099/jgv.0.001780][PDF]

Aerosolized Hydrogen Peroxide Decontamination of N95 Respirators, with Fit-Testing and Viral Inactivation, Demonstrates Feasibility for Reuse during the COVID-19 Pandemic.
Derr TH, James MA, Kuny CV, Patel DR, Kandel PP, Field C, Beckman MD, Hockett KL, Bates MA, Sutton TC, Szpara ML – MSphere, 2022. e00303-22. [DOI: https://doi.org/10.1128/msphere.00303-22][PDF]

Herpes Simplex Virus-2 Variation Contributes to Neurovirulence During Neonatal Infection.
Hayes CK, Villota CK, McEnany FB, Cerón S, Awasthi S, Szpara ML, Friedman HM, Leib DA, Longnecker R, Weitzman MD, Akhtar LN – Journal of Infectious Diseases, 2022. Apr 22;jiac151. [DOI: https://doi.org/10.1093/infdis/jiac151][PDF]

Comparison of herpes simplex virus 1 genetic diversity between adult sexual transmission partners with genital infection.
Rathbun MM, Shipley MM, Bowen CD, Selke S, Wald A, Johnston CM, Szpara ML – PLOS Pathogens 18, no. 5 (May 19, 2022): e1010437. [DOI: https://doi.org/10.1371/journal.ppat.1010437] [PDF]

Dermatitis during Spaceflight Associated with HSV-1 Reactivation.
Mehta SK, Szpara ML, Rooney BV, Diak DM, Shipley MM, Renner DW, Krieger SS, Nelman-Gonzalez MA, Zwart SR, Smith SM, Crucian BE – Viruses, 2022. 14:789. [DOI: https://doi.org/10.3390/v14040789][PDF]

2021

A holistic perspective on herpes simplex virus (HSV) ecology and evolution.
Rathbun MM and Szpara ML – Advances in Virus Research, 2021. 110:27–57. [DOI: https://doi.org/10.1016/bs.aivir.2021.05.001][PDF]

ICTV Virus Taxonomy Profile: Herpesviridae 2021.
Gatherer D, Depledge DP, Hartley CA, Szpara ML, Vaz PK, Benkő M, Brandt CR, et al – Journal of General Virology, 2021. 102(10): October 27. [DOI: https://doi.org/10.1099/jgv.0.001673][PDF]

Viral infection of human neurons triggers strain-specific differences in host neuronal and viral transcriptomes.
Mangold CA, Rathbun MM, Renner DW, Kuny CV, Szpara ML – PLOS Pathogens, 2021. 17(3): e1009441. [DOI: https://doi.org/10.1371/journal.ppat.1009441][PDF]

Genome sequence of the virulent model herpes simplex virus 1 strain McKrae demonstrates the presence of at least two widely used variant strains.
Renner DW, Parsons L, Shreve JT, Engel EA, Kuny CV, Enquist L, Neumann D, Mangold C, Szpara ML – Microbiology Resource Announcements, 2021. 10(12): e01146-19. [DOI: https://doi.org/10.1128/MRA.01146-19][PDF]

2020

Alphaherpesvirus Genomics: Past, Present and Future.
Kuny CV and Szpara ML – Current Issues in Molecular Biology, 2020. 42: 41–80. [DOI: https://doi.org/10.21775/cimb.042.041][PDF]

Interferon-independent STING signaling promotes resistance to HSV-1 in vivo.
Yamashiro LH, Wilson SC, Morrison HM, Karalis V, Chung JJ, Chen KJ, Bateup HS, Szpara ML, Lee AY, Cox JS, Vance RE – Nature Communications, 2020. December; 11(1). [DOI: https://doi.org/10.1038/s41467-020-17156-x][PDF]

In vitro evolution of herpes simplex virus 1 (HSV-1) reveals selection for syncytia and other minor variants in cell culture.
Kuny CV, Bowen CD, Renner DW, Johnston CM, Szpara ML – Virus Evolution, 2020. April 12; 6(1). [DOI: https://doi.org/10.1093/ve/veaa013][PDF]

Mechanisms of DNA virus evolution.
Szpara ML, Van Doorslaer K – Encyclopedia of Virology, 2020. 4th edition, Elsevier Ltd; Chapter 00006: 1-8. [DOI: https://doi.org/10.1016/B978-0-12-809633-8.20993-X][PDF]

Oligonucleotide enrichment of HSV-1 genomic DNA from clinical specimens for use in high-throughput sequencing.
Shipley MM, Rathbun MM, Szpara ML – Chapter in: Methods in Molecular Biology, Herpes Simplex Virus, 2020. 2060:199–217. [DOI: https://doi.org/10.1007/978-1-4939-9814-2_11][PDF]

2019

Personalized viral genomic investigation of herpes simplex virus 1 perinatal viremic transmission with dual fatality.
Shipley MM, Renner DW, Pandey U, Ford B, Bloom DC, Grose C, Szpara ML – Molecular Case Studies (Cold Spring Harbor Press), 2019. December; 5(6): a004382.[DOI: https://doi.org/10.1101/mcs.a004382][PDF]

Persistent Infection with Herpes Simplex Virus 1 and Alzheimer’s Disease—A Call to Study How Variability in Both Virus and Host May Impact Disease.
Mangold CA, Szpara ML – Viruses (Invited for Special Issue: Viruses Ten-Year Anniversary), 2019. 11(10), 966 [DOI: https://doi.org/10.3390/v11100966] [PDF]

Viral genetic diversity and its potential contributions to the development and progression of neonatal herpes simplex virus (HSV) disease.
Akhtar LN, Szpara ML – Current Clinical Microbiology Reports, 2019. 23 Nov. [DOI: https://doi.org/10.1007/s40588-019-00131-6] [PDF]

Molecular epidemiology of Marek’s disease virus in central Pennsylvania, USA.
Bell AS, Kennedy DA, Jones MJ, Cairns CL, Pandey U, Dunn PA, Szpara ML, Read AF – Virus Evolution, 2019. Apr 23;5(1). [DOI: https://doi.org/10.1093/ve/vey042] [PDF]

Genotypic and phenotypic diversity of herpes simplex virus 2 within the infected neonatal population.
Akhtar LN, Bowen CD, Renner DW, Pandey U, Della Fera AN, Kimberlin DW, Prichard MN, Whitley RJ, Weitzman MW, Szpara ML – mSphere, 2019. 4(1). [DOI: https://doi.org/10.1128/mSphere.00590-18] [PDF]

Comparison of HSV-1 strains circulating in Finland demonstrates the uncoupling of whole-genome relatedness and phenotypic outcomes of viral infection.
Bowen CD, Paavilainen H, Renner DW, Palomäki J, Lehtinen J, Vuorinen T, Norberg P, Hukkanen V, Szpara ML – Journal of Virology, 2019. Apr 3;93(8). pii: e01824-18. [DOI: https://doi.org/10.1128/JVI.01824-18] [PDF]

Herpes simplex virus (HSV) disease management and diagnostics in the era of high throughput sequencing.
Pandey U and Szpara ML – Clinical Microbiology Newsletter, 2019. 41(5): 41–48. [DOI: https://doi.org/10.1016/j.clinmicnews.2019.02.003] [PDF]

2018

Genome-wide surveillance of genital HSV-1 from multiple anatomic sites over time.
Shipley MM, Renner DW, Ott M, Bloom DC, Koelle DM, Johnston C, Szpara ML – Journal of Infectious Diseases, 2018. 218(4): 595–605. [DOI:https://doi.org/10.1093/infdis/jiy216] [PDF]

Expression of the purine biosynthetic enzyme phosphoribosyl formylglycinamidine synthase (FGAMS) in neurons.
Mangold CA, Yao PJ, Du M, Freeman WM, Benkovic SJ, Szpara ML – Journal of Neurochemistry, 2018. 144(6): 723–35. [DOI: https://doi.org/10.1111/jnc.14304]  [PDF]

Impacts of genome-wide analyses on our understanding of human herpesvirus diversity and evolution.
Renner DW and Szpara ML – Journal of Virology (Invited minireview), 2018. 92:e00908-17.  [DOI: https://doi.org/10.1128/JVI.00908-17]  [PDF]

2017

Inferred father-to-son transmission of herpes simplex virus results in near-perfect preservation of viral genome identity and in vivo phenotypes.
Pandey U, Renner DW, Thompson RL, Szpara ML, Sawtell NM – Scientific Reports, 2017. 7(1):13666. [DOI: https://doi.org/10.1038/s41598-017-13936-6] [PDF]

Differentiated SH-SY5Y human cells provide a reductionist model of HSV-1 neurotropism.
Shipley MM, Mangold CA, Kuny CV, Szpara ML – Journal of Virology, 2017. 91(23):e00958-17. [DOI: https://doi.org/10.1128/JVI.00958-17] [PDF]

Experimental Oral Herpes Simplex Virus-1 (HSV-1) Co-infection in Simian Immunodeficiency Virus (SIV)-Infected Rhesus Macaques.
Aravantinou M, Mizenina O, Calenda G, Kenney J, Frank I, Lifson JD, Szpara M, Jing L, Koelle DM, Teleshova N, Grasperge B, Blanchard J, Gettie A, Martinelli E, Derby N – Frontiers in Microbiology, 2017. 8. [DOI: https://doi.org/10.3389/fmicb.2017.02342] [PDF]

A phylogenomic analysis of Marek’s disease virus reveals independent paths to virulence in Eurasia and North America.
Trimpert J, Groenke N, Jenckel M, He S, Kunec D, Szpara ML, Spatz SJ, Osterrieder N, McMahon DP – Evolutionary Applications, 2017. 10:1091–1101. [DOI: https://doi.org/10.1111/eva.12515] [PDF]

A model of genital herpes simplex virus Type 1 infection in Rhesus Macaques.
Aravantinou M, Frank I, Arrode-Bruses G, Szpara M, Grasperge B, Blanchard J, Gettie A, Derby N, Martinelli E – Journal of Medical Primatology, 2017. 46:121–128. [DOI: https://doi.org/10.1111/jmp.12293] [PDF]

2016

DNA from dust: comparative genomics of large DNA viruses in field surveillance samples
Pandey U, Bell AS, Renner D, Kennedy DA, Shreve J, Cairns CL, Jones MJ, Dunn PA, Read AF,  Szpara ML – mSphere, 2016. 1:e00132-16. [DOI: https://doi.org/10.1128/mSphere.00132-16] [PDF]

• Public repository for data from this paper: https://scholarsphere.psu.edu/collections/1544bp14j

Viral forensic genomics reveals the relatedness of classic herpes simplex virus strains KOS, KOS63, and KOS79
Bowen CD, Renner DW, Shreve JT, Tafuri Y, PayneKM, Dix RD, Kinchington PR, Gatherer D, Szpara ML – Virology (Elsevier), 2016. 492, 179–186. [DOI: https://doi.org/10.1016/j.virol.2016.02.013] [PDF]

Differentiation of the SH-SY5Y human neuroblastoma cell line
Shipley MM, Mangold CA, Szpara ML – Journal of Visualized Experiments (JoVE), 2016. Feb 17(108). [DOI: https://doi.org/10.3791/53193] [PDF] [Movie]

2015

VirAmp: A Galaxy-based viral genome assembly pipeline
Wan Y, Renner DW, Albert I, Szpara ML – GigaScience, 2015. Apr 28;4:19. [DOI: https://doi.org/10.1186/s13742-015-0060-y] [PDF]

Rapid genome assembly and comparison decodes intra-strain variation in human alpha-herpesviruses
Parsons LR, Tafuri YR, Shreve JT, Bowen CD, Shipley MM, Enquist LW, Szpara ML – mBio, 2015. Mar 31;6(2). pii: e02213-14. [DOI: https://doi.org/10.1128/mBio.02213-14] [PDF]

• How-to documentation for VirGA: http://virga.readthedocs.org/en/latest/
• Code repository for VirGA: https://bitbucket.org/szparalab
• A freely-accessible Virtual Machine (VM) that can run VirGA:     https://www.dropbox.com/sh/szsnelelpbs4qip/AAAohfvHWBGG_HMLL6pJgmTca?dl=0
• Public repository for data used in this paper:        https://scholarsphere.psu.edu/collections/sf268c193

2014

Genome sequence of the anterograde-spread defective herpes simplex virus 1 strain MacIntyre
Szpara ML, Tafuri YR, Parsons L, Shreve JT, Engel EA, Enquist LW – Genome Announcements, 2014. 2(6):e01161-14. [DOI: https://doi.org/10.1128/genomeA.01161-14] [PDF]

Isolation of Herpes Simplex Virus Nucleocapsid DNA
ML Szpara – Methods in Molecular Biology, 2014. 1144: 31–41. [online book chapter link: http://link.springer.com/10.1007/978-1-4939-0428-0_3] [PDF]

2013

Evolution and diversity in human herpes simplex virus genomes
ML Szpara, D Gatherer, A Ochoa, B Greenbaum, A Dolan, RJ Bowden, LW Enquist, M Legendre, AJ Davison – Journal of Virology, 2013 (online). 2014 Jan (print); 88(2): 1209-27. [DOI: https://doi.org/10.1128/JVI.01987-13] [PDF]

• Data website:  http://szparalab.psu.edu/hsv-diversity/

2011

A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses
ML Szpara, YR Tafuri, L Parsons, SR Shamim, KJ Verstrepen, M Legendre, LW Enquist – PLoS Pathogens, 2011. 7(10): e1002282. [DOI: https://doi.org/10.1371/journal.ppat.1002282] [PDF]

• Data website: http://viro-genome.princeton.edu/PRV
• How-to documentation: http://genomics-pubs.princeton.edu/prv/

Herpes simplex virus 1 pUL34 plays a critical role in cell-to-cell spread of virus in addition to its role in virus replication
AC Haugo, ML Szpara, L Parsons, LW Enquist, RJ Roller – Journal of Virology (Recommended, Faculty of 1000), 2011. Jul; 85(14): 7203-15. [DOI: https://doi.org/10.1128/JVI.00262-11] [PDF]

Preparation of viral DNA from nucleocapsids
ML Szpara, YR Tafuri, LW Enquist – Journal of Visualized Experiments (JoVE video protocols), 2011. e3151. [DOI: https://doi.org/10.3791/3151] [PDF] [Movie]

2010

A common neuronal response to alphaherpesvirus infection
ML Szpara, O Kobiler, LW Enquist – Journal of Neuroimmune Pharmacology, 2010. Sep; 5(3): 418-27. [DOI: https://doi.org/10.1007/s11481-010-9212-0] [PDF]

Sequence variability in clinical and laboratory isolates of herpes simplex virus 1 reveals new mutations
ML Szpara, L Parsons, LW Enquist – Journal of Virology, 2010. May; 84(10): 5303-13. [DOI: https://doi.org/10.1128/JVI.00312-10  ] [PDF] [Data website]

• Data website: http://viro-genome.princeton.edu/HSV

2009

Fluorescence-based monitoring of in vivo neural activity using a circuit-tracing pseudorabies virus
AE Granstedt, ML Szpara, B Kuhn, SS Wang, LW Enquist – PLoS One, 2009. Sep 9; 4 (9): e6923. [DOI: https://doi.org/10.1371/journal.pone.0006923] [PDF]

Compartmented neuron cultures for directional infection by alpha herpesviruses
D Curanović*, TH Ch’ng*, M Szpara*, L Enquist (*equal author contributions) – Chapter 26: Current Protocols in Cell Biology, 2009. Jun: Unit 26.4.  [DOI: https://doi.org/10.1002/0471143030.cb2604s43] [PDF]

2007

Analysis of gene expression during neurite outgrowth and regeneration
ML Szpara, K Vranizan, YC Tai, CS Goodman, TP Speed, J Ngai – BMC Neuroscience, 2007. 8 (1): 100. [DOI: https://doi.org/10.1186/1471-2202-8-100] [PDF]

2004

Regulation of pontine neurite morphology by target-derived signals
SK Hansen, ML Szpara, TA Serafini – Molecular Brain Research, 2004. 124 (2): 165-177. [DOI: https://doi.org/10.1016/j.molbrainres.2004.02.017] [PDF]