Nischay Mishra, PhD

  • Assistant Professor of Epidemiology (In the Center for Infection and Immunity) at CUMC
Profile Headshot


Dr. Mishra is a virologist and molecular biologist with over 15 years of experience in rapid and broad-spectrum molecular and serological techniques for identifying known/unknown infectious agents, genomic and evolutionary phylogenetic analysis of emerging viruses, genome mutation and changes in virulence and transmissibility of viral agents, association of disease and disease progression with changes in the microbiome and virome. Mishra has devoted his career to finding new ways to detect and reduce the threat of infectious diseases to human health. For his doctoral research at National Institute of Virology, India, he discovered host cytokine polymorphisms and viral mutations in hepatitis E virus-associated with fulminant hepatitis in pregnant women.

Dr. Mishra moved to the Center for Infection and Immunity as a post-doctoral research scientist in 2011 and contributed to the development of three platforms that have revolutionized diagnosis and surveillance of infectious diseases, including VirCapSeq-VERT, BacCapSeq, and the SeroChip. Each of these methods has been highlighted by the NIH director and multiple media outlets and also in development as a certified laboratory test for clinical use. In 2014, he reported the identification and implication of a new polyomavirus as the cause of retinal artery occlusion and myositis in a woman exposed to Superstorm Sandy floodwaters. In other work, he discovered tilapia lake virus, a novel virus that has undermined global food security, and pursued bat and camel sequencing in an effort to understand the origin of the MERS.

In 2017, at the request of NIAID for support of the Zika in Pregnant Women (ZIP) project, he developed a multiplex PCR assay for differential diagnosis of Zika virus, dengue virus, Chikungunya virus, and other arboviruses and received an Emergency Use Authorization (EUA) by the FDA. It is the only EUA for Zika diagnosis awarded to an academic institution and the only EUA ever awarded to Columbia University. In 2019, he was the senior lead on a study that focused finding traces for the origins of Chikungunya in Brazil using VirCapSeq-VERT method. He also piloted the development of the first highly multiplexed serological array.  He has developed the first multiplex diagnostic serologic platforms for arboviral diseases, Acute flaccid myelitis and also contributed in the development of a SeroChip for tick-borne diseases that were cited the NIH Director's blog on June 26, 2018.

Dr. Mishra is also working on a project between the Columbia University-Indian Academy of Medical Sciences investigations of the acute encephalitis syndrome outbreak in Gorakhpur. He is using these high throughput molecular and serological tools for the discovery of infectious agents causing deaths of hundreds of children in northern India last 25 years or more. Mishra is also working with the US CDC to investigate the pathogenesis of acute flaccid myelitis in children in the United States. When tests of cerebrospinal fluid for the presence of infectious agents using VirCapSeq-VERT failed to yield pathogen sequences, he built and implemented a SeroChip that provided unequivocal evidence of enteroviral infection in the central nervous system.


Academic Appointments

  • Assistant Professor of Epidemiology (In the Center for Infection and Immunity) at CUMC

Credentials & Experience

Education & Training

  • MSc, Institute of Biotechnology and Biosciences
  • BSc, University of Lucknow
  • PhD, 2012 National Institute of Virology

Honors & Awards

2016-2017 Calderone Junior Faculty Awards to Study differential serodiagnosis of Flaviviruses infections, which include Zika, dengue, yellow fever, and West Nile virus.


Discovery, Characterization, and diagnosis for known and novel pathogens.

Research Interests

  • Child and Adolescent Health
  • Chronic disease
  • Environmental Health
  • Genetics
  • Infectious diseases

Selected Publications

Mishra N, Ng J, Strom MA, Jain K, Thakkar R, Joshi S, Pereira M, Shah L, Grossman ME, Lee MJ, De Michele S, Silvers DN, Faust PL, Lipkin WI, Gallitano SM.Human Polyomavirus 9-An Emerging Cutaneous and Pulmonary Pathogen in Solid Organ Transplant Recipients. JAMA Dermatol. 2022 Mar 1;158(3):293-298. doi: 10.1001/jamadermatol.2021.5853. PMID: 35138364

Mishra N, Huang X, Joshi S, Guo C, Ng J, Thakkar R, Wu Y, Dong X, Li Q, Pinapati RS, Sullivan E, Caciula A, Tokarz R, Briese T, Lu J, Lipkin WI. Immunoreactive peptide maps of SARS-CoV-2. Nature Commun Biol. 2021 Feb 12;4(1):225. doi: 10.1038/s42003-021-01743-9. PMID: 33580175

Dugue R, Cay-Martínez KC, Thakur KT, Garcia JA, Chauhan LV, Williams SH, Briese T, Jain K, Foca M, McBrian DK, Bain JM, Lipkin WI, Mishra N. Neurologic manifestations in an infant with COVID-19. Neurology. 2020 Jun 16;94(24):1100-1102. doi: 10.1212/WNL.0000000000009653. Epub 2020 Apr 23. PMID: 32327489

Mishra, N., Ng, T. F. F., Marine, R. L., Jain, K., Ng, J., Thakkar, R., Caciula, A., Price, A., Garcia, J. A., Burns, J. C., Thakur, K. T., Hetzler, K. L., Routh, J. A., Konopka-Anstadt, J. L., Nix, W. A., Tokarz, R., Briese, T., Oberste, M. S., Lipkin, W. I, Antibodies to Enteroviruses in Cerebrospinal Fluid of Patients with Acute Flaccid Myelitis, mBio 2019 10: p. e01903-19-e01903-19.

Mishra N, Caciula A, Price A, Thakkar R, Ng J, Chauhan LV, Jain K, Che X, Espinosa DA, Montoya Cruz M, Balmaseda A, Sullivan EH, Patel JJ, Jarman RG, Rakeman JL, Egan CT, Reusken C, Koopmans MPG, Harris E, Tokarz R, Briese T, Lipkin WI. 2018. Diagnosis of Zika Virus Infection by Peptide Array and Enzyme-Linked Immunosorbent Assay. MBio 9.

Mishra N, Ng J, Rakeman JL, Perry MJ, Centurioni DA, Dean AB, Price A, Thakkar R, Angus AG, Williamson P, Delwart E, Carrington C, Sahadeo N, Che X, Briese T, Tokarz R, Lipkin WI. 2019. One-step pentaplex real-time polymerase chain reaction assay for detection of zika, dengue, chikungunya, West nile viruses and a human housekeeping gene. J Clin Virol 120:44-50.

Mishra N, Fagbo SF, Alagaili AN, Nitido A, Williams SH, Ng J, Lee B, Durosinlorun A, Garcia JA, Jain K, Kapoor V, Epstein JH, Briese T, Memish ZA, Olival KJ, Lipkin WI. 2019. A viral metagenomic survey identifies known and novel mammalian viruses in bats from Saudi Arabia. PLoS One 14:e0214227.

Tokarz R, Mishra N, Tagliafierro T, Sameroff S, Caciula A, Chauhan L, Patel J, Sullivan E, Gucwa A, Fallon B, Golightly M, Molins C, Schriefer M, Marques A, Briese T, Lipkin WI. 2018. A multiplex serologic platform for diagnosis of tick-borne diseases. Sci Rep 8:3158.

Briese T, Kapoor A, Mishra N, Jain K, Kumar A, Jabado OJ, Lipkin WI. 2015. Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis. MBio 6:e01491-01415.

Bacharach E, Mishra N, Briese T, Zody MC, Kembou Tsofack JE, Zamostiano R, Berkowitz A, Ng J, Nitido A, Corvelo A, Toussaint NC, Abel Nielsen SC, Hornig M, Del Pozo J, Bloom T, Ferguson H, Eldar A, Lipkin WI. 2016. Characterization of a Novel Orthomyxo-like Virus Causing Mass Die-Offs of Tilapia. MBio 7:e00431-00416.

Global Health Activities

Investigation of pathogens in children suffering from Acute Encephalitis Syndrome in Uttar Pradesh, Northern India