Nischay Mishra, PhD

  • Assistant Professor of Epidemiology (In the Center for Infection and Immunity) at CUMC
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Dr. Mishra is a virologist and molecular biologist with over 20 years of experience at the Center for Infection and Immunity (CII) in emerging infectious diseases, investigation of host and virus determinants of zoonotic virus spillover, high-throughput sequencing and serology, viral metagenomics, pathogen discovery, viral evolution, pandemic response and preparedness, and role of microbial infections in chronic diseases like ME/CFS, Long-Covid, Alzheimer’s disease, MIS-C, and unexplained neurological infections. His work includes two FDA EUA diagnostic devices and ten patents, with other advance molecular and serological diagnostic inventions in the pipeline. Mishra was also pivotal in developing and validating the patented VirCapSeq-VERT and BacCapSeq methods for detecting viruses and bacteria. These technologies provide the foundation for capture sequencing for the CII's Global Alliance for Preventing Pandemics (GAPP).

Mishra discovered Rickettsia and several viruses as the causative agents of unexplained acute encephalitis syndrome (AES) in children in India. He also identified and characterized Tilapia lake virus (TiLV), which declared a threat to global food security by UN's Food and Agricultural Organization, particularly in low and middle-income countries. Additionally, Mishra discovered New Jersey Polyomavirus as the cause of blindness and myositis in a woman exposed to Superstorm Sandy floodwaters, reported the pathogenicity of human polyomavirus 9 in solid organ transplant recipients, and pathogenesis of SARS-CoV-2 in children and immunocompromised patients. Mishra also conducted viral discovery and serology in bats and camels to study origin and evolution of MERS.

Mishra leads serology projects at the CII that focus on the detection of infection footprints in samples when methods for direct detection of microbial nucleic acids and proteins are no longer applicable. Such examples include determining enterovirus D68 in pediatric cases of acute flaccid myelitis who had no viral sequencings in blood or CSF, Zika virus in microcephaly in offspring of women who had no viral sequencing in blood, Abs against microbial agents in the CSF of pediatric cases of acute encephalitis, and contributions to tick-borne disease serodiagnostic development. Mishra and his team have successfully built high density multiplex serological assays to profile distinctive immune responses for henipaviruses, nairoviruses, arboviruses, pox viruses, hemorrhagic-fever viruses, human papillomaviruses, persistent and latent viruses, and human respiratory viruses. By using these assays, we can specifically detect and quantify Abs to each viral protein distinguishably, that is critical to discovering immune markers for accurate diagnosis, differentiate between infection and immunization, spillover, zoonoses, and future therapeutic interventions.

Classes Taught

EPID P8475: Emerging Infectious Diseases (MPH degree program; Epidemiology)

Academic Appointments

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

Credentials & Experience

Education & Training

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

Committees, Societies, Councils

Committee member, MSPH Epidemiology Masters Admission Committee

Member, Pan American Society for Clinical Virology (PASCV)

Member, Emerging Infections Network, Infectious Disease Society of America (IDSA)

Member, Association of Public Health Laboratories (APHL)

Member, American Society of Microbiology (ASM)

Member, American Society of Virology (ASV)

Steering committee member, MSPH Food Related Science (establishing a program focusing on food, nutrition, climate, and public health)

Steering Committee Member, MSPH IFTF Public Health 2035 Initiative

Honors & Awards

2021: Yusuf Hamied Fellowship for Capacity building for SARS-CoV-2 sequencing and Tuberculosis diagnosis in India

2020: Mailman School of Health Innovation Award for Serodiagnosis of Lymphatic Filariasis

2016: Calderone Junior Faculty Award


One Health - The whole world is one family (Vasudhaiva Kutumbakam)

FDA EUA Approvals
Triplex CII-SARS-CoV-2 rRT PCR assay for two regions of the nucleocapsid gene as well as a human housekeeping gene (RNase P). (Used to detect asymptomatic and symptomatic SARS-CoV-2 infections and licensed for use in Santa Clara County (CA), the Los Angeles County Unified School District, the 2020 Democratic National Convention, and the 93rd Annual Academy Awards.)

CII-ArboViroPlex rRT-PCR assay for Zika virus (ZIKV), dengue virus types 1-4 (DENV), Chikungunya virus (CHIKV), West Nile virus (WNV), and a human housekeeping gene (RNase P).

Visit Columbia Technology Ventures or Google Patents for current patent information.

Research Interests

  • Chronic disease
  • CNS infections
  • Diagnostic Microbiology
  • Emergency response and preparedness
  • Global Health
  • Infectious Diseases
  • Mobile health interventions
  • Rapid Clinical Diagnostics
  • Syndromic molecular diagnostics for infectious diseases

Selected Publications

Boruah AP, Kroopnick A, Thakkar R, Wapniarski AE, Kim C, Dugue R, Harrigan E, Lipkin WI, Mishra N, Thakur KT. Application of VirCapSeq-VERT and BacCapSeq in the diagnosis of presumed and definitive neuroinfectious diseases. J Neurovirol. 2023 Dec;29(6):678-691. doi: 10.1007/s13365-023-01172-w. Epub 2023 Oct 18. PMID: 37851324.

Mishra N, Ng J, Strom MA, Jain K, Thakkar R, Joshi S, Pereira M, Shah L, Grossman ME, Lee MJ. 2022. Human polyomavirus 9—an emerging cutaneous and pulmonary pathogen in solid organ transplant recipients. JAMA dermatology 158:293-298.

Mishra N, Huang X, Joshi S, Guo C, Ng J, Thakkar R, Wu Y, Dong X, Li Q, Pinapati RS. 2021. Immunoreactive peptide maps of SARS-CoV-2. Communications Biology 4:225.

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. 2020. Neurologic manifestations in an infant with COVID-19. Neurology 94:1100-1102.

Souza TML, Vieira YR, Delatorre E, Barbosa-Lima G, Luiz RLF, Vizzoni A, Jain K, Miranda MM, Bhuva N, Gogarten JF, Ng J, Thakkar R, Calheiros AS, Monteiro APT, Bozza PT, Bozza FA, Tschoeke DA, Leomil L, Mendonça MCL, Rodrigues CDDS, Torres MC, Filippis AMB, Nogueira RMR, Thompson FL, Lemos C, Durovni B, Cerbino- Neto J, Morel CM, Lipkin WI, Mishra N. 2019. The emergence of the East-Central-South-African genotype of the Chikungunya virus in Brazil and the city of Rio de Janeiro may have occurred years before surveillance detection. Scientific Reports 9:2760.

Mishra N, Ng TFF, Marine RL, Jain K, Ng J, Thakkar R, Caciula A, Price A, Garcia JA, Burns JC. 2019. Antibodies to enteroviruses in cerebrospinal fluid of patients with acute flaccid myelitis. MBio 10:e01903-19.

Mishra N, Ng J, Rakeman JL, Perry MJ, Centurioni DA, Dean AB, Price A, Thakkar R, Angus AG, Williamson P. 2019. One-step pentaplex real-time polymerase chain reaction assay for detection of zika, dengue, chikungunya, West Nile viruses, and a human housekeeping gene. Journal of Clinical Virology 120:44-50.

Mishra N, Fagbo SF, Alagaili AN, Nitido A, Williams SH, Ng J, Lee B, Durosinlorun A, Garcia JA, Jain K. 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. 2018. A multiplex serologic platform for diagnosis of tick-borne diseases. Scientific reports 8:3158.

Mishra N, Caciula A, Price A, Thakkar R, Ng J, Chauhan LV, Jain K, Che X, Espinosa DA, Montoya Cruz M. 2018. Diagnosis of Zika virus infection by peptide array and enzyme-linked immunosorbent assay. MBio 9:e00095-18.

Briese T, Mishra N, Jain K, Zalmout IS, Jabado OJ, Karesh WB, Daszak P, Mohammed OB, Alagaili AN, Lipkin WI. 2014. Middle East respiratory syndrome coronavirus quasispecies that includes homologs of human isolates revealed through whole-genome analysis and virus cultured from dromedary camels in Saudi Arabia. MBio 5:e01146-14.

Global Health Activities

Bangladesh/India: zoonoses of henipaviruses and cross-species spillover

Ecuador/Israel: characterization of a novel orthomyxo-like virus as the causative agent in Tilapia Lake Virus (TiLV), which is implicated in the mass die-off of tilapia in two continents and having significant risk of global food security

India: investigation of pathogens in a pediatric epidemic of Acute Encephalitis Syndrome (AES) identifying rickettsia diseases and a broad range of viral infections

Liberia: efficacy study of ebolavirus vaccination and SARS-CoV-2 surge in 2021

Mongolia: efficacy study of COVID-19 inactivated virus vaccines to assess unexplained case surge in a 90% vaccinated population

Saudi Arabia: conducted viral discovery and serology in bats and camels to identified the origin and evolution of the MERS-CoV outbreak.