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Article ; Online: Molecular and Serologic Investigation of the 2021 COVID-19 Case Surge Among Vaccine Recipients in Mongolia.

Dashdorj, Naranjargal J / Dashdorj, Naranbaatar D / Mishra, Mitali / Danzig, Lisa / Briese, Thomas / Lipkin, W Ian / Mishra, Nischay

JAMA network open

2022 Volume 5, Issue 2, Page(s) e2148415

MeSH term(s)	COVID-19/blood ; COVID-19/epidemiology ; COVID-19 Vaccines/blood ; Communicable Disease Control/organization & administration ; Cross-Sectional Studies ; Female ; Humans ; Male ; Mongolia/epidemiology ; Retrospective Studies ; SARS-CoV-2 ; Vaccination Coverage/statistics & numerical data
Chemical Substances	COVID-19 Vaccines
Language	English
Publishing date	2022-02-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2574-3805
ISSN (online)	2574-3805
DOI	10.1001/jamanetworkopen.2021.48415
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Article ; Online: High-throughput Sequencing to Identify Bacteremia in Children with Cancer.

McLaren, Son H / Mishra, Nischay / Hijiya, Nobuko / Ng, James / Guo, Cheng / Whittier, Susan / Mariani, Erica / Glaser, Laura / Frantzis, Irene / Vindas, Marc T / Leu, Cheng-Shiun / Dayan, Peter S

The Pediatric infectious disease journal

2023 Volume 42, Issue 8, Page(s) 695–697

Abstract: Current methods to diagnose bacteremia are limited. In this pilot study of children with cancer presenting with fever, we determined the concordance between a novel high-throughput sequencing platform called BacCapSeq and blood culture. High-throughput ... ...

Abstract	Current methods to diagnose bacteremia are limited. In this pilot study of children with cancer presenting with fever, we determined the concordance between a novel high-throughput sequencing platform called BacCapSeq and blood culture. High-throughput sequencing had modest concordance with blood culture. Discordant organisms included those with both unlikely or potential clinical relevance.
MeSH term(s)	Child ; Humans ; Infant ; Pilot Projects ; Bacteremia/diagnosis ; Neoplasms/complications ; High-Throughput Nucleotide Sequencing
Language	English
Publishing date	2023-04-27
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	392481-6
ISSN	1532-0987 ; 0891-3668
ISSN (online)	1532-0987
ISSN	0891-3668
DOI	10.1097/INF.0000000000003948
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Article ; Online: Zika Virus Peptide ELISA (ZIKV-NS2B-Concat ELISA) for Detection of IgG Antibodies to Zika Virus Infection.

Mishra, Nischay / Thakkar, Riddhi / Ng, James / Lipkin, W Ian

Methods in molecular biology (Clifton, N.J.)

2020 Volume 2142, Page(s) 113–122

Abstract: Maternal Zika virus (ZIKV) infection during pregnancy can have profound teratogenic effects including microcephaly and intracranial calcification. In adults, infection may cause acute inflammatory polyneuropathy. These complications appear after ... ...

Abstract	Maternal Zika virus (ZIKV) infection during pregnancy can have profound teratogenic effects including microcephaly and intracranial calcification. In adults, infection may cause acute inflammatory polyneuropathy. These complications appear after resolution of viremia. Thus, molecular assays of blood are typically insufficient to make the link between ZIKV infection and disease. An alternative approach to testing for ZIKV exposure is serology. However, specific serological implication of ZIKV can be confounded by cross-reactivity with closely related flaviviruses. We used high-density peptide arrays that tile the proteomes of a selection of arboviruses to search for ZIKV-specific linear epitopes that would enable the development of accurate serological tests. We identified a 20-amino-acid-long diagnostic peptide sequence in the NS2B protein of ZIKV that was immunoreactive with sera from patients with a confirmed history of infection with ZIKV but not other flaviviruses. We then established a ZIKV peptide ELISA (ZIKV-NS2B-concat ELISA) that enables sensitive and specific diagnosis of exposure to ZIKV.
MeSH term(s)	Adult ; Antibodies, Viral/analysis ; Antibodies, Viral/blood ; Antibodies, Viral/isolation & purification ; Antibody Specificity ; Biotinylation ; Enzyme-Linked Immunosorbent Assay/methods ; Epitopes/chemistry ; Epitopes/immunology ; Female ; Humans ; Immunoglobulin G/blood ; Immunoglobulin G/isolation & purification ; Peptide Fragments/chemistry ; Peptide Fragments/immunology ; Pregnancy ; Pregnancy Complications, Infectious/blood ; Pregnancy Complications, Infectious/diagnosis ; Serologic Tests/methods ; Viral Nonstructural Proteins/chemistry ; Viral Nonstructural Proteins/immunology ; Zika Virus/immunology ; Zika Virus Infection/blood ; Zika Virus Infection/diagnosis ; Zika Virus Infection/virology
Chemical Substances	Antibodies, Viral ; Epitopes ; Immunoglobulin G ; Peptide Fragments ; Viral Nonstructural Proteins
Language	English
Publishing date	2020-05-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-0581-3_10
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Article ; Online: A potential role for SARS-CoV-2 small viral RNAs in targeting host microRNAs and modulating gene expression.

Neeb, Zachary T / Ritter, Alexander J / Chauhan, Lokendra V / Katzman, Sol / Lipkin, W Ian / Mishra, Nischay / Sanford, Jeremy R

Scientific reports

2022 Volume 12, Issue 1, Page(s) 21694

Abstract: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease (COVID-19) in humans, with symptoms ranging from mild to severe, including fatality. The molecular mechanisms surrounding the effects of viral infection on the host ... ...

Abstract	Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes coronavirus disease (COVID-19) in humans, with symptoms ranging from mild to severe, including fatality. The molecular mechanisms surrounding the effects of viral infection on the host RNA machinery remain poorly characterized. We used a comparative transcriptomics approach to investigate the effects of SARS-CoV-2 infection on the host mRNA and sRNA expression machinery in a human lung epithelial cell line (Calu-3) and an African green monkey kidney cell line (Vero-E6). Upon infection, we observed global changes in host gene expression and differential expression of dozens of host miRNAs, many with known links to viral infection and immune response. Additionally, we discovered an expanded landscape of more than a hundred SARS-CoV-2-derived small viral RNAs (svRNAs) predicted to interact with differentially expressed host mRNAs and miRNAs. svRNAs are derived from distinct regions of the viral genome and sequence signatures suggest they are produced by a non-canonical biogenesis pathway. 52 of the 67 svRNAs identified in Calu-3 cells are predicted to interact with differentially expressed miRNAs, with many svRNAs having multiple targets. Accordingly, we speculate that these svRNAs may play a role in SARS-CoV-2 propagation by modulating post-transcriptional gene regulation, and that methods for antagonizing them may have therapeutic value.
MeSH term(s)	Animals ; Humans ; Chlorocebus aethiops ; MicroRNAs/genetics ; MicroRNAs/metabolism ; SARS-CoV-2/genetics ; SARS-CoV-2/metabolism ; COVID-19/genetics ; Lung/metabolism ; RNA, Viral/genetics ; RNA, Viral/metabolism ; Gene Expression
Chemical Substances	MicroRNAs ; RNA, Viral
Language	English
Publishing date	2022-12-15
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-022-26135-9
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Article ; Online: Cross-Reactive Antibody Responses against Nonpoliovirus Enteroviruses.

Rosenfeld, Amy B / Shen, Edmund Qian Long / Melendez, Michaela / Mishra, Nischay / Lipkin, W Ian / Racaniello, Vincent R

mBio

2022 Volume 13, Issue 1, Page(s) e0366021

Abstract: Enteroviruses are among the most common human viral pathogens. Infection with members of a subgroup of viruses within this genus, the nonpoliovirus enteroviruses (NPEVs), can result in a broad spectrum of serious illnesses, including acute flaccid ... ...

Abstract	Enteroviruses are among the most common human viral pathogens. Infection with members of a subgroup of viruses within this genus, the nonpoliovirus enteroviruses (NPEVs), can result in a broad spectrum of serious illnesses, including acute flaccid myelitis (AFM), a polio-like childhood paralysis; neonatal sepsis; aseptic meningitis; myocarditis; and hand-foot-mouth disease. Despite the diverse primary sites of virus infection, including the respiratory and alimentary tracts, and an array of diseases associated with these infections, there is significant genetic and antigenic similarity among NPEVs. This conservation results in the induction of cross-reactive antibodies that are either able to bind and neutralize or bind but not neutralize multiple NPEVs. Using plaque reduction and enzyme-linked immunosorbent assay (ELISA)-based binding assays, we define the antigenic relationship among poliovirus and NPEVs, including multiple isolates of EV-D68, EV-A71, EV-D70, EV-94, EV-111, Coxsackievirus A24v, and rhinovirus. The results reveal extensive cross-reactivity among EVs that cannot be predicted from phylogenetic analysis. Determining the immunologic relationship among EVs is critical to understanding the humoral response elicited during homologous and heterologous virus infections.
MeSH term(s)	Humans ; Infant, Newborn ; Animals ; Child ; Phylogeny ; Antibody Formation ; Enterovirus/genetics ; Enterovirus Infections ; Enterovirus A, Human ; Antigens, Viral/genetics ; Poliomyelitis ; Antibodies/metabolism
Chemical Substances	Antigens, Viral ; Antibodies
Language	English
Publishing date	2022-01-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2557172-2
ISSN	2150-7511 ; 2161-2129
ISSN (online)	2150-7511
ISSN	2161-2129
DOI	10.1128/mbio.03660-21
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Article ; Online: Compassionate-use pocapavir and immunoglobulin therapy for treatment of rituximab-associated enterovirus meningoencephalitis.

Epstein, Samantha / Thakkar, Riddhi / Fong, Kathryn T / Ng, James / Bearden, David R / Mishra, Nischay / Thakur, Kiran T / Riley, Claire S

Journal of neurovirology

2022 Volume 28, Issue 2, Page(s) 329–334

Abstract: A 71-year-old woman previously on rituximab treatment for rheumatoid arthritis presented with 2 years of progressive neurologic symptoms. She was found to have persistent hypogammaglobulinemia and B cell depletion despite rituximab discontinuation a year ...

Abstract	A 71-year-old woman previously on rituximab treatment for rheumatoid arthritis presented with 2 years of progressive neurologic symptoms. She was found to have persistent hypogammaglobulinemia and B cell depletion despite rituximab discontinuation a year prior. MRI revealed diffuse meningeal enhancement along the entire neuroaxis. LP showed a CSF lymphocytic pleocytosis, elevated protein, and presence of enterovirus by PCR. The patient was hospitalized several times for progressive clinical and radiologic decline, though she had transient improvements following treatment with immunoglobulin therapy. Her CSF remained positive for enterovirus PCR for at least 12 months. Though two brain biopsies were non-diagnostic, pan-Enterovirus was ultimately identified using a high-throughput next-generation sequencing technique. She was treated with compassionate-use pocapavir with clinical stabilization at 4-month follow-up; however, she expired 8 months later from a bacterial pneumonia.
MeSH term(s)	Aged ; Enterovirus/genetics ; Enterovirus Infections/drug therapy ; Female ; Humans ; Immunization, Passive ; Meningoencephalitis ; Phenyl Ethers ; Rituximab/therapeutic use
Chemical Substances	Phenyl Ethers ; Rituximab (4F4X42SYQ6) ; pocapavir (4ILA3VOV97)
Language	English
Publishing date	2022-01-03
Publishing country	United States
Document type	Case Reports ; Journal Article
ZDB-ID	1283265-0
ISSN	1538-2443 ; 1355-0284
ISSN (online)	1538-2443
ISSN	1355-0284
DOI	10.1007/s13365-021-01038-z
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Article: Application of VirCapSeq-VERT and BacCapSeq In the Diagnosis of Presumed and Definitive Neuroinfectious Diseases.

Boruah, Abhilasha P / Kroopnick, Adam / Thakkar, Riddhi / Wapniarski, Annie E / Kim, Carla / Dugue, Rachelle / Harrigan, Eileen / Lipkin, W Ian / Mishra, Nischay / Thakur, Kiran T

Research square

2023

Abstract: Background: Unbiased high-throughput sequencing (HTS) has enabled new insights into the diversity of agents implicated in central nervous system (CNS) infections. The addition of positive selection capture methods to HTS has enhanced the sensitivity ... ...

Abstract	Background: Unbiased high-throughput sequencing (HTS) has enabled new insights into the diversity of agents implicated in central nervous system (CNS) infections. The addition of positive selection capture methods to HTS has enhanced the sensitivity while reducing sequencing costs and complexity of bioinformatic analysis. Here we report the use of virus capture based sequencing for vertebrate viruses (VirCapSeq-VERT) and bacterial capture sequencing (BacCapSeq) in investigating CNS infections. Design/methods: Thirty-four samples were categorized: (1) Patients with definitive CNS infection by routine testing; (2) Patients meeting clinically Brighton Criteria (BC) for meningoencephalitis (3) Patients with presumptive infectious etiology highest on the differential. RNA extracts from cerebrospinal fluid (CSF) were used for VirCapSeq-VERT and DNA extracts were used for BacCapSeq analysis. Results: Among 8 samples from known CNS infections in group 1, VirCapSeq and BacCapSeq confirmed 3 expected diagnoses (42.8%), were negative in 2 (25%), yielded an alternative result in 1 (11.1%), and did not detect 2 expected negative pathogens. The confirmed cases identified HHV-6, HSV-2, and VZV while the negative samples included JCV and HSV-2. In groups 2 and 3,11/26 samples (42%) were positive for at least one pathogen, however 27% of the total samples (7/26) were positive for commensal organisms. No microbial nucleic acids were detected in negative control samples. Conclusions: HTS showed limited promise for pathogen identification in presumed CNS infectious diseases in our small sample. Before conducting larger-scale prospective studies to assess clinical value of this novel technique, clinicians should understand benefits and limitations of using this modality.
Language	English
Publishing date	2023-07-11
Publishing country	United States
Document type	Preprint
DOI	10.21203/rs.3.rs-2675665/v1
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Article ; Online: Application of VirCapSeq-VERT and BacCapSeq in the diagnosis of presumed and definitive neuroinfectious diseases.

Boruah, Abhilasha P / Kroopnick, Adam / Thakkar, Riddhi / Wapniarski, Anne E / Kim, Carla / Dugue, Rachelle / Harrigan, Eileen / Lipkin, W Ian / Mishra, Nischay / Thakur, Kiran T

Journal of neurovirology

2023 Volume 29, Issue 6, Page(s) 678–691

Abstract: Unbiased high-throughput sequencing (HTS) has enabled new insights into the diversity of agents implicated in central nervous system (CNS) infections. The addition of positive selection capture methods to HTS has enhanced the sensitivity while reducing ... ...

Abstract	Unbiased high-throughput sequencing (HTS) has enabled new insights into the diversity of agents implicated in central nervous system (CNS) infections. The addition of positive selection capture methods to HTS has enhanced the sensitivity while reducing sequencing costs and the complexity of bioinformatic analysis. Here we report the use of virus capture-based sequencing for vertebrate viruses (VirCapSeq-VERT) and bacterial capture sequencing (BacCapSeq) in investigating CNS infections. Thirty-four samples were categorized: (1) patients with definitive CNS infection by routine testing; (2) patients meeting clinically the Brighton criteria (BC) for meningoencephalitis; (3) patients with presumptive infectious etiology highest on the differential. RNA extracts from cerebrospinal fluid (CSF) were used for VirCapSeq-VERT, and DNA extracts were used for BacCapSeq analysis. Among 8 samples from known CNS infections in group 1, VirCapSeq and BacCapSeq confirmed 3 expected diagnoses (42.8%), were negative in 2 (25%), yielded an alternative result in 1 (11.1%), and did not detect 2 expected negative pathogens. The confirmed cases identified HHV-6, HSV-2, and VZV while the negative samples included JCV and HSV-2. In groups 2 and 3, 11/26 samples (42%) were positive for at least one pathogen; however, 27% of the total samples (7/26) were positive for commensal organisms. No microbial nucleic acids were detected in negative control samples. HTS showed limited promise for pathogen identification in presumed CNS infectious diseases in our small sample. Before conducting larger-scale prospective studies to assess the clinical value of this novel technique, clinicians should understand the benefits and limitations of using this modality.
MeSH term(s)	Humans ; Prospective Studies ; Viruses ; High-Throughput Nucleotide Sequencing/methods ; Meningoencephalitis ; Herpesvirus 2, Human/genetics
Language	English
Publishing date	2023-10-18
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	1283265-0
ISSN	1538-2443 ; 1355-0284
ISSN (online)	1538-2443
ISSN	1355-0284
DOI	10.1007/s13365-023-01172-w
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Article ; Online: A Short Series of Case Reports of COVID-19 in Immunocompromised Patients.

Mishra, Mitali / Zahra, Aleena / Chauhan, Lokendra V / Thakkar, Riddhi / Ng, James / Joshi, Shreyas / Spitzer, Eric D / Marcos, Luis A / Lipkin, W Ian / Mishra, Nischay

Viruses

2022 Volume 14, Issue 5

Abstract: Immunocompromised individuals are at risk of prolonged SARS-CoV-2 infection due to weaker immunity, co-morbidities, and lowered vaccine effectiveness, which may evolve highly mutated variants of SARS-CoV-2. Nonetheless, limited data are available on the ... ...

Abstract	Immunocompromised individuals are at risk of prolonged SARS-CoV-2 infection due to weaker immunity, co-morbidities, and lowered vaccine effectiveness, which may evolve highly mutated variants of SARS-CoV-2. Nonetheless, limited data are available on the immune responses elicited by SARS-CoV-2 infection, reinfections, and vaccinations with emerging variants in immunocompromised patients. We analyzed clinical samples that were opportunistically collected from eight immunocompromised individuals for mutations in SARS-CoV-2 genomes, neutralizing antibody (NAb) titers against different SARS-CoV-2 variants, and the identification of immunoreactive epitopes using a high-throughput coronavirus peptide array. The viral genome analysis revealed two SARS-CoV-2 variants (20A from a deceased patient and an Alpha variant from a recovered patient) with an eight amino-acid (aa) deletion within the N-terminal domain (NTD) of the surface glycoprotein. A higher NAb titer was present against the prototypic USA/WA1/2020 strain in vaccinated immunocompromised patients. NAb titer was absent against the Omicron variant and the cultured virus of the 20A variant with eight aa deletions in non-vaccinated patients. Our data suggest that fatal SARS-CoV-2 infections may occur in immunocompromised individuals even with high titers of NAb post-vaccination. Moreover, persistent SARS-CoV-2 infection may lead to the emergence of newer variants with additional mutations favoring the survival and fitness of the pathogen that include deletions in NAb binding sites in the SARS-CoV-2 surface glycoprotein.
MeSH term(s)	COVID-19 ; Humans ; Immunocompromised Host ; Membrane Glycoproteins ; SARS-CoV-2/genetics ; Viral Vaccines
Chemical Substances	Membrane Glycoproteins ; Viral Vaccines
Language	English
Publishing date	2022-04-29
Publishing country	Switzerland
Document type	Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v14050934
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Article ; Online: Detection of antibodies to Anaplasma phagocytophilum and Babesia microti using linear peptides.

Tagliafierro, Teresa / Joshi, Shreyas / Sameroff, Stephen / Marques, Adriana / Dumler, J Stephen / Mishra, Nischay / Sanchez-Vicente, Santiago / Wormser, Gary P / Marcos, Luis A / Lipkin, W Ian / Tokarz, Rafal

Ticks and tick-borne diseases

2022 Volume 13, Issue 5, Page(s) 101999

Abstract: Anaplasma phagocytophilum and Babesia microti are emerging tick-borne pathogens in the United States. Although active infection is typically diagnosed by direct diagnostic tests, such as blood smear or polymerase chain reaction assay, serologic assays ... ...

Abstract	Anaplasma phagocytophilum and Babesia microti are emerging tick-borne pathogens in the United States. Although active infection is typically diagnosed by direct diagnostic tests, such as blood smear or polymerase chain reaction assay, serologic assays can be helpful to identify past infections, and the use of acute plus convalescent testing can potentially identify recent infections. We employed a peptide array to select sets of linear peptides for serologic diagnosis of infections with A. phagocytophilum and B. microti. Three optimal peptides were selected for each agent based on their performance with clinical specimens. All three A. phagocytophilum peptides were located within the conserved fragments of the MSP2 antigen. Two B. microti peptides were located in the N terminus of the SA-1 antigen; the third was in the BMN 1-17 antigen. We found that these peptides can be a useful tool for detection of antibody reactivity to both of these pathogens.
MeSH term(s)	Anaplasma phagocytophilum ; Antibodies ; Babesia microti ; Babesiosis/diagnosis ; Borrelia burgdorferi ; Humans ; Peptides
Chemical Substances	Antibodies ; Peptides
Language	English
Publishing date	2022-07-01
Publishing country	Netherlands
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
ZDB-ID	2541872-5
ISSN	1877-9603 ; 1877-959X
ISSN (online)	1877-9603
ISSN	1877-959X
DOI	10.1016/j.ttbdis.2022.101999
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