Matthew (Matt) Hernandez

All Publications

• RT-PCR/MALDI-TOF Diagnostic Target Performance Reflects Circulating SARS-CoV-2 Variant Diversity in New York City. The Journal of molecular diagnostics : JMD Hernandez, M. M., Banu, R., Gonzalez-Reiche, A. S., Gray, B., Shrestha, P., Cao, L., Chen, F., Shi, H., Hanna, A., Ramírez, J. D., van de Guchte, A., Sebra, R., Gitman, M. R., Nowak, M. D., Cordon-Cardo, C., Schutzbank, T. E., Simon, V., van Bakel, H., Sordillo, E. M., Paniz-Mondolfi, A. E. 2022; 24 (7): 738-749

  Abstract

  As severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to circulate, multiple variants of concern have emerged. New variants pose challenges for diagnostic platforms because sequence diversity can alter primer/probe-binding sites (PBSs), causing false-negative results. The MassARRAY SARS-CoV-2 Panel (Agena Bioscience) uses RT-PCR and mass spectrometry to detect five multiplex targets across N and ORF1ab genes. Herein, we use a data set of 256 SARS-CoV-2-positive specimens collected between April 11, 2021, and August 28, 2021, to evaluate target performance with paired sequencing data. During this time frame, two targets in the N gene (N2 and N3) were subject to the greatest sequence diversity. In specimens with N3 dropout, 69% harbored the Alpha-specific A28095U polymorphism that introduces a 3'-mismatch to the N3 forward PBS and increases risk of target dropout relative to specimens with 28095A (relative risk, 20.02; 95% CI, 11.36 to 35.72; P < 0.0001). Furthermore, among specimens with N2 dropout, 90% harbored the Delta-specific G28916U polymorphism that creates a 3'-mismatch to the N2 probe PBS and increases target dropout risk (relative risk, 11.92; 95% CI, 8.17 to 14.06; P < 0.0001). These findings highlight the robust capability of MassARRAY SARS-CoV-2 Panel target results to reveal circulating virus diversity, and they underscore the power of multitarget design to capture variants of concern.

  View details for DOI 10.1016/j.jmoldx.2022.04.003

  View details for PubMedID 35525388

  View details for PubMedCentralID PMC9067105

• Molecular evidence of SARS-CoV-2 in New York before the first pandemic wave. Nature communications Hernandez, M. M., Gonzalez-Reiche, A. S., Alshammary, H., Fabre, S., Khan, Z., van De Guchte, A., Obla, A., Ellis, E., Sullivan, M. J., Tan, J., Alburquerque, B., Soto, J., Wang, C. Y., Sridhar, S. H., Wang, Y. C., Smith, M., Sebra, R., Paniz-Mondolfi, A. E., Gitman, M. R., Nowak, M. D., Cordon-Cardo, C., Luksza, M., Krammer, F., van Bakel, H., Simon, V., Sordillo, E. M. 2021; 12 (1): 3463

  Abstract

  Numerous reports document the spread of SARS-CoV-2, but there is limited information on its introduction before the identification of a local case. This may lead to incorrect assumptions when modeling viral origins and transmission. Here, we utilize a sample pooling strategy to screen for previously undetected SARS-CoV-2 in de-identified, respiratory pathogen-negative nasopharyngeal specimens from 3,040 patients across the Mount Sinai Health System in New York. The patients had been previously evaluated for respiratory symptoms or influenza-like illness during the first 10 weeks of 2020. We identify SARS-CoV-2 RNA from specimens collected as early as 25 January 2020, and complete SARS-CoV-2 genome sequences from multiple pools of samples collected between late February and early March, documenting an increase prior to the later surge. Our results provide evidence of sporadic SARS-CoV-2 infections a full month before both the first officially documented case and emergence of New York as a COVID-19 epicenter in March 2020.

  View details for DOI 10.1038/s41467-021-23688-7

  View details for PubMedID 34103497

  View details for PubMedCentralID PMC8187428

• Introductions and early spread of SARS-CoV-2 in the New York City area. Science (New York, N.Y.) Gonzalez-Reiche, A. S., Hernandez, M. M., Sullivan, M. J., Ciferri, B., Alshammary, H., Obla, A., Fabre, S., Kleiner, G., Polanco, J., Khan, Z., Alburquerque, B., van de Guchte, A., Dutta, J., Francoeur, N., Melo, B. S., Oussenko, I., Deikus, G., Soto, J., Sridhar, S. H., Wang, Y. C., Twyman, K., Kasarskis, A., Altman, D. R., Smith, M., Sebra, R., Aberg, J., Krammer, F., García-Sastre, A., Luksza, M., Patel, G., Paniz-Mondolfi, A., Gitman, M., Sordillo, E. M., Simon, V., van Bakel, H. 2020; 369 (6501): 297-301

  Abstract

  New York City (NYC) has emerged as one of the epicenters of the current severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. To identify the early transmission events underlying the rapid spread of the virus in the NYC metropolitan area, we sequenced the virus that causes coronavirus disease 2019 (COVID-19) in patients seeking care at the Mount Sinai Health System. Phylogenetic analysis of 84 distinct SARS-CoV-2 genomes indicates multiple, independent, but isolated introductions mainly from Europe and other parts of the United States. Moreover, we found evidence for community transmission of SARS-CoV-2 as suggested by clusters of related viruses found in patients living in different neighborhoods of the city.

  View details for DOI 10.1126/science.abc1917

  View details for PubMedID 32471856

  View details for PubMedCentralID PMC7259823

• Impact of Suboptimal APOBEC3G Neutralization on the Emergence of HIV Drug Resistance in Humanized Mice. Journal of virology Hernandez, M. M., Fahrny, A., Jayaprakash, A., Gers-Huber, G., Dillon-White, M., Audigé, A., Mulder, L. C., Sachidanandam, R., Speck, R. F., Simon, V. 2020; 94 (5)

  Abstract

  HIV diversification facilitates immune escape and complicates antiretroviral therapy. In this study, we take advantage of a humanized-mouse model to probe the contribution of APOBEC3 mutagenesis to viral evolution. Humanized mice were infected with isogenic HIV molecular clones (HIV-WT, HIV-45G, and HIV-ΔSLQ) that differ in their abilities to counteract APOBEC3G (A3G). Infected mice remained naive or were treated with the reverse transcriptase (RT) inhibitor lamivudine (3TC). Viremia, emergence of drug-resistant variants, and quasispecies diversification in the plasma compartment were determined throughout infection. While both HIV-WT and HIV-45G achieved robust infection, over time, HIV-45G replication was significantly reduced compared to that of HIV-WT in the absence of 3TC treatment. In contrast, treatment responses differed significantly between HIV-45G- and HIV-WT-infected mice. Antiretroviral treatment failed in 91% of HIV-45G-infected mice, while only 36% of HIV-WT-infected mice displayed a similar negative outcome. Emergence of 3TC-resistant variants and nucleotide diversity were determined by analyzing 155,462 single HIV reverse transcriptase gene (RT) and 6,985 vif sequences from 33 mice. Prior to treatment, variants with genotypic 3TC resistance (RT-M184I/V) were detected at low levels in over a third of all the animals. Upon treatment, the composition of the plasma quasispecies rapidly changed, leading to a majority of circulating viral variants encoding RT-184I. Interestingly, increased viral diversity prior to treatment initiation correlated with higher plasma viremia in HIV-45G-infected animals, but not in HIV-WT-infected animals. Taken together, HIV variants with suboptimal anti-A3G activity were attenuated in the absence of selection but displayed a fitness advantage in the presence of antiretroviral treatment.IMPORTANCE Both viral (e.g., RT) and host (e.g., A3G) factors can contribute to HIV sequence diversity. This study shows that suboptimal anti-A3G activity shapes viral fitness and drives viral evolution in the plasma compartment in humanized mice.

  View details for DOI 10.1128/JVI.01543-19

  View details for PubMedID 31801862

  View details for PubMedCentralID PMC7022346

• Phylogenetic landscape of Monkeypox Virus (MPV) during the early outbreak in New York City, 2022. Emerging microbes & infections Patiño, L. H., Guerra, S., Muñoz, M., Luna, N., Farrugia, K., van de Guchte, A., Khalil, Z., Gonzalez-Reiche, A. S., Hernandez, M. M., Banu, R., Shrestha, P., Liggayu, B., Firpo Betancourt, A., Reich, D., Cordon-Cardo, C., Albrecht, R., Pearl, R., Simon, V., Rooker, A., Sordillo, E. M., van Bakel, H., García-Sastre, A., Bogunovic, D., Palacios, G., Paniz Mondolfi, A., Ramírez, J. D. 2023; 12 (1): e2192830

  Abstract

  Monkeypox (MPOX) is a zoonotic disease endemic to regions of Central/Western Africa. The geographic endemicity of MPV has expanded, broadening the human-monkeypox virus interface and its potential for spillover. Since May 2022, a large multi-country MPV outbreak with no proven links to endemic countries has originated in Europe and has rapidly expanded around the globe, setting off genomic surveillance efforts. Here, we conducted a genomic analysis of 23 MPV-infected patients from New York City during the early outbreak, assessing the phylogenetic relationship of these strains against publicly available MPV genomes. Additionally, we compared the genomic sequences of clinical isolates versus culture-passaged samples from a subset of samples. Phylogenetic analysis revealed that MPV genomes included in this study cluster within the B.1 lineage (Clade IIb), with some of the samples displaying further differentiation into five different sub-lineages of B.1. Mutational analysis revealed 55 non-synonymous polymorphisms throughout the genome, with some of these mutations located in critical regions required for viral multiplication, structural and assembly functions, as well as the target region for antiviral treatment. In addition, we identified a large majority of polymorphisms associated with GA > AA and TC > TT nucleotide replacements, suggesting the action of human APOBEC3 enzyme. A comparison between clinical isolates and cell culture-passaged samples failed to reveal any difference. Our results provide a first glance at the mutational landscape of early MPV-2022 (B.1) circulating strains in NYC.

  View details for DOI 10.1080/22221751.2023.2192830

  View details for PubMedID 36927408

  View details for PubMedCentralID PMC10114986

• Multidisciplinary management of a pregnancy complicated by Glanzmann thrombasthenia: A case report. Transfusion Hernandez, M. M., Buckley, A., Mills, A., Meislin, R., Cromwell, C., Bianco, A., Strong, N., Arinsburg, S. 2023; 63 (12): 2384-2391

  Abstract

  Glanzmann thrombasthenia (GT) is a rare, autosomal recessive disorder of platelet glycoprotein IIb-IIIa receptors. Pregnant patients with GT are at increased risk of maternal and fetal bleeding. There is a paucity of literature on the peripartum management of patients.We present the antepartum through the postpartum course of a patient with GT who was managed by a multidisciplinary approach that included communication across maternal-fetal medicine, hematology, transfusion medicine, and anesthesiology services. In addition to routine prepartum obstetric imaging and hematologic laboratory studies, we proactively monitored the patient for anti-platelet antibodies every 4-6 weeks to gauge the risk for neonatal alloimmune thrombocytopenia. Furthermore, we prioritized uterotonics, tranexamic acid, and transfusion of HLA-matched platelets to manage bleeding for mother and fetus intrapartum through the postpartum periods.To date, there are limited guidelines for managing bleeding or preventing alloimmunization during pregnancy in patients with GT. Here, we present a complex case with aggressive management of bleeding prophylactically for the mother while serially monitoring both mother and fetus for peripartum bleeding risks and events. Moreover, future studies warrant continued evaluation of these approaches to mitigate increased bleeding risks in subsequent pregnancies.

  View details for DOI 10.1111/trf.17594

  View details for PubMedID 37952246

• Genomic and ultrastructural analysis of monkeypox virus in skin lesions and in human/animal infected cells reveals further morphofunctional insights into viral pathogenicity. Journal of medical virology Paniz-Mondolfi, A., Reidy, J., Pagani, N., Lednicky, J. A., McGrail, J. P., Kasminskaya, Y., Patino, L. H., Garcia-Sastre, A., Palacios, G., Gonzalez-Reiche, A. S., van Bakel, H., Firpo Betancourt, A., Hernandez, M. M., Cordon-Cardo, C., Simon, V., Sordillo, E. M., Ramírez, J. D., Guerra, S. 2023; 95 (6): e28878

  Abstract

  Monkeypox (MPOX) is a zoonotic disease that affects humans and other primates, resulting in a smallpox-like illness. It is caused by monkeypox virus (MPXV), which belongs to the Poxviridae family. Clinically manifested by a range of cutaneous and systemic findings, as well as variable disease severity phenotypes based on the genetic makeup of the virus, the cutaneous niche and respiratory mucosa are the epicenters of MPXV pathogenicity. Herein, we describe the ultrastructural features of MPXV infection in both human cultured cells and cutaneous clinical specimens collected during the 2022-2023 MPOX outbreak in New York City that were revealed through electron microscopy. We observed typical enveloped virions with brick-shaped morphologies that contained surface protrusions, consistent with the classic ultrastructural features of MPXV. In addition, we describe morpho-functional evidence that point to roles of distinct cellular organelles in viral assembly during clinical MPXV infection. Interestingly, in skin lesions, we found abundant melanosomes near viral assembly sites, particularly in the vicinity of mature virions, which provides further insight into virus-host interactions at the subcellular level that contribute to MPXV pathogenesis. These findings not only highlight the importance of electron microscopic studies for further investigation of this emerging pathogen but also in characterizing MPXV pathogenesis during human infection.

  View details for DOI 10.1002/jmv.28878

  View details for PubMedID 37322614

• Evaluation and validation of an RT-PCR assay for specific detection of monkeypox virus (MPXV). Journal of medical virology Paniz-Mondolfi, A., Guerra, S., Muñoz, M., Luna, N., Hernandez, M. M., Patino, L. H., Reidy, J., Banu, R., Shrestha, P., Liggayu, B., Umeaku, A., Chen, F., Cao, L., Patel, A., Hanna, A., Li, S., Look, A., Pagani, N., Albrecht, R., Pearl, R., Garcia-Sastre, A., Bogunovic, D., Palacios, G., Bonnier, L., Cera, F., Lopez, H., Calderon, Y., Eiting, E., Mullen, K., Shin, S. J., Lugo, L. A., Urbina, A. E., Starks, C., Koo, T., Uychiat, P., Look, A., van Bakel, H., Gonzalez-Reiche, A., Betancourt, A. F., Reich, D., Cordon-Cardo, C., Simon, V., Sordillo, E. M., Ramírez, J. D. 2023; 95 (1): e28247

  Abstract

  Monkeypox virus (MPXV) is a zoonotic orthopoxvirus within the Poxviridae family. MPXV is endemic to Central and West Africa. However, the world is currently witnessing an international outbreak with no clear epidemiological links to travel or animal exposure and with ever-increasing numbers of reported cases worldwide. Here, we evaluated and validated a new, sensitive, and specific real-time PCR-assay for MPXV diagnosis in humans and compare the performance of this novel assay against a Food & Drug Administration-cleared pan-Orthopox RT-PCR assay. We determined specificity, sensitivity, and analytic performance of the PKamp™ Monkeypox Virus RT-PCR assay targeting the viral F3L-gene. In addition, we further evaluated MPXV-PCR-positive specimens by viral culture, electron microscopy, and viral inactivation assays. The limit of detection was established at 7.2 genome copies/reaction, and MPXV was successfully identified in 20 clinical specimens with 100% correlation against the reference method with 100% sensitivity and specificity. Our results demonstrated the validity of this rapid, robust, and reliable RT-PCR assay for specific and accurate diagnosis of MPXV infection in human specimens collected both as dry swabs and in viral transport media. This assay has been approved by NYS Department of Health for clinical use.

  View details for DOI 10.1002/jmv.28247

  View details for PubMedID 36271493

• A Robust, Highly Multiplexed Mass Spectrometry Assay to Identify SARS-CoV-2 Variants. Microbiology spectrum Hernandez, M. M., Banu, R., Shrestha, P., Gonzalez-Reiche, A. S., van de Guchte, A., Farrugia, K., Sebra, R., Gitman, M. R., Nowak, M. D., Cordon-Cardo, C., Simon, V., van Bakel, H., Sordillo, E. M., Luna, N., Ramirez, A., Castañeda, S. A., Patiño, L. H., Ballesteros, N., Muñoz, M., Ramírez, J. D., Paniz-Mondolfi, A. E. 2022; 10 (5): e0173622

  Abstract

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole-genome sequencing (WGS) is the "gold standard" for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA and Bogotá, Colombia (September 2, 2020 to March 2, 2022). We demonstrated almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls (κ ≥ 0.856) and 25 of 30 targets (κ ≥ 0.820) tested on the panel. The assay had a high diagnostic sensitivity (≥93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, and Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants (≥96.15%) and all 30 targets (≥94.34%) tested. Moreover, we highlighted distinct target patterns that could be utilized to identify variants not yet defined on the panel, including the Omicron BA.2 and other sublineages. These findings exemplified the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones. IMPORTANCE The continued circulation of SARS-CoV-2 amid limited surveillance efforts and inconsistent vaccination of populations has resulted in the emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to informing diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlighted the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated from September 2, 2020 to March 2, 2022 among patients seeking care in our health systems. This assay demonstrated variant-specific signatures of nucleotide/amino acid polymorphisms and underscored its utility for the detection of contemporary and emerging SARS-CoV-2 variants of concern.

  View details for DOI 10.1128/spectrum.01736-22

  View details for PubMedID 36069609

  View details for PubMedCentralID PMC9604185

• Hotspots for SARS-CoV-2 Omicron variant spread: Lessons from New York City. Journal of medical virology Ramírez, J. D., Castañeda, S., Ballesteros, N., Muñoz, M., Hernández, M., Banu, R., Shrestha, P., Chen, F., Shi, H., van Bakel, H., Simon, V., Cordon-Cardo, C., Sordillo, E. M., Paniz-Mondolfi, A. E. 2022; 94 (7): 2911-2914

  Abstract

  The coronavirus disease-2019 (COVID-19) pandemic is still challenging public health systems worldwide, particularly with the emergence of novel SARS-CoV-2 variants with mutations that increase their transmissibility and immune escape. This is the case of the variant of concern Omicron that rapidly spread globally. Here, using epidemiological and genomic data we compared the situations in South Africa as the epicenter of emergence, United Kingdom, and with particular interest New York City. This rapid global dispersal from the place of first report reemphasizes the high transmissibility of Omicron, which needed only two weeks to become dominant in the United Kingdom and New York City. Our analyses suggest that as SARS-CoV-2 continues to evolve, global authorities must prioritize equity in vaccine access and continued genomic surveillance. Future studies are still needed to fully unveil the biological properties of Omicron, but what is certain is that vaccination, large-scale testing, and infection prevention efforts are the greatest arsenal against the COVID-19 pandemic.

  View details for DOI 10.1002/jmv.27691

  View details for PubMedID 35243662

  View details for PubMedCentralID PMC9088473

• Food for thought: Eating before saliva collection and interference with SARS-CoV-2 detection. Journal of medical virology Hernandez, M. M., Riollano-Cruz, M., Boyle, M. C., Banu, R., Shrestha, P., Gray, B., Cao, L., Chen, F., Shi, H., Paniz-Perez, D. E., Paniz-Perez, P. A., Rishi, A. L., Dubinsky, J., Dubinsky, D., Dubinsky, O., Baine, S., Baine, L., Arinsburg, S., Baine, I., Ramirez, J. D., Cordon-Cardo, C., Sordillo, E. M., Paniz-Mondolfi, A. E. 2022; 94 (6): 2471-2478

  Abstract

  Saliva is a promising specimen for the detection of viruses that cause upper respiratory infections including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) due to its cost-effectiveness and noninvasive collection. However, together with intrinsic enzymes and oral microbiota, children's unique dietary habits may introduce substances that interfere with diagnostic testing. To determine whether children's dietary choices impact SARS-CoV-2 molecular detection in saliva, we performed a diagnostic study that simulates testing of real-life specimens provided from healthy children (n = 5) who self-collected saliva at home before and at 0, 20, and 60 min after eating 20 foods they selected. Each of 72 specimens was split into two volumes and spiked with SARS-CoV-2-negative or SARS-CoV-2-positive clinical standards before side-by-side testing by reverse-transcription polymerase chain reaction matrix-assisted laser desorption ionization time-of-flight (RT-PCR/MALDI-TOF) assay. Detection of internal extraction control and SARS-CoV-2 nucleic acids was reduced in replicates of saliva collected at 0 min after eating 11 of 20 foods. Interference resolved at 20 and 60 min after eating all foods except hot dogs in one participant. This represented a significant improvement in the detection of nucleic acids compared to saliva collected at 0 min after eating (p = 0.0005). We demonstrate successful detection of viral nucleic acids in saliva self-collected by children before and after eating a variety of foods. Fasting is not required before saliva collection for SARS-CoV-2 testing by RT-PCR/MALDI-TOF, but waiting for 20 min after eating is sufficient for accurate testing. These findings should be considered for SARS-CoV-2 testing and broader viral diagnostics in saliva specimens.

  View details for DOI 10.1002/jmv.27660

  View details for PubMedID 35171508

  View details for PubMedCentralID PMC9088375

• A robust, highly multiplexed mass spectrometry assay to identify SARS-CoV-2 variants. medRxiv : the preprint server for health sciences Hernandez, M. M., Banu, R., Shrestha, P., Gonzalez-Reiche, A. S., van de Guchte, A., Farrugia, K., Sebra, R., Mount Sinai PSP Study Group, Gitman, M. R., Nowak, M. D., Cordon-Cardo, C., Simon, V., van Bakel, H., Sordillo, E. M., Luna, N., Ramirez, A., Castaneda, S. A., Patino, L. H., Ballesteros, N., Munoz, M., Ramirez, J. D., Paniz-Mondolfi, A. E. 2022

  Abstract

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are characterized by differences in transmissibility and response to therapeutics. Therefore, discriminating among them is vital for surveillance, infection prevention, and patient care. While whole viral genome sequencing (WGS) is the "gold standard" for variant identification, molecular variant panels have become increasingly available. Most, however, are based on limited targets and have not undergone comprehensive evaluation. We assessed the diagnostic performance of the highly multiplexed Agena MassARRAY SARS-CoV-2 Variant Panel v3 to identify variants in a diverse set of 391 SARS-CoV-2 clinical RNA specimens collected across our health systems in New York City, USA as well as in Bogota, Colombia (September 2, 2020 - March 2, 2022). We demonstrate almost perfect levels of interrater agreement between this assay and WGS for 9 of 11 variant calls (kappa ≥ 0.856) and 25 of 30 targets (kappa ≥ 0.820) tested on the panel. The assay had a high diagnostic sensitivity (≥93.67%) for contemporary variants (e.g., Iota, Alpha, Delta, Omicron [BA.1 sublineage]) and a high diagnostic specificity for all 11 variants (≥96.15%) and all 30 targets (≥94.34%) tested. Moreover, we highlight distinct target patterns that can be utilized to identify variants not yet defined on the panel including the Omicron BA.2 and other sublineages. These findings exemplify the power of highly multiplexed diagnostic panels to accurately call variants and the potential for target result signatures to elucidate new ones.Importance: The continued circulation of SARS-CoV-2 amidst limited surveillance efforts and inconsistent vaccination of populations has resulted in emergence of variants that uniquely impact public health systems. Thus, in conjunction with functional and clinical studies, continuous detection and identification are quintessential to inform diagnostic and public health measures. Furthermore, until WGS becomes more accessible in the clinical microbiology laboratory, the ideal assay for identifying variants must be robust, provide high resolution, and be adaptable to the evolving nature of viruses like SARS-CoV-2. Here, we highlight the diagnostic capabilities of a highly multiplexed commercial assay to identify diverse SARS-CoV-2 lineages that circulated at over September 2, 2020 - March 2, 2022 among patients seeking care at our health systems. This assay demonstrates variant-specific signatures of nucleotide/amino acid polymorphisms and underscores its utility for detection of contemporary and emerging SARS-CoV-2 variants of concern.

  View details for DOI 10.1101/2022.05.28.22275691

  View details for PubMedID 35665019

• Robust clinical detection of SARS-CoV-2 variants by RT-PCR/MALDI-TOF multitarget approach. Journal of medical virology Hernandez, M. M., Banu, R., Gonzalez-Reiche, A. S., van de Guchte, A., Khan, Z., Shrestha, P., Cao, L., Chen, F., Shi, H., Hanna, A., Alshammary, H., Fabre, S., Amoako, A., Obla, A., Alburquerque, B., Patiño, L. H., Ramírez, J. D., Sebra, R., Gitman, M. R., Nowak, M. D., Cordon-Cardo, C., Schutzbank, T. E., Simon, V., van Bakel, H., Sordillo, E. M., Paniz-Mondolfi, A. E. 2022; 94 (4): 1606-1616

  Abstract

  The coronavirus disease 2019 (COVID-19) pandemic has sparked the rapid development of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnostics. However, emerging variants pose the risk for target dropout and false-negative results secondary to primer/probe binding site (PBS) mismatches. The Agena MassARRAY® SARS-CoV-2 Panel combines reverse-transcription polymerase chain reaction and matrix-assisted laser desorption/ionization time-of-flight mass-spectrometry to probe for five targets across N and ORF1ab genes, which provides a robust platform to accommodate PBS mismatches in divergent viruses. Herein, we utilize a deidentified data set of 1262 SARS-CoV-2-positive specimens from Mount Sinai Health System (New York City) from December 2020 to April 2021 to evaluate target results and corresponding sequencing data. Overall, the level of PBS mismatches was greater in specimens with target dropout. Of specimens with N3 target dropout, 57% harbored an A28095T substitution that is highly specific for the Alpha (B.1.1.7) variant of concern. These data highlight the benefit of redundancy in target design and the potential for target performance to illuminate the dynamics of circulating SARS-CoV-2 variants.

  View details for DOI 10.1002/jmv.27510

  View details for PubMedID 34877674

  View details for PubMedCentralID PMC8854350

• Remitting neuropsychiatric symptoms in COVID-19 patients: Viral cause or drug effect? Journal of medical virology Forero-Peña, D. A., Hernandez, M. M., Mozo Herrera, I. P., Collado Espinal, I. B., Páez Paz, J., Ferro, C., Flora-Noda, D. M., Maricuto, A. L., Velásquez, V. L., Camejo-Avila, N. A., Sordillo, E. M., Delgado-Noguera, L. A., Perez-Garcia, L. A., Morantes Rodríguez, C. G., Landaeta, M. E., Paniz-Mondolfi, A. E. 2022; 94 (3): 1154-1161

  Abstract

  Numerous reports of neuropsychiatric symptoms highlighted the pathologic potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its relationship the onset and/or exacerbation of mental disease. However, coronavirus disease 2019 (COVID-19) treatments, themselves, must be considered as potential catalysts for new-onset neuropsychiatric symptoms in COVID-19 patients. To date, immediate and long-term neuropsychiatric complications following SARS-CoV-2 infection are currently unknown. Here we report on five patients with SARS-CoV-2 infection with possible associated neuropsychiatric involvement, following them clinically until resolution of their symptoms. We will also discuss the contributory roles of chloroquine and dexamethasone in these neuropsychiatric presentations.

  View details for DOI 10.1002/jmv.27443

  View details for PubMedID 34755347

  View details for PubMedCentralID PMC8661670

• Profiling Selective Packaging of Host RNA and Viral RNA Modification in SARS-CoV-2 Viral Preparations. Frontiers in cell and developmental biology Peña, N., Zhang, W., Watkins, C., Halucha, M., Alshammary, H., Hernandez, M. M., Liu, W. C., Albrecht, R. A., Garcia-Sastre, A., Simon, V., Katanski, C., Pan, T. 2022; 10: 768356

  Abstract

  Viruses package host RNAs in their virions which are associated with a range of functions in the viral life cycle. Previous transcriptomic profiling of host RNA packaging mostly focused on retroviruses. Which host RNAs are packaged in other viruses at the transcriptome level has not been thoroughly examined. Here we perform proof-of-concept studies using both small RNA and large RNA sequencing of six different SARS-CoV-2 viral isolates grown on VeroE6 cells to profile host RNAs present in cell free viral preparations and to explore SARS-CoV-2 genomic RNA modifications. We find selective enrichment of specific host transfer RNAs (tRNAs), tRNA fragments and signal recognition particle (SRP) RNA in SARS-CoV-2 viral preparations. Different viral preparations contain the same set of host RNAs, suggesting a common mechanism of packaging. We estimate that a single SARS-CoV-2 particle likely contains up to one SRP RNA and four tRNA molecules. We identify tRNA modification differences between the tRNAs present in viral preparations and those in the uninfected VeroE6 host cells. Furthermore, we find uncharacterized candidate modifications in the SARS-CoV-2 genomic RNA. Our results reveal an under-studied aspect of viral-host interactions that may be explored for viral therapeutics.

  View details for DOI 10.3389/fcell.2022.768356

  View details for PubMedID 35186917

  View details for PubMedCentralID PMC8851031

• Human Anti-neuraminidase Antibodies Reduce Airborne Transmission of Clinical Influenza Virus Isolates in the Guinea Pig Model. Journal of virology Tan, J., O'Dell, G., Hernandez, M. M., Sordillo, E. M., Kahn, Z., Kriti, D., van Bakel, H., Ellebedy, A. H., Wilson, P. C., Simon, V., Krammer, F., McMahon, M. 2022; 96 (2): e0142121

  Abstract

  The public health burden caused by influenza virus infections is not adequately addressed with existing vaccines and antivirals. Identifying approaches that interfere with human-to-human transmission of influenza viruses remains a pressing need. The importance of neuraminidase (NA) activity for the replication and spread of influenza viruses led us to investigate whether broadly reactive human anti-NA monoclonal antibodies (MAbs) could affect airborne transmission of the virus using the guinea pig model. In that model, infection with recent influenza virus clinical isolates resulted in 100% transmission from inoculated donors to recipients in an airborne transmission setting. Anti-NA MAbs were administered either to the inoculated animals on days 1, 2, and 4 after infection or to the naive contacts on days 2 and 4 after donor infection. Administration of NA-1G01, a broadly cross-reactive anti-NA MAb, to either the donor or recipient reduced transmission of the A/New York City/PV02669/2019 (H1N1) and A/New York City/PV01148/2018 (H3N2) viruses. Administration of 1000-3C05, an anti-N1 MAb, to either the donor or recipient reduced transmission of A/New York City/PV02669/2019 (H1N1) virus but did not reduce transmission of A/New York City/PV01148 (H3N2) virus. Conversely, 229-2C06, an anti-N2 MAb, reduced transmission of A/New York City/PV01148 (H3N2) but did not impact transmission of A/New York City/PV02669/2019 (H1N1) virus. Our work demonstrates that anti-NA MAbs could be further developed into prophylactic or therapeutic agents to prevent influenza virus transmission to control viral spread. IMPORTANCE The burden of influenza remains substantial despite unremitting efforts to reduce the magnitude of seasonal influenza epidemics and prepare for pandemics. Although vaccination remains the mainstay of these efforts, current vaccines are designed to stimulate an immune response against the viral hemagglutinin. Interest in the role immunity against neuraminidase plays in influenza virus infection and transmission has recently surged. Human antibodies that bind broadly to neuraminidases of diverse influenza viruses and protect mice against lethal viral challenge have previously been characterized. Here, we show that three such antibodies inhibit the neuraminidase activity of recent isolates and reduce their airborne transmission in a guinea pig model. In addition to contributing to the accumulating support for incorporating neuraminidase as a vaccine antigen, these findings also demonstrate the potential of direct administration of anti-neuraminidase antibodies to individuals infected with influenza virus and to individuals for postexposure prophylaxis to prevent the spread of influenza virus.

  View details for DOI 10.1128/JVI.01421-21

  View details for PubMedID 34669506

  View details for PubMedCentralID PMC8791283

• Real-Time Investigation of a Large Nosocomial Influenza A Outbreak Informed by Genomic Epidemiology. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America Javaid, W., Ehni, J., Gonzalez-Reiche, A. S., Carreño, J. M., Hirsch, E., Tan, J., Khan, Z., Kriti, D., Ly, T., Kranitzky, B., Barnett, B., Cera, F., Prespa, L., Moss, M., Albrecht, R. A., Mustafa, A., Herbison, I., Hernandez, M. M., Pak, T. R., Alshammary, H. A., Sebra, R., Smith, M. L., Krammer, F., Gitman, M. R., Sordillo, E. M., Simon, V., van Bakel, H. 2021; 73 (11): e4375-e4383

  Abstract

  Nosocomial respiratory virus outbreaks represent serious public health challenges. Rapid and precise identification of cases and tracing of transmission chains is critical to end outbreaks and to inform prevention measures.We combined conventional surveillance with influenza A virus (IAV) genome sequencing to identify and contain a large IAV outbreak in a metropolitan healthcare system. A total of 381 individuals, including 91 inpatients and 290 healthcare workers (HCWs), were included in the investigation.During a 12-day period in early 2019, infection preventionists identified 89 HCWs and 18 inpatients as cases of influenza-like illness (ILI), using an amended definition without the requirement for fever. Sequencing of IAV genomes from available nasopharyngeal specimens identified 66 individuals infected with a nearly identical strain of influenza A H1N1pdm09 (43 HCWs, 17 inpatients, and 6 with unspecified affiliation). All HCWs infected with the outbreak strain had received the seasonal influenza virus vaccination. Characterization of 5 representative outbreak viral isolates did not show antigenic drift. In conjunction with IAV genome sequencing, mining of electronic records pinpointed the origin of the outbreak as a single patient and a few interactions in the emergency department that occurred 1 day prior to the index ILI cluster.We used precision surveillance to delineate a large nosocomial IAV outbreak, mapping the source of the outbreak to a single patient rather than HCWs as initially assumed based on conventional epidemiology. These findings have important ramifications for more-effective prevention strategies to curb nosocomial respiratory virus outbreaks.

  View details for DOI 10.1093/cid/ciaa1781

  View details for PubMedID 33252647

  View details for PubMedCentralID PMC8653627

• Comparison of real-time RT-PCR and RT-PCR/MALDI-TOF methods for SARS-CoV-2 detection in saliva Hernandez, M. M., Banu, R., Shrestha, P., Patel, A., Chen, F., Cao, L., Fabre, S., Tan, J., Lopez, H., Chiu, N. OXFORD UNIV PRESS INC. 2021: S9

  View details for Web of Science ID 000714901300017

• SARS-CoV-2 in Transit: Characterization of SARS-CoV-2 Genomes From Venezuelan Migrants in Colombia. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases Patiño, L. H., Ballesteros, N., Muñoz, M., Castañeda, S., Hernández, C., Gomez, S., Florez, C., Rico, A., Pardo, L., Hernandez-Pereira, C. E., Delgado-Noguera, L., Grillet, M. E., Hernandez, M. M., Khan, Z., van de Guchte, A., Dutta, J., Gonzalez-Reiche, A. S., Simon, V., van Bakel, H., Sordillo, E. M., Ramírez, J. D., Paniz-Mondolfi, A. E. 2021; 110: 410-416

  Abstract

  To evaluate the genomic epidemiology of SARS-CoV-2 from Venezuelan migrants living in Colombia.This study sequenced SARS-CoV-2 from 30 clinical specimens collected from Venezuelan migrants. Genomes were compared with the Wuhan reference genome to identify polymorphisms, reconstruct phylogenetic relationships and perform comparative genomic analyses. Geographic, sociodemographic and clinical data were also studied across genotypes.This study demonstrated the presence of six distinct SARS-CoV-2 lineages circulating among Venezuelan migrants, as well as a close relationship between SARS-CoV-2 genomic sequences obtained from individuals living in the Venezuelan-Colombian border regions of La Guajira (Colombia) and Zulia (Venezuela). Three clusters (C-1, C-2 and C-3) were well supported by phylogenomic inference, supporting the hypothesis of three potential transmission routes across the Colombian-Venezuelan border. These genomes included point mutations previously associated with increased infectivity. A mutation (L18F) in the N-terminal domain of the spike protein that has been associated with compromised binding of neutralizing antibodies was found in 2 of 30 (6.6%) genomes. A statistically significant association was identified with symptomatology for cluster C2.The close phylogenetic relationships between SARS-CoV-2 genomes from Venezuelan migrants and from people living at the Venezuela-Colombian border support the importance of human movements for the spread of COVID-19 and for emerging virus variants.

  View details for DOI 10.1016/j.ijid.2021.07.069

  View details for PubMedID 34333122

  View details for PubMedCentralID PMC10130730

• RT-PCR/MALDI-TOF mass spectrometry-based detection of SARS-CoV-2 in saliva specimens. Journal of medical virology Hernandez, M. M., Banu, R., Shrestha, P., Patel, A., Chen, F., Cao, L., Fabre, S., Tan, J., Lopez, H., Chiu, N., Shifrin, B., Zapolskaya, I., Flores, V., Lee, P. Y., Castañeda, S., Ramírez, J. D., Jhang, J., Osorio, G., Gitman, M. R., Nowak, M. D., Reich, D. L., Cordon-Cardo, C., Sordillo, E. M., Paniz-Mondolfi, A. E. 2021; 93 (9): 5481-5486

  Abstract

  As severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections continue, there is a substantial need for cost-effective and large-scale testing that utilizes specimens that can be readily collected from both symptomatic and asymptomatic individuals in various community settings. Although multiple diagnostic methods utilize nasopharyngeal specimens, saliva specimens represent an attractive alternative as they can rapidly and safely be collected from different populations. While saliva has been described as an acceptable clinical matrix for the detection of SARS-CoV-2, evaluations of analytic performance across platforms for this specimen type are limited. Here, we used a novel sensitive RT-PCR/MALDI-TOF mass spectrometry-based assay (Agena MassARRAY®) to detect SARS-CoV-2 in saliva specimens. The platform demonstrated high diagnostic sensitivity and specificity when compared to matched patient upper respiratory specimens. We also evaluated the analytical sensitivity of the platform and determined the limit of detection of the assay to be 1562.5 copies/ml. Furthermore, across the five individual target components of this assay, there was a range in analytic sensitivities for each target with the N2 target being the most sensitive. Overall, this system also demonstrated comparable performance when compared to the detection of SARS-CoV-2 RNA in saliva by the cobas® 6800/8800 SARS-CoV-2 real-time RT-PCR Test (Roche). Together, we demonstrate that saliva represents an appropriate matrix for SARS-CoV-2 detection on the novel Agena system as well as on a conventional real-time RT-PCR assay. We conclude that the MassARRAY® system is a sensitive and reliable platform for SARS-CoV-2 detection in saliva, offering scalable throughput in a large variety of clinical laboratory settings.

  View details for DOI 10.1002/jmv.27069

  View details for PubMedID 33963565

  View details for PubMedCentralID PMC8242556

• Catheter-related bloodstream infection due to biofilm-producing Capnocytophaga sputigena. IDCases Fabre, S., Malik, Y., van De Guchte, A., Delgado-Noguera, L. A., Gitman, M. R., Nowak, M. D., Sordillo, E. M., Hernandez, M. M., Paniz-Mondolfi, A. E. 2021; 25: e01231

  Abstract

  Capnocytophaga sputigena is a facultatively-anaerobic bacterium that is part of the human oropharyngeal microflora. Although C. sputigena bacteremia is uncommon, systemic infections have been reported in both immunocompetent and immunocompromised patients. We report a case of catheter-related bloodstream infection by C. sputigena and highlight its enhanced biofilm-forming capacity in vitro.

  View details for DOI 10.1016/j.idcr.2021.e01231

  View details for PubMedID 34377666

  View details for PubMedCentralID PMC8329477

• Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin. PLoS neglected tropical diseases Ballesteros, N., Muñoz, M., Patiño, L. H., Hernández, C., González-Casabianca, F., Carroll, I., Santos-Vega, M., Cascante, J., Angel, A., Feged-Rivadeneira, A., Palma-Cuero, M., Flórez, C., Gomez, S., van de Guchte, A., Khan, Z., Dutta, J., Obla, A., Alshammary, H. A., Gonzalez-Reiche, A. S., Hernandez, M. M., Sordillo, E. M., Simon, V., van Bakel, H., Paniz-Mondolfi, A. E., Ramírez, J. D. 2021; 15 (4): e0009327

  Abstract

  The SARS-CoV-2 pandemic has forced health authorities across the world to take important decisions to curtail its spread. Genomic epidemiology has emerged as a valuable tool to understand introductions and spread of the virus in a specific geographic location.Here, we report the sequences of 59 SARS-CoV-2 samples from inhabitants of the Colombian Amazonas department. The viral genomes were distributed in two robust clusters within the distinct GISAID clades GH and G. Spatial-temporal analyses revealed two independent introductions of SARS-CoV-2 in the region, one around April 1, 2020 associated with a local transmission, and one around April 2, 2020 associated with other South American genomes (Uruguay and Brazil). We also identified ten lineages circulating in the Amazonas department including the P.1 variant of concern (VOC).This study represents the first genomic epidemiology investigation of SARS-CoV-2 in one of the territories with the highest report of indigenous communities of the country. Such findings are essential to decipher viral transmission, inform on global spread and to direct implementation of infection prevention and control measures for these vulnerable populations, especially, due to the recent circulation of one of the variants of concern (P.1) associated with major transmissibility and possible reinfections.

  View details for DOI 10.1371/journal.pntd.0009327

  View details for PubMedID 33857136

  View details for PubMedCentralID PMC8078805

• Repeated cross-sectional sero-monitoring of SARS-CoV-2 in New York City. Nature Stadlbauer, D., Tan, J., Jiang, K., Hernandez, M. M., Fabre, S., Amanat, F., Teo, C., Arunkumar, G. A., McMahon, M., Capuano, C., Twyman, K., Jhang, J., Nowak, M. D., Simon, V., Sordillo, E. M., van Bakel, H., Krammer, F. 2021; 590 (7844): 146-150

  Abstract

  In late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first detected in China and has since caused a pandemic of coronavirus disease 2019 (COVID-19). The first case of COVID-19 in New York City was officially confirmed on 1 March 2020 followed by a severe local epidemic1. Here, to understand seroprevalence dynamics, we conduct a retrospective, repeated cross-sectional analysis of anti-SARS-CoV-2 spike antibodies in weekly intervals from the beginning of February to July 2020 using more than 10,000 plasma samples from patients at Mount Sinai Hospital in New York City. We describe the dynamics of seroprevalence in an 'urgent care' group, which is enriched in cases of COVID-19 during the epidemic, and a 'routine care' group, which more closely represents the general population. Seroprevalence increased at different rates in both groups; seropositive samples were found as early as mid-February, and levelled out at slightly above 20% in both groups after the epidemic wave subsided by the end of May. From May to July, seroprevalence remained stable, suggesting lasting antibody levels in the population. Our data suggest that SARS-CoV-2 was introduced in New York City earlier than previously documented and describe the dynamics of seroconversion over the full course of the first wave of the pandemic in a major metropolitan area.

  View details for DOI 10.1038/s41586-020-2912-6

  View details for PubMedID 33142304

  View details for PubMedCentralID 7259823

• The arrival and spread of SARS-CoV-2 in Colombia. Journal of medical virology Ramírez, J. D., Florez, C., Muñoz, M., Hernández, C., Castillo, A., Gomez, S., Rico, A., Pardo, L., Barros, E. C., Castañeda, S., Ballesteros, N., Martínez, D., Vega, L., Jaimes, J. E., Cruz-Saavedra, L., Herrera, G., Patiño, L. H., Teherán, A. A., Gonzalez-Reiche, A. S., Hernandez, M. M., Sordillo, E. M., Simon, V., van Bakel, H., Paniz-Mondolfi, A. 2021; 93 (2): 1158-1163

  Abstract

  We performed phylogenomic analysis of severe acute respiratory syndrome coronavirus-2 from 88 infected individuals across different regions of Colombia. Eleven different lineages were detected, suggesting multiple introduction events. Pangolin lineages B.1 and B.1.5 were the most frequent, with B.1 being associated with prior travel to high-risk areas.

  View details for DOI 10.1002/jmv.26393

  View details for PubMedID 32761908

  View details for PubMedCentralID PMC7436700

• SARS-CoV-2 spread across the Colombian-Venezuelan border. Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases Paniz-Mondolfi, A., Muñoz, M., Florez, C., Gomez, S., Rico, A., Pardo, L., Barros, E. C., Hernández, C., Delgado, L., Jaimes, J. E., Pérez, L., Teherán, A. A., Alshammary, H. A., Obla, A., Khan, Z., Dutta, J., van de Guchte, A., Gonzalez-Reiche, A. S., Hernandez, M. M., Sordillo, E. M., Simon, V., van Bakel, H., Llewellyn, M. S., Ramírez, J. D. 2020; 86: 104616

  Abstract

  Venezuela and Colombia both adopted measures of containment early in response to the COVID-19 pandemic. However, Venezuela's ongoing humanitarian crisis has decimated its health care system, and forced millions of Venezuelans to flee through its porous border with Colombia. The extensive shared border, and illegal cross-border transit through improvised trails between the two countries are major challenges for public health authorities. We report the first SARS-CoV-2 genomes from Venezuela, and present a snapshot of the SARS-CoV-2 epidemiologic landscape in the Colombian-Venezuelan border region.We sequenced and assembled viral genomes from total RNA extracted from nasopharyngeal (NP) clinical specimens using a custom reference-based analysis pipeline. Three assemblies obtained were subjected to typing using the Phylogenetic Assignment of Named Global Outbreak LINeages 'Pangolin' tool. A total of 376 publicly available SARS-CoV-2 genomes from South America were obtained from the GISAID database to perform comparative genomic analyses. Additionally, the Wuhan-1 strain was used as reference.We found that two of the SARS-CoV-2 genomes from Venezuela belonged to the B1 lineage, and the third to the B.1.13 lineage. We observed a point mutation in the Spike protein gene (D614G substitution), previously reported to be associated with increased infectivity, in all three Venezuelan genomes. Additionally, three mutations (R203K/G204R substitution) were present in the nucleocapsid (N) gene of one Venezuelan genome.Genomic sequencing demonstrates similarity between SARS-CoV-2 lineages from Venezuela and viruses collected from patients in bordering areas in Colombia and from Brazil, consistent with cross-border transit despite administrative measures including lockdowns. The presence of mutations associated with increased infectivity in the 3 Venezuelan genomes we report and Colombian SARS-CoV-2 genomes from neighboring borders areas may pose additional challenges for control of SARS-CoV-2 spread in the complex epidemiological landscape in Latin American countries. Public health authorities should carefully follow the progress of the pandemic and its impact on displaced populations within the region.

  View details for DOI 10.1016/j.meegid.2020.104616

  View details for PubMedID 33157300

  View details for PubMedCentralID PMC7609240

• Comparison of SARS-CoV-2 detection from nasopharyngeal swab samples by the Roche cobas 6800 SARS-CoV-2 test and a laboratory-developed real-time RT-PCR test. Journal of medical virology Pujadas, E., Ibeh, N., Hernandez, M. M., Waluszko, A., Sidorenko, T., Flores, V., Shiffrin, B., Chiu, N., Young-Francois, A., Nowak, M. D., Paniz-Mondolfi, A. E., Sordillo, E. M., Cordon-Cardo, C., Houldsworth, J., Gitman, M. R. 2020; 92 (9): 1695-1698

  Abstract

  The urgent need to implement and rapidly expand testing for severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has led to the development of multiple assays. How these tests perform relative to one another is poorly understood. We evaluated the concordance between the Roche Diagnostics cobas 6800 SARS-CoV-2 test and a laboratory-developed test (LDT) real-time reverse transcription-polymerase chain reaction based on a modified Centers for Disease Control and Prevention protocol, for the detection of SARS-CoV-2 in samples submitted to the Clinical Laboratories of the Mount Sinai Health System. A total of 1006 nasopharyngeal swabs in universal transport medium from persons under investigation were tested for SARS-CoV-2 as part of routine clinical care using the cobas SARS-CoV-2 test with subsequent evaluation by the LDT. Cycle threshold values were analyzed and interpreted as either positive ("detected" or "presumptive positive"), negative (not detected), inconclusive, or invalid. Statistical analysis was performed using GraphPad Prism 8. The cobas SARS-CoV-2 test reported 706 positive and 300 negative results. The LDT reported 640 positive, 323 negative, 34 inconclusive, and 9 invalid results. When excluding inconclusive and invalid results, the overall percent agreement between the two platforms was 95.8%. Cohen's κ coefficient was 0.904 (95% confidence interval, 0.875-0.933), suggesting almost perfect agreement between both platforms. An overall discordance rate of 4.2% between the two systems may reflect differences in primer sequences, assay limit of detection, or other factors, highlighting the importance of comparing the performance of different testing platforms.

  View details for DOI 10.1002/jmv.25988

  View details for PubMedID 32383179

  View details for PubMedCentralID PMC7267546

• Real-Time Outbreak Investigation Informed by Whole Genome Sequencing and Data Mining: Expecting the Unexpected Hernandez, M. M., Gitman, M., Altman, D., Woods, K. L., Javaid, W., Gabasan, A., Schwing, D., Ehni, J., Moss, M. K., Tan, J., Khan, Z., Kriti, D., Ly, T., Samaroo, F., Hirsch, E. L., Polanco, J., Luksza, M., Mustafa, A., Powell, J. C., Carreno-Quiroz, J., Pak, T., Kasarskis, A., Sebra, R., Smith, M. L., Garcia-Sastre, A., Krammer, F., Simon, V., van Bakel, H., Sordillo, E. M. ELSEVIER SCIENCE INC. 2019: 1181

  View details for Web of Science ID 000496996500210

• IL-15 regulates susceptibility of CD4+ T cells to HIV infection. Proceedings of the National Academy of Sciences of the United States of America Manganaro, L., Hong, P., Hernandez, M. M., Argyle, D., Mulder, L. C., Potla, U., Diaz-Griffero, F., Lee, B., Fernandez-Sesma, A., Simon, V. 2018; 115 (41): E9659-E9667

  Abstract

  HIV integrates into the host genome to create a persistent viral reservoir. Stimulation of CD4+ memory T lymphocytes with common γc-chain cytokines renders these cells more susceptible to HIV infection, making them a key component of the reservoir itself. IL-15 is up-regulated during primary HIV infection, a time when the HIV reservoir established. Therefore, we investigated the molecular and cellular impact of IL-15 on CD4+ T-cell infection. We found that IL-15 stimulation induces SAM domain and HD domain-containing protein 1 (SAMHD1) phosphorylation due to cell cycle entry, relieving an early block to infection. Perturbation of the pathways downstream of IL-15 receptor (IL-15R) indicated that SAMHD1 phosphorylation after IL-15 stimulation is JAK dependent. Treating CD4+ T cells with Ruxolitinib, an inhibitor of JAK1 and JAK2, effectively blocked IL-15-induced SAMHD1 phosphorylation and protected CD4+ T cells from HIV infection. Using high-resolution single-cell immune profiling using mass cytometry by TOF (CyTOF), we found that IL-15 stimulation altered the composition of CD4+ T-cell memory populations by increasing proliferation of memory CD4+ T cells, including CD4+ T memory stem cells (TSCM). IL-15-stimulated CD4+ TSCM, harboring phosphorylated SAMHD1, were preferentially infected. We propose that IL-15 plays a pivotal role in creating a self-renewing, persistent HIV reservoir by facilitating infection of CD4+ T cells with stem cell-like properties. Time-limited interventions with JAK1 inhibitors, such as Ruxolitinib, should prevent the inactivation of the endogenous restriction factor SAMHD1 and protect this long-lived CD4+ T-memory cell population from HIV infection.

  View details for DOI 10.1073/pnas.1806695115

  View details for PubMedID 30257946

  View details for PubMedCentralID PMC6187195

• Histology Education in the Next Generation Shaw, P., Hernandez, M. WILEY. 2017

  View details for Web of Science ID 000405461400496

• Genome sequencing of Giardia lamblia genotypes A2 and B isolates (DH and GS) and comparative analysis with the genomes of genotypes A1 and E (WB and Pig). Genome biology and evolution Adam, R. D., Dahlstrom, E. W., Martens, C. A., Bruno, D. P., Barbian, K. D., Ricklefs, S. M., Hernandez, M. M., Narla, N. P., Patel, R. B., Porcella, S. F., Nash, T. E. 2013; 5 (12): 2498-511

  Abstract

  Giardia lamblia (syn G. intestinalis, G. duodenalis) is the most common pathogenic intestinal parasite of humans worldwide and is a frequent cause of endemic and epidemic diarrhea. G. lamblia is divided into eight genotypes (A-H) which infect a wide range of mammals and humans, but human infections are caused by Genotypes A and B. To unambiguously determine the relationship among genotypes, we sequenced GS and DH (Genotypes B and A2) to high depth coverage and compared the assemblies with the nearly completed WB genome and draft sequencing surveys of Genotypes E (P15; pig isolate) and B (GS; human isolate). Our results identified DH as the smallest Giardia genome sequenced to date, while GS is the largest. Our open reading frame analyses and phylogenetic analyses showed that GS was more distant from the other three genomes than any of the other three were from each other. Whole-genome comparisons of DH_A2 and GS_B with the optically mapped WB_A1 demonstrated substantial synteny across all five chromosomes but also included a number of rearrangements, inversions, and chromosomal translocations that were more common toward the chromosome ends. However, the WB_A1/GS_B alignment demonstrated only about 70% sequence identity across the syntenic regions. Our findings add to information presented in previous reports suggesting that GS is a different species of Giardia as supported by the degree of genomic diversity, coding capacity, heterozygosity, phylogenetic distance, and known biological differences from WB_A1 and other G. lamblia genotypes.

  View details for DOI 10.1093/gbe/evt197

  View details for PubMedID 24307482

  View details for PubMedCentralID PMC3879983

• Effect of the Leptin Receptor Q223R Polymorphism on the Host Transcriptome following Infection with <i>Entamoeba histolytica</i> (vol 81, pg 1460, 2013) INFECTION AND IMMUNITY Mackey-Lawrence, N. M., Guo, X., Sturdevant, D. E., Virtaneva, K., Hernandez, M. M., Houpt, E., Sher, A., Porcella, S. F., Petri, W. A. 2013; 81 (11): 4322

  View details for DOI 10.1128/IAI.00689-13

  View details for Web of Science ID 000325719900038

• Effect of the leptin receptor Q223R polymorphism on the host transcriptome following infection with Entamoeba histolytica. Infection and immunity Mackey-Lawrence, N. M., Guo, X., Sturdevant, D. E., Virtaneva, K., Hernandez, M. M., Houpt, E., Sher, A., Porcella, S. F., Petri, W. A. 2013; 81 (5): 1460-70

  Abstract

  Resistance to amebiasis is associated with a polymorphism in the leptin receptor. Previous studies demonstrated that humans with the ancestral Q223 leptin receptor allele were nearly four times less likely to be infected with Entamoeba histolytica than those carrying the mutant R223 allele. We hypothesized that the Q223 allele protected against E. histolytica via STAT3-mediated transcription of genes required for mucosal immunity. To test this, mice containing the humanized LEPR Q or R allele at codon 223 were intracecally infected with E. histolytica. Susceptibility to amebiasis was assessed, and cecal tissues were analyzed for changes in gene expression. By 72 h postchallenge, all Q223 mice had cleared E. histolytica, whereas 39% of 223R mice were infected. Thirty-seven genes were differentially expressed in response to infection at 72 h, including proinflammatory genes (CXCL2, S100A8/9, PLA2G7, ITBG2, and MMP9) and functions pertaining to the movement and activity of immune cells. A comparison at 12 h postchallenge of infected Q223 versus R223 mice identified a subset of differentially expressed genes, many of which were closely linked to leptin signaling. Further analyses indicated that the Q223 gene expression pattern was consistent with a suppressed apoptotic response to infection, while 223R showed increased cellular proliferation and recruitment. These studies are the first to illuminate the downstream effects of leptin receptor polymorphisms on intestinal infection by E. histolytica. As such, they are important for the insight that they provide into this previously uncharacterized mechanism of mucosal immunity.

  View details for DOI 10.1128/IAI.01383-12

  View details for PubMedID 23429533

  View details for PubMedCentralID PMC3647980