Biology subjects

Xiang, J.

Publications and source records attributed to Xiang, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2022

Identification of secreted proteins by comparison of protein abundance in conditioned media and cell lysates.

Analysis of the full spectrum of secreted proteins in cell culture is complicated by leakage of intracellular proteins from damaged cells. To address this issue, we compared the abundance of individual proteins between the cell lysate and the conditioned medium, reasoning that secreted proteins should be relatively more abundant in the conditioned medium. Marked enrichment for signal-peptide-bearing proteins with increasing conditioned media to cell lysate ratio, as well loss of this signal following brefeldin A treatment, confirmed the sensitivity and specificity of this approach. The subset of proteins demonstrating increased conditioned media to cell lysate ratio in the presence of Brefeldin A identified candidates for unconventional secretion via a pathway independent of ER to Golgi trafficking.

biochemistry↗

bioRxiv2022

Genomic analyses provide new insights into the evolutionary history and reproduction of the Paleogene relictual Kingdonia (Circaeasteraceae, Ranunculales)

Asexual lineages are perceived to be short-lived on evolutionary timescales due to accumulation of deleterious mutations. Hence reports for exceptional cases of putative ancient asexual species usually raise doubts about whether such species are recently derived or engage in some undocumented sexual reproduction. However, there have been few studies to solve the mystery. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having closely related congeneric sexual species, seeming to have persisted under strict asexuality for long periods of time. In this study, we use population genomic analyses to test for reproduction mode and infer the evolutionary process and mechanisms facilitating the survival of the species. Our results indicate the presence of three differentiating genetic lineages within the species and support that asexual reproduction in K. uniflora indicated by high allelic heterozygosity had occurred prior to the lineage differentiation ([~]0.5 mya). We also detected DNA recombination events in some populations, in line with occurrence of unseen and unevenly distributed sexual reproduction among populations. However the observation of high linkage disequilibrium, relatively high ratio of{pi} N/{pi}S (nonsynonymous versus synonymous nucleotide diversity), together with high allelic heterozygosity suggest the sexual reproduction is infrequent. Furthermore, we found that genes containing SNPs with elevated Fst values are significantly enriched in functions associated with seed development, suggesting differentiation in genes regulating seed development is likely to be the key reason of the uneven distribution of sexual reproduction in K. uniflora. Evidence from our study supports predominate asexual reproduction in K. uniflora, but unseen sexual reproduction must have played a key role to ensure the long-term survival of the lineage in general. Uneven distribution of sexual reproduction in the species may be a key factor underlying the observed genetic differentiation between populations. This study provides novel insights into the reproduction and evolution of Kingdonia, a relict lineage evolved in the Paleogene and known for asexual reproduction, and demonstrate the power of data from population genome sequencing in resolving long-standing evolutionary questions.

genomics↗

bioRxiv2022

A CRISPR-based instant DNA repositioning system and the early intranuclear life of HSV-1

The intranuclear localization of viral DNA genomes in relation to the intranuclear environment plays critical roles in determining virus fate. Recent advances in the application of chromosome conformation capture-based sequencing analysis (3C technologies) have revealed valuable aspects of the spatiotemporal interplay of viral genomes with host chromosomes. However, to elucidate the causal relationship between the subnuclear localization of viral genomes and the pathogenic outcome of the infection, manipulative tools are needed. Instant repositioning of viral DNAs to specific subnuclear compartments amid infection is a powerful approach to synchronize and interrogate this dynamically changing process in space and time. Herein, we report an inducible CRISPR-based two-component platform that relocates extrachromosomal DNA pieces (5 kb to 170 kb) to the nuclear periphery instantly (CRISPR-nuPin). Based on this system, investigations of herpes simplex virus 1 (HSV-1), a prototype member of the human herpesvirus family, revealed unprecedently reported insights into the early intranuclear life of the pathogen: I) Viral genomes tethered to the nuclear periphery upon entry, compared with those in the nuclear interior, were wrapped around histones with increased suppressive modifications and subjected to stronger transcriptional silencing and prominent inhibition. II) Relocating HSV-1 genomes at 1 hour post infection significantly promoted transcription of viral {beta} and {gamma} genes, termed an "Escaping" effect. III) Early accumulation of ICP0 was a sufficient but not necessary condition mediating "Escaping". IV) Subnuclear localization was only critical during early infection. Importantly, the CRISPR-nuPin tactic should be widely applicable to many DNA viruses. SummaryThe intranuclear localization of viral DNA genomes plays a critical role in determining virus fate. To elucidate the causal relationship between subnuclear localization and the pathogenic outcome of DNA viruses, manipulative tools are needed. Herein, we report an inducible CRISPR-based two-component platform that relocates DNA pieces (5 kb to 170 kb) to the nuclear periphery instantly (CRISPR-nuPin). Utilizing this tactic, we interrogated the early intranuclear life of herpes simplex virus 1 (HSV-1), a prototype of human herpesviruses, in space and time and revealed that I) viral genomes tethered to the nuclear edge upon entry were prone to suppressive histone packaging and severe inhibition. II) Relocating HSV-1 genomes to the nuclear fringe at 1 hour post infection promoted transcription of viral genes ("Escaping"). III) Early accumulation of ICP0 was a sufficient but not necessary condition mediating "Escaping". IV) Subnuclear localization was a critical factor only during early infection. HighlightsO_LICRISPR-nuPin is an inducible two-component DNA repositioning system C_LIO_LIIt mediates instant nuclear edging of viral DNA during infection C_LIO_LIA powerful approach to interrogate DNA viruses in space and time C_LIO_LIViral DNA at the nuclear periphery upon entry is strongly silenced C_LI In briefAn inducible two-component CRISPR-based platform that instantly repositions HSV-1 genomes to the nuclear edge unveils intranuclear space heterogeneity for the incoming viral genomes and dynamic stages of the host-virus interplay during early infection of the pathogen.

microbiology↗

bioRxiv2021

Comprehensive simulation and interpretation of single nucleotide substitutions in GJB2 reveals the genetic and phenotypic landscape of GJB2-related hearing loss

Genetic variants in the GJB2 gene are the most frequent causes of congenital and childhood hearing loss worldwide. In addition to nonsyndromic hearing loss, GJB2 pathogenic variants are also correlated with syndromic phenotypes, showing high genetic and phenotypic heterogeneity. To comprehensively delineate the genetic and phenotypic landscape of GJB2 variants, we interpreted and manually curated all the 2043 possible single-nucleotide substitution (SNS) coding variants in this gene following the hearing loss-specific ACMG/AMP guidelines. As a result, 61 (3.0%), 188 (9.2%), 1487 (72.8%), 301 (14.7%) and 6 (0.3%) variants were classified as pathogenic, likely pathogenic, variant of uncertain significance, likely benign and benign, respectively. Interestingly, 54% (84/156) of pathogenic/likely pathogenic missense variants were not recorded in ClinVar. Further analysis showed that the second transmembrane domain (TM2) and the 310 helix are highly enriched for pathogenic missense variants. The N-terminal tail and the extracellular loop (E1) showed a high density of variants that are associated with syndromic or dominant nonsyndromic hearing loss. On the other hand, the intracellular loops (CL and CT) were extremely tolerant to variation. Based on this new information, we propose refinements of the guidelines for variant interpretation in GJB2. In summary, our study interpreted all possible SNS variants in the coding region of the GJB2 gene, characterized novel clinically significant (N = 249) and benign or likely benign (N = 307) in this gene, and revealed significant genotype-phenotype correlations at this common hearing loss locus. The interpretation of GJB2 SNS variants in the coding region provides a prototype for genes with similarly high genetic and phenotypic heterogeneity.

genetics↗

bioRxiv2021

Reduced neutralization of SARS-CoV-2 B.1.617 variant by inactivated and RBD-subunit vaccine

Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The Spike protein that mediates coronavirus entry into host cells is a major target for COVID-19 vaccines and antibody therapeutics. However, multiple variants of SARS-CoV-2 have emerged, which may potentially compromise vaccine effectiveness. Using a pseudovirus-based assay, we evaluated SARS-CoV-2 cell entry mediated by the viral Spike B.1.617 and B.1.1.7 variants. We also compared the neutralization ability of monoclonal antibodies from convalescent sera and neutralizing antibodies (NAbs) elicited by CoronaVac (inactivated vaccine) and ZF2001 (RBD-subunit vaccine) against B.1.617 and B.1.1.7 variants. Our results showed that, compared to D614G and B.1.1.7 variants, B.1.617 shows enhanced viral entry and membrane fusion, as well as more resistant to antibody neutralization. These findings have important implications for understanding viral infectivity and for immunization policy against SARS-CoV-2 variants.

microbiology↗

bioRxiv2021

The role of AUX1 during lateral root development in the domestication of the model C4 grass Setaria italica

C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from rubisco. The specialized leaf anatomy required for this separation evolved independently many times. C4 root systems are highly branched, an adaptation thought to support high rates of photosynthesis; however, little is known about the molecular mechanisms that have driven the evolution of C4 root system architecture (RSA). Using a mutant screen in the C4 model plant Setaria italica, we identify siaux1-1 and siaux1-2 as RSA mutants, and use CRISPR/cas9-mediated genome editing and overexpression to confirm the importance of the locus. As AUX1 is not necessary for lateral root emergence in S. viridis, the species from which S. italica was domesticated, we conducted an analysis of auxin responsive elements in the promoters of auxin-responsive gene families in S. italica, and explore the molecular basis of SiAUX1s role in seedling development using an RNAseq analysis of wild type and siaux1-1 plants. Finally, we use a root coordinate system to compare cell-by-cell meristem structures in siaux1-1 and wild type Setaria plants, observing changes in the distribution of cell volumes in all cell layers and a dependence in the frequency of protophloem and protoxylem strands on siAUX1.

plant biology↗

bioRxiv2021

HyMM: Hybrid method for disease-gene prediction by integrating multiscale module structures

MotivationIdentifying disease-related genes is important for the study of human complex diseases. Module structures or community structures are ubiquitous in biological networks. Although the modular nature of human diseases can provide useful insights, the mining of information hidden in multiscale module structures has received less attention in disease-gene prediction. ResultsWe propose a hybrid method, HyMM, to predict disease-related genes more effectively by integrating the information from multiscale module structures. HyMM consists of three key steps: extraction of multiscale modules, gene rankings based on multiscale modules and integration of multiple gene rankings. The statistical analysis of multiscale modules extracted by three multiscale-module-decomposition algorithms (MO, AS and HC) shows that the functional consistency of the modules gradually improves as the resolution increases. This suggests the existence of different levels of functional relationships in the multiscale modules, which may help reveal disease-gene associations. We display the effectiveness of multiscale module information in the disease-gene prediction and confirm the excellent performance of HyMM by 5-fold cross-validation and independent test. Specifically, HyMM with MO can more effectively enhance the ability of disease-gene prediction; HyMM (MO, RWR) and HyMM (MO, RWRH) are especially preferred due to their excellent comprehensive performance, and HyMM (AS, RWRH) is also good choice due to its local performance. We anticipate that this work could provide useful insights for disease-module analysis and disease-gene prediction based on multi-scale module structures. Availabilityhttps://github.com/xiangiu0208/HvMM Contactlimin@mail.csu.edu.cn Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

bioRxiv2021

Age and Race related changes in Gene Expression during Human PBMC aging

Human immune system functions over an entire lifetime, yet how and why the immune system becomes less effective with age are not well understood. Here, we characterize peripheral blood mononuclear cells transcriptome from 172 healthy adults with 21~90 years of age using RNA-seq and the weighted gene correlation network analyses (WGCNA). These data reveal a set of insightful gene expression modules and representative gene biomarkers for human immune system aging from Asian and Caucasian ancestry, respectively. Among them, the aging-specific modules show an age-related gene expression variation spike around early-seventies. In addition, it is not known whether Asian and Caucasian immune systems go through similar gene expression changes throughout their lifespan, and to what extent these aging-associated changes are shared among ethnicities. We find the top hub genes including NUDT7, CLPB, OXNAD1 and MLLT3 are shared between Asian and Caucasian aging related modules and further validated in human PBMCs from different age groups. Overall, the impact of age and race on transcriptional variation elucidated from this study provide insights into the transcriptional driver of immune aging.

immunology↗

bioRxiv2020

Methylation of Dual Specificity Phosphatase 4 Controls Cell Differentiation

A collection of signaling and epigenetic events needs to be orchestrated for normal development of hematopoietic lineages. While mitogen-activated protein (MAP) kinases (MAPKs) and multiple epigenetic modulators have been implicated in the megakaryocytic (Mk) cell differentiation, the underlying molecular mechanisms of signaling-epigenetic crosstalk remain unclear. MAPKs are in general inactivated by dual specificity phosphatases (DUSPs), whose activities are tightly regulated by various posttranslational modifications. Using knockdown screening and single-cell transcriptional analysis, we determined that DUSP4 is the phosphatase that inactivates p38 MAPK in hematopoietic cells and serves as a key regulator to promote Mk differentiation. With the nextgeneration Bioorthogonal Profiling of Protein Methylation technology for live cells, we identified DUSP4 as a PRMT1 substrate. Mechanistically, PRMT1-mediated Arg351 methylation of DUSP4 triggers its ubiquitinylation by HUWE1 (an E3 ligase) and then degradation, which results in p38 MAPK activation and inhibition of Mk differentiation in vitro and in vivo. Interestingly, the mechanistic axis of the DUSP4 degradation and p38 activation is also associated with a transcriptional signature of immune activation and thus argues immunological roles of Mk cells. Collectively, these results demonstrate a critical role of PRMT1-mediated posttranslational modification of DUSP4 in regulation of Mk differentiation and maturation. In the context of thrombocytopenia observed in myelodysplastic syndromes (MDS), we demonstrated that high levels of p38 MAPK and PRMT1 are associated with low platelet counts and adverse prognosis, while pharmacological inhibition of p38 MAPK or PRMT1 stimulates megakaryopoiesis in MDS samples. These findings provide novel mechanistic insights into the role of the PRMT1-DUSP4-p38 axis on Mk differentiation and present a targeting strategy for treatment of thrombocytopenia associated with myeloid malignancies such as MDS.

cell biology↗

bioRxiv2020

Intranasal administration of SARS-CoV-2 neutralizing human antibody prevents infection in mice

Prevention of SARS-CoV-2 infection at the point of nasal entry is a novel strategy that has the potential to help contain the ongoing pandemic. Using our proprietary technologies, we have engineered a human antibody that recognizes SARS-CoV-2 S1 spike protein with an enhanced affinity for mucin to improve the antibodys retention in respiratory mucosa. The modified antibody, when administered into mouse nostrils, was shown to block infection in mice that were exposed to high titer SARS-CoV-2 pseudovirus 10 hours after the initial antibody treatment. Our data show that the protection against SARS-CoV-2 infection is effective in both nasal and lung areas 7 days after viral exposure. The modified antibody is stable in a nasal spray formulation and maintains its SARS-CoV-2 neutralizing activity. Nasal spray of the modified antibody can be developed as an affordable and effective prophylactic product to protect people from infection by exposure to SARS-CoV-2 virus in the air. One-sentence summaryA Fc-modified human antibody prevents SARS-CoV-2 viral infection via nasal administration

bioengineering↗

bioRxiv2020

Detection of melanin-mediated false-positive for BaxΔ2 immunohistochemical staining in human skin tissue

Bax{Delta}2 is a pro-apoptotic isoform of the Bax family. We have previously shown that Bax{Delta}2 protein expression is low in most healthy human tissues with the protein mainly scattered in the connective tissues. Surprisingly, in skin tissue, the Bax{Delta}2-positive staining was strikingly strong, especially in the basal layer of the epidermis. It has been documented that melanin in the basal cells displays a brown color that could give false-positive staining in the commonly used DAB-based (3-3-diaminobenzidine) immunostaining. To avoid the false-positive staining from DAB-melanin, we performed immunofluorescent staining on the same set of tissues which were positive for Bax{Delta}2 in the DAB immunostaining. The results from co-immunofluorescent staining of Bax{Delta}2 and a basal cell marker CK-14 showed that the previously detected DAB-stained Bax{Delta}2-positive epidermal cells were CK-14 positive but Bax{Delta}2 negative. Consistent with our previous finding, the Bax{Delta}2-positive cells in the dermis connective tissues are positive in both DAB-based and fluorescence-based immunostainings. These data indicate that the DAB-stained Bax{Delta}2 positive cells in the basal layer of skin tissue are false-positive due to a misinterpretation of the melanin color, but the dermal connective tissue still presents real Bax{Delta}2 positive staining.

cell biology↗

bioRxiv2020

Single extracellular vesicles protein profiling classifies renal fibrosis stages in mice model

Renal fibrosis is a common consequence of various chronic kidney diseases (CKD), leading to the loss of renal function and even end-stage renal failure. Extracellular vesicles (EVs) were shown to be involved in development of CKD and renal fibrosis. In this study, we induced renal fibrosis in mice model through unilateral ureteral obstruction (UUO) and extracted EVs from the kidney with induced fibrosis. Proximity barcoding assay (PBA) was performed to detect the expression of 112 proteins at individual EVs level for renal fibrosis of Grade I to IV and sham control group as well. The single EVs are classified into subpopulations according to the surface proteomic characteristics. We discovered several EV subpopulations, with presence of ITGAM, ITGA6, CD73, CD13 and ALDH1, increase significantly with development of renal fibrosis. These findings indicate that besides protein expression, proteomic fingerprints of single EVs can be potential biomarkers for surveillance of CKD and renal fibrosis.

molecular biology↗

bioRxiv2020

VIP-HL: Semi-automated ACMG/AMP variant interpretation platform for genetic hearing loss

PurposeThe American College of Medical Genetics and Genomics, and the Association for Molecular Pathology (ACMG/AMP) have proposed a set of evidence-based guidelines to support sequence variant interpretation. The ClinGen hearing loss expert panel (HL-EP) introduced further specifications into the ACMG/AMP framework for genetic hearing loss. This study aimed to semi-automate the HL ACMG/AMP rules. MethodsVIP-HL aggregates information from external databases to automate 13 out of 24 ACMG/AMP rules specified by HL-EP, namely PVS1, PS1, PM1, PM2, PM4, PM5, PP3, BA1, BS1, BS2, BP3, BP4, and BP7. ResultsWe benchmarked VIP-HL using 50 variants where 83 rules were activated by the HL expert panel. VIP-HL concordantly activated 96% (80/83) rules, significantly higher than that of by InterVar (47%; 39/83). Of 4948 ClinVar star 2+ variants from 142 deafness-related genes, VIP-HL achieved an overall variant interpretation concordance in 88.0% (4353/4948). VIP-HL is available with a user-friendly web interface at http://hearing.genetics.bgi.com/. ConclusionVIP-HL is an integrated online tool for reliable automated variant classification in hearing loss genes. It assists curators in variant interpretation and provides a platform for users to share classifications with each other.

bioinformatics↗

bioRxiv2020

Gluconeogenic Enzyme PCK1 Deficiency Is Critical for CHK2 O-GlcNAcylation and Hepatocellular Carcinoma Growth upon Glucose Deprivation

Elevated hexosamine-biosynthesis pathway (HBP) activity and O-GlcNAcylation are emerging hallmarks of hepatocellular carcinoma (HCC). Inhibiting O-GlcNAcylation could be a promising anti-cancer strategy. Here, we investigate this possibility and demonstrate that deficiency of phosphoenolpyruvate carboxykinase 1 (PCK1), a rate-limiting enzyme in gluconeogenesis, promotes O-GlcNAcylation and hepatoma cell proliferation under low-glucose conditions. PCK1 loss results in oxaloacetate accumulation and AMPK inactivation, promoting uridine diphosphate-N-acetylglucosamine (UDP-GlcNAc) synthesis and CHK2 threonine 378 O-GlcNAcylation and counteracting its ubiquitination and degradation. O-GlcNAcylation also promotes CHK2-dependent Rb phosphorylation and HCC cell proliferation. Therefore, blocking HBP-mediated O-GlcNAcylation suppresses tumor progression in liver-specific Pck1-knockout mice. We reveal a link between PCK1 depletion and hyper-O-GlcNAcylation that underlies HCC oncogenesis and suggest therapeutic targets for HCC that act by inhibiting O-GlcNAcylation.

cancer biology↗

bioRxiv2020

Performance characterization of PCR-free whole genome sequencing for clinical diagnosis

PurposeTo evaluate the performance of PCR-free whole genome sequencing (WGS) for clinical diagnosis, and thereby revealing how experimental parameters affect variant detection. MethodsAll the 5 NA12878 samples were sequenced using MGISEQ-2000. NA12878 samples underwent WGS with differing DNA input and library preparation protocol (PCR-based versus PCR-free protocols for library preparation). The DP (depth of coverage) and GQ (genotype quality) of each sample were compared. We developed a systematic WGS pipeline for the analysis of down-sampling samples of the 5 NA12878 samples. The performance of each sample was measured for sensitivity, coverage of depth and breadth of coverage of disease-related genes and CNVs. ResultsIn general, NA12878-2 (PCR-free WGS) showed better DP and GQ distribution than NA12878-1 (PCR-based WGS). With a mean depth of ~40X, the sensitivity of homozyous and heterozygous SNPs of NA12878-2 showed higher sensitivity (>99.77% and > 99.82%) than NA12878-1, and positive predictive value (PPV) exceeded 99.98% and 99.07%. The sensitivity and PPV of homozygous and heterozygous indels for NA12878-2 (PCR-free WGS) showed great improvement than NA128878-1. The breadths of coverage for disease-related genes and CNVs are slightly better for samples with PCR-free library preparation protocol than the sample with PCR-based library preparation protocol. DNA input also influences the performance of variant detection in samples with PCR-free WGS. ConclusionDifferent experimental parameters may affect variant detection for clinical WGS. Clinical scientists should know the range of sensitivity of variants for different methods of WGS, which would be useful when interpreting and delivering clinical reports.

genetics↗

bioRxiv2020

A multiplexed, automated evolution pipeline enablesscalable discovery and characterization of biosensors

Biosensors are key components in engineered biological systems, providing a means of measuring and acting upon the large biochemical space in living cells. However, generating small molecule sensing elements and integrating them into in vivo biosensors have been challenging. Using aptamer-coupled ribozyme libraries and a novel ribozyme regeneration method, we developed de novo rapid in vitro evolution of RNA biosensors (DRIVER) that enables multiplexed discovery of biosensors. With DRIVER and high-throughput characterization (CleaveSeq) fully automated on liquid-handling systems, we identified and validated biosensors against six small molecules, including five for which no aptamers were previously found. DRIVER-evolved biosensors were applied directly to regulate gene expression in yeast, displaying activation ratios up to 33-fold. DRIVER biosensors were also applied in detecting metabolite production from a multi-enzyme biosynthetic pathway. This work demonstrates DRIVER as a scalable pipeline for engineering de novo biosensors with wide-ranging applications in biomanufacturing, diagnostics, therapeutics, and synthetic biology.

bioengineering↗

bioRxiv2020

Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids

Summary ParagraphThe SARS-CoV-2 virus has caused already over 3.5 million COVID-19 cases and 250,000 deaths globally. There is an urgent need to create novel models to study SARS-CoV-2 using human disease-relevant cells to understand key features of virus biology and facilitate drug screening. As primary SARS-CoV-2 infection is respiratory-based, we developed a lung organoid model using human pluripotent stem cells (hPSCs) that could be adapted for drug screens. The lung organoids, particularly aveolar type II cells, express ACE2 and are permissive to SARS-CoV-2 infection. Transcriptomic analysis following SARS-CoV-2 infection revealed a robust induction of chemokines and cytokines with little type I/III interferon signaling, similar to that observed amongst human COVID-19 pulmonary infections. We performed a high throughput screen using hPSC-derived lung organoids and identified FDA-approved drug candidates, including imatinib and mycophenolic acid, as inhibitors of SARS-CoV-2 entry. Pre- or post-treatment with these drugs at physiologically relevant levels decreased SARS-CoV-2 infection of hPSC-derived lung organoids. Together, these data demonstrate that hPSC-derived lung cells infected by SARS-CoV-2 can model human COVID-19 disease and provide a valuable resource to screen for FDA-approved drugs that might be repurposed and should be considered for COVID-19 clinical trials.

microbiology↗

bioRxiv2020

Host, Viral, and Environmental Transcriptome Profiles of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2)

The Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused thousands of deaths worldwide, including >18,000 in New York City (NYC) alone. The sudden emergence of this pandemic has highlighted a pressing clinical need for rapid, scalable diagnostics that can detect infection, interrogate strain evolution, and identify novel patient biomarkers. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs, plus a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, bacterial, and viral profiling. We applied both technologies across 857 SARS-CoV-2 clinical specimens and 86 NYC subway samples, providing a broad molecular portrait of the COVID-19 NYC outbreak. Our results define new features of SARS-CoV-2 evolution, nominate a novel, NYC-enriched viral subclade, reveal specific host responses in interferon, ACE, hematological, and olfaction pathways, and examine risks associated with use of ACE inhibitors and angiotensin receptor blockers. Together, these findings have immediate applications to SARS-CoV-2 diagnostics, public health, and new therapeutic targets.

molecular biology↗