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1.
medRxiv ; 2024 Jun 05.
Article in English | MEDLINE | ID: mdl-38883802

ABSTRACT

Background: Assessing COVID-19 vaccine effectiveness (VE) and severity of SARS-CoV-2 variants can inform public health risk assessments and decisions about vaccine composition. BA.2.86 and its descendants, including JN.1 (referred to collectively as "JN lineages"), emerged in late 2023 and exhibited substantial genomic divergence from co-circulating XBB lineages. Methods: We analyzed patients hospitalized with COVID-19-like illness at 26 hospitals in 20 U.S. states admitted October 18, 2023-March 9, 2024. Using a test-negative, case-control design, we estimated the effectiveness of an updated 2023-2024 (Monovalent XBB.1.5) COVID-19 vaccine dose against sequence-confirmed XBB and JN lineage hospitalization using logistic regression. Odds of severe outcomes, including intensive care unit (ICU) admission and invasive mechanical ventilation (IMV) or death, were compared for JN versus XBB lineage hospitalizations using logistic regression. Results: 585 case-patients with XBB lineages, 397 case-patients with JN lineages, and 4,580 control-patients were included. VE in the first 7-89 days after receipt of an updated dose was 54.2% (95% CI = 36.1%-67.1%) against XBB lineage hospitalization and 32.7% (95% CI = 1.9%-53.8%) against JN lineage hospitalization. Odds of ICU admission (adjusted odds ratio [aOR] 0.80; 95% CI = 0.46-1.38) and IMV or death (aOR 0.69; 95% CI = 0.34-1.40) were not significantly different among JN compared to XBB lineage hospitalizations. Conclusions: Updated 2023-2024 COVID-19 vaccination provided protection against both XBB and JN lineage hospitalization, but protection against the latter may be attenuated by immune escape. Clinical severity of JN lineage hospitalizations was not higher relative to XBB lineage hospitalizations.

2.
bioRxiv ; 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38895234

ABSTRACT

Natural killer (NK) cells recognize target cells through germline-encoded activation and inhibitory receptors enabling effective immunity against viruses and cancer. The Ly49 receptor family in the mouse and killer immunoglobin-like receptor family in humans play a central role in NK cell immunity through recognition of MHC class I and related molecules. Functionally, these receptor families are involved in licensing and rejection of MHC-I-deficient cells through missing-self. The Ly49 family is highly polymorphic, making it challenging to detail the contributions of individual Ly49 receptors to NK cell function. Herein, we showed mice lacking expression of all Ly49s were unable to reject missing-self target cells in vivo, were defective in NK cell licensing, and displayed lower KLRG1 on the surface of NK cells. Expression of Ly49A alone on a H-2Dd background restored missing-self target cell rejection, NK cell licensing, and NK cell KLRG1 expression. Thus, a single inhibitory Ly49 receptor is sufficient to license NK cells and mediate missing-self in vivo.

3.
Microbiol Spectr ; : e0422523, 2024 Jun 24.
Article in English | MEDLINE | ID: mdl-38912809

ABSTRACT

SARS-CoV-2 molecular testing coupled with whole-genome sequencing is instrumental for real-time genomic surveillance. Genomic surveillance is critical for monitoring the spread of variants of concern (VOCs) as well as discovery of novel variants. Since the beginning of the pandemic, millions of SARS-CoV-2 genomes have been deposited into public sequence databases. This is the result of efforts of both national and regional diagnostic laboratories. In this study, we describe the results of SARS-CoV-2 genomic surveillance from February 2021 to June 2022 at a metropolitan hospital in the United States. We demonstrate that consistent daily sampling is sufficient to track the regional prevalence and emergence of VOCs and recapitulate national trends. Similar sampling efforts should be considered a viable option for local SARS-CoV-2 genomic surveillance at other regional laboratories. IMPORTANCE: In our manuscript, we describe the results of SARS-CoV-2 genomic surveillance from February 2021 to June 2022 at a metropolitan hospital in the United States. We demonstrate that consistent daily sampling is sufficient to track the regional prevalence and emergence of variants of concern (VOCs). Similar sampling efforts should be considered a viable option for local SARS-CoV-2 genomic surveillance at other regional laboratories. While the SARS-CoV-2 pandemic has evolved into a more endemic form, we still believe that additional real-world information about sampling, procedures, and data interpretation is valuable for ongoing as well as future genomic surveillance efforts. Our study should be of substantial interest to clinical virologists.

4.
Nat Commun ; 15(1): 4839, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38844462

ABSTRACT

Comparative genomics has revealed the rapid expansion of multiple gene families involved in immunity. Members within each gene family often evolved distinct roles in immunity. However, less is known about the evolution of their epigenome and cis-regulation. Here we systematically profile the epigenome of the recently expanded murine Ly49 gene family that mainly encode either inhibitory or activating surface receptors on natural killer cells. We identify a set of cis-regulatory elements (CREs) for activating Ly49 genes. In addition, we show that in mice, inhibitory and activating Ly49 genes are regulated by two separate sets of proximal CREs, likely resulting from lineage-specific losses of CRE activity. Furthermore, we find that some Ly49 genes are cross-regulated by the CREs of other Ly49 genes, suggesting that the Ly49 family has begun to evolve a concerted cis-regulatory mechanism. Collectively, we demonstrate the different modes of cis-regulatory evolution for a rapidly expanding gene family.


Subject(s)
Evolution, Molecular , Multigene Family , NK Cell Lectin-Like Receptor Subfamily A , Animals , Mice , NK Cell Lectin-Like Receptor Subfamily A/genetics , NK Cell Lectin-Like Receptor Subfamily A/metabolism , Regulatory Sequences, Nucleic Acid/genetics , Gene Expression Regulation , Killer Cells, Natural/immunology , Mice, Inbred C57BL
6.
J Intensive Care Med ; 39(6): 525-533, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38629466

ABSTRACT

RATIONALE: Recent studies suggest that both hypo- and hyperinflammatory acute respiratory distress syndrome (ARDS) phenotypes characterize severe COVID-19-related pneumonia. The role of lung Severe Acute Respiratory Syndrome - Coronavirus 2 (SARS-CoV-2) viral load in contributing to these phenotypes remains unknown. OBJECTIVES: To redefine COVID-19 ARDS phenotypes when considering quantitative SARS-CoV-2 RT-PCR in the bronchoalveolar lavage of intubated patients. To compare the relevance of deep respiratory samples versus plasma in linking the immune response and the quantitative viral loads. METHODS: Eligible subjects were adults diagnosed with COVID-19 ARDS who required mechanical ventilation and underwent bronchoscopy. We recorded the immune response in the bronchoalveolar lavage and plasma and the quantitative SARS-CoV-2 RT-PCR in the bronchoalveolar lavage. Hierarchical clustering on principal components was applied separately on the 2 compartments' datasets. Baseline characteristics were compared between clusters. MEASUREMENTS AND RESULTS: Twenty subjects were enrolled between August 2020 and March 2021. Subjects underwent bronchoscopy on average 3.6 days after intubation. All subjects were treated with dexamethasone prior to bronchoscopy, 11 of 20 (55.6%) received remdesivir and 1 of 20 (5%) received tocilizumab. Adding viral load information to the classic 2-cluster model of ARDS revealed a new cluster characterized by hypoinflammatory responses and high viral load in 23.1% of the cohort. Hyperinflammatory ARDS was noted in 15.4% of subjects. Bronchoalveolar lavage clusters were more stable compared to plasma. CONCLUSIONS: We identified a unique group of critically ill subjects with COVID-19 ARDS who exhibit hypoinflammatory responses but high viral loads in the lower airways. These clusters may warrant different treatment approaches to improve clinical outcomes.


Subject(s)
Bronchoalveolar Lavage Fluid , COVID-19 , Critical Illness , Cytokines , SARS-CoV-2 , Viral Load , Humans , COVID-19/immunology , COVID-19/diagnosis , Male , Female , Middle Aged , Bronchoalveolar Lavage Fluid/virology , Bronchoalveolar Lavage Fluid/chemistry , Cytokines/analysis , Cytokines/blood , Aged , Phenotype , Respiration, Artificial , Respiratory Distress Syndrome/virology , Bronchoscopy , Adult , COVID-19 Nucleic Acid Testing , Antibodies, Monoclonal, Humanized
7.
Nano Lett ; 24(1): 229-237, 2024 Jan 10.
Article in English | MEDLINE | ID: mdl-38146928

ABSTRACT

Rapid and accurate quantification of low-abundance protein biomarkers in biofluids can transform the diagnosis of a range of pathologies, including infectious diseases. Here, we harness ultrabright plasmonic fluors as "digital nanolabels" and demonstrate the detection and quantification of subfemtomolar concentrations of human IL-6 and SARS-CoV-2 alpha and variant proteins in clinical nasopharyngeal swab and saliva samples from COVID-19 patients. The resulting digital plasmonic fluor-linked immunosorbent assay (digital p-FLISA) enables detection of SARS-CoV-2 nucleocapsid protein, both in solution and in live virions. Digital p-FLISA outperforms the "gold standard" enzyme-linked immunosorbent assay (ELISA), having a nearly 7000-fold lower limit-of-detection, and outperforms a commercial antigen test, having over 5000-fold improvement in analytical sensitivity. Detection and quantification of very low concentrations of target proteins holds potential for early detection of pathological conditions, treatment monitoring, and personalized medicine.


Subject(s)
COVID-19 , Humans , Enzyme-Linked Immunosorbent Assay , COVID-19/diagnosis , Fluoroimmunoassay , SARS-CoV-2 , Biomarkers , Sensitivity and Specificity
8.
Open Forum Infect Dis ; 10(11): ofad518, 2023 Nov.
Article in English | MEDLINE | ID: mdl-37953814

ABSTRACT

Background: Despite improvements in prevention and treatment, severe coronavirus disease 2019 (COVID-19) is associated with high mortality. Phosphoinositide 3-kinase (PI3K) pathways contribute to cytokine and cell-mediated lung inflammation. We conducted a randomized, placebo-controlled, double-blind pilot trial to determine the feasibility, safety, and preliminary activity of duvelisib, a PI3Kδγ inhibitor, for the treatment of COVID-19 critical illness. Methods: We enrolled adults aged ≥18 years with a primary diagnosis of COVID-19 with hypoxic respiratory failure, shock, and/or new cardiac disease, without improvement after at least 48 hours of corticosteroid. Participants received duvelisib (25 mg) or placebo for up to 10 days. Participants had daily semi-quantitative viral load measurements performed. Dose modifications were protocol driven due to adverse events (AEs) or logarithmic change in viral load. The primary endpoint was 28-day overall survival (OS). Secondary endpoints included hospital and intensive care unit length of stay, 60-day OS, and duration of critical care interventions. Safety endpoints included viral kinetics and AEs. Exploratory endpoints included serial cytokine measurements and cytometric analysis. Results: Fifteen patients were treated in the duvelisib cohort, and 13 in the placebo cohort. OS at 28 days was 67% (95% confidence interval [CI], 38%-88%) compared to 62% (95% CI, 32%-86%) for placebo (P = .544). Sixty-day OS was 60% versus 46%, respectively (hazard ratio, 0.66 [95% CI, .22-1.96]; P = .454). Other secondary outcomes were comparable. Duvelisib was associated with lower inflammatory cytokines. Conclusions: In this pilot study, duvelisib did not significantly improve 28-day OS compared to placebo for severe COVID-19. Duvelisib appeared safe in this critically ill population and was associated with reduction in cytokines implicated in COVID-19 and acute respiratory distress syndrome, supporting further investigation. Clinical Trials Registration: NCT04372602.

9.
J Virol ; 97(6): e0063523, 2023 06 29.
Article in English | MEDLINE | ID: mdl-37223945

ABSTRACT

The stem-loop II motif (s2m) is an RNA structural element that is found in the 3' untranslated region (UTR) of many RNA viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Though the motif was discovered over 25 years ago, its functional significance is unknown. In order to understand the importance of s2m, we created viruses with deletions or mutations of the s2m by reverse genetics and also evaluated a clinical isolate harboring a unique s2m deletion. Deletion or mutation of the s2m had no effect on growth in vitro or on growth and viral fitness in Syrian hamsters in vivo. We also compared the secondary structure of the 3' UTR of wild-type and s2m deletion viruses using selective 2'-hydroxyl acylation analyzed by primer extension and mutational profiling (SHAPE-MaP) and dimethyl sulfate mutational profiling and sequencing (DMS-MaPseq). These experiments demonstrate that the s2m forms an independent structure and that its deletion does not alter the overall remaining 3'-UTR RNA structure. Together, these findings suggest that s2m is dispensable for SARS-CoV-2. IMPORTANCE RNA viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), contain functional structures to support virus replication, translation, and evasion of the host antiviral immune response. The 3' untranslated region of early isolates of SARS-CoV-2 contained a stem-loop II motif (s2m), which is an RNA structural element that is found in many RNA viruses. This motif was discovered over 25 years ago, but its functional significance is unknown. We created SARS-CoV-2 with deletions or mutations of the s2m and determined the effect of these changes on viral growth in tissue culture and in rodent models of infection. Deletion or mutation of the s2m element had no effect on growth in vitro or on growth and viral fitness in Syrian hamsters in vivo. We also observed no impact of the deletion on other known RNA structures in the same region of the genome. These experiments demonstrate that s2m is dispensable for SARS-CoV-2.


Subject(s)
Nucleotide Motifs , SARS-CoV-2 , Animals , Cricetinae , 3' Untranslated Regions/genetics , COVID-19/virology , Mesocricetus , Mutation , SARS-CoV-2/genetics , Nucleotide Motifs/genetics , RNA, Viral/chemistry , RNA, Viral/genetics
10.
medRxiv ; 2023 May 10.
Article in English | MEDLINE | ID: mdl-37214888

ABSTRACT

SARS-CoV-2 molecular testing coupled with whole genome sequencing is instrumental for real-time genomic surveillance. Genomic surveillance is critical for monitoring the spread of variants of concern (VOC) as well as novel variant discovery. Since the beginning of the pandemic millions of SARS-CoV-2 genomes have been deposited into public sequence databases. This is the result of efforts of both national and regional diagnostic laboratories. Here we describe the results of SARS-CoV-2 genomic surveillance from February 2021 to June 2022 at a metropolitan hospital in the USA. We demonstrate that consistent daily sampling is sufficient to track the regional prevalence and emergence of VOC. Similar sampling efforts should be considered a viable option for local SARS-CoV-2 genomic surveillance at other regional laboratories.

11.
bioRxiv ; 2023 Mar 16.
Article in English | MEDLINE | ID: mdl-36993345

ABSTRACT

The stem-loop II motif (s2m) is a RNA structural element that is found in the 3' untranslated region (UTR) of many RNA viruses including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Though the motif was discovered over twenty-five years ago, its functional significance is unknown. In order to understand the importance of s2m, we created viruses with deletions or mutations of the s2m by reverse genetics and also evaluated a clinical isolate harboring a unique s2m deletion. Deletion or mutation of the s2m had no effect on growth in vitro , or growth and viral fitness in Syrian hamsters in vivo . We also compared the secondary structure of the 3' UTR of wild type and s2m deletion viruses using SHAPE-MaP and DMS-MaPseq. These experiments demonstrate that the s2m forms an independent structure and that its deletion does not alter the overall remaining 3'UTR RNA structure. Together, these findings suggest that s2m is dispensable for SARS-CoV-2. IMPORTANCE: RNA viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) contain functional structures to support virus replication, translation and evasion of the host antiviral immune response. The 3' untranslated region of early isolates of SARS-CoV-2 contained a stem-loop II motif (s2m), which is a RNA structural element that is found in many RNA viruses. This motif was discovered over twenty-five years ago, but its functional significance is unknown. We created SARS-CoV-2 with deletions or mutations of the s2m and determined the effect of these changes on viral growth in tissue culture and in rodent models of infection. Deletion or mutation of the s2m element had no effect on growth in vitro , or growth and viral fitness in Syrian hamsters in vivo . We also observed no impact of the deletion on other known RNA structures in the same region of the genome. These experiments demonstrate that the s2m is dispensable for SARS-CoV-2.

12.
Nat Biomed Eng ; 7(12): 1556-1570, 2023 Dec.
Article in English | MEDLINE | ID: mdl-36732621

ABSTRACT

Lateral-flow assays (LFAs) are rapid and inexpensive, yet they are nearly 1,000-fold less sensitive than laboratory-based tests. Here we show that plasmonically active antibody-conjugated fluorescent gold nanorods can make conventional LFAs ultrasensitive. With sample-to-answer times within 20 min, plasmonically enhanced LFAs read out via a standard benchtop fluorescence scanner attained about 30-fold improvements in dynamic range and in detection limits over 4-h-long gold-standard enzyme-linked immunosorbent assays, and achieved 95% clinical sensitivity and 100% specificity for antibodies in plasma and for antigens in nasopharyngeal swabs from individuals with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Comparable improvements in the assay's performance can also be achieved via an inexpensive portable scanner, as we show for the detection of interleukin-6 in human serum samples and of the nucleocapsid protein of SARS-CoV-2 in nasopharyngeal samples. Plasmonically enhanced LFAs outperform standard laboratory tests in sensitivity, speed, dynamic range, ease of use and cost, and may provide advantages in point-of-care diagnostics.


Subject(s)
Immunoconjugates , Nanoparticles , Humans , SARS-CoV-2 , Enzyme-Linked Immunosorbent Assay , Antibodies , Point-of-Care Testing
13.
Am J Perinatol ; 40(4): 341-347, 2023 03.
Article in English | MEDLINE | ID: mdl-35714654

ABSTRACT

OBJECTIVE: The management of incidentally found short cervical length (CL) without prior spontaneous preterm birth (PTB) can vary. While most agree on starting vaginal progesterone, management after CL shortens <10 mm varies. The purpose of this study was to elucidate current practice patterns amongst maternal-fetal medicine (MFM) specialists. STUDY DESIGN: We conducted an online survey of MFM attending physicians and fellows in the United States from May 2019 to April 2020. The primary outcome was management of varying CL based on gestational age. Variations in management were assessed descriptively. RESULTS: There were 236 respondents out of 400 eligible surveyed, with a response rate of 59.2%. Universal CL screening was reported by 93.6% (49.6% abdominal and 44.1% transvaginal). Management of short CL varied based on CL measurement, rather than gestational age at presentation. At CL <10 mm, management included cerclage (17.4-18.7%), vaginal progesterone (41.3-41.7%), or cerclage plus vaginal progesterone (43.4%). Between CL of 10 to 20 mm, the majority (77.4-91.9%) would start vaginal progesterone. At CL 21 to 25 mm, management varied between expectant management (45.5-48.5%) or vaginal progesterone (51.1-52.8%). Suture material used was ethylene terephthalate (47.4%) or polypropelene (31.2). Preoperative antibiotic use was reported by 22.3%, while 45.5% used them only if the amniotic membranes were exposed, and 32.2% reported no antibiotic use. Postoperative tocolytic use varied with 19.3% reporting no use, 32.6% using it always, 8.2% only after significant cervical manipulation, 22.7% after the patient is experiencing symptoms, and 17.6% using it only if the cervix is dilated on exam. After cerclage placement, 44.5% continued CL surveillance. CONCLUSION: Substantial differences of opinion exist among MFM physicians regarding management of incidentally found short CL in patients without history of PTB. The differences in responses obtained highlight the need for evidence-based guidelines for managing this clinical scenario. KEY POINTS: · There is lack of consensus on the management of incidentally found shortened CL.. · The purpose of this study was to elucidate current trends in CL screening and management.. · Substantial differences of opinion exist regarding management of incidentally found short CL..


Subject(s)
Cerclage, Cervical , Premature Birth , Pregnancy , Female , Infant, Newborn , Humans , Progesterone/therapeutic use , Pregnancy Trimester, Second , Cervix Uteri , Premature Birth/prevention & control , Premature Birth/epidemiology , Perinatology , Cervical Length Measurement
14.
Blood Adv ; 7(2): 236-245, 2023 01 24.
Article in English | MEDLINE | ID: mdl-36251745

ABSTRACT

Patients with multiple myeloma (MM) who are treated with lenalidomide rarely develop a secondary B-cell acute lymphoblastic leukemia (B-ALL). The clonal and biological relationship between these sequential malignancies is not yet clear. We identified 17 patients with MM treated with lenalidomide, who subsequently developed B-ALL. Patient samples were evaluated through sequencing, cytogenetics/fluorescence in situ hybridization (FISH), immunohistochemical (IHC) staining, and immunoglobulin heavy chain (IgH) clonality assessment. Samples were assessed for shared mutations and recurrently mutated genes. Through whole exome sequencing and cytogenetics/FISH analysis of 7 paired samples (MM vs matched B-ALL), no mutational overlap between samples was observed. Unique dominant IgH clonotypes between the tumors were observed in 5 paired MM/B-ALL samples. Across all 17 B-ALL samples, 14 (83%) had a TP53 variant detected. Three MM samples with sufficient sequencing depth (>500×) revealed rare cells (average of 0.6% variant allele frequency, or 1.2% of cells) with the same TP53 variant identified in the subsequent B-ALL sample. A lack of mutational overlap between MM and B-ALL samples shows that B-ALL developed as a second malignancy arising from a founding population of cells that likely represented unrelated clonal hematopoiesis caused by a TP53 mutation. The recurrent variants in TP53 in the B-ALL samples suggest a common path for malignant transformation that may be similar to that of TP53-mutant, treatment-related acute myeloid leukemia. The presence of rare cells containing TP53 variants in bone marrow at the initiation of lenalidomide treatment suggests that cellular populations containing TP53 variants expand in the presence of lenalidomide to increase the likelihood of B-ALL development.


Subject(s)
Burkitt Lymphoma , Lenalidomide , Multiple Myeloma , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma , Humans , Bone Marrow/pathology , Burkitt Lymphoma/pathology , Immunoglobulin Heavy Chains/genetics , In Situ Hybridization, Fluorescence , Lenalidomide/adverse effects , Lenalidomide/therapeutic use , Multiple Myeloma/drug therapy , Mutation , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/pathology
15.
Genet Med ; 25(3): 100348, 2023 03.
Article in English | MEDLINE | ID: mdl-36571464

ABSTRACT

PURPOSE: RAS genes (HRAS, KRAS, and NRAS) are commonly found to be mutated in cancers, and activating RAS variants are also found in disorders of somatic mosaicism (DoSM). A survey of the mutational spectrum of RAS variants in DoSM has not been performed. METHODS: A total of 938 individuals with suspected DoSM underwent high-sensitivity clinical next-generation sequencing-based testing. We investigated the mutational spectrum and genotype-phenotype associations of mosaic RAS variants. RESULTS: In this article, we present a series of individuals with DoSM with RAS variants. Classic hotspots, including Gly12, Gly13, and Gln61 constituted the majority of RAS variants observed in DoSM. Furthermore, we present 12 individuals with HRAS and KRAS in-frame duplication/insertion (dup/ins) variants in the switch II domain. Among the 18.3% individuals with RAS in-frame dup/ins variants, clinical findings were mainly associated with vascular malformations. Hotspots were associated with a broad phenotypic spectrum, including vascular tumors, vascular malformations, nevoid proliferations, segmental overgrowth, digital anomalies, and combinations of these. The median age at testing was higher and the variant allelic fraction was lower in individuals with in-frame dup/ins variants than those in individuals with mosaic RAS hotspots. CONCLUSION: Our work provides insight into the allelic and clinical heterogeneity of mosaic RAS variants in nonmalignant conditions.


Subject(s)
Mosaicism , Vascular Malformations , Humans , Proto-Oncogene Proteins p21(ras)/genetics , Mutation , Alleles , Vascular Malformations/genetics
16.
HLA ; 100(6): 662-664, 2022 12.
Article in English | MEDLINE | ID: mdl-35933577

ABSTRACT

DQA1*01:99 differs from DQA1*01:01 by a missense nucleotide substitution in exon 4.


Subject(s)
High-Throughput Nucleotide Sequencing , Humans , Alleles , Sequence Analysis, DNA , HLA-DQ alpha-Chains/genetics
17.
J Clin Microbiol ; 60(6): e0060022, 2022 06 15.
Article in English | MEDLINE | ID: mdl-35582905

ABSTRACT

Mutations in the genome of SARS-CoV-2 can affect the performance of molecular diagnostic assays. In some cases, such as S-gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here, we describe partial ORF1ab gene target failure (pOGTF) on the cobas SARS-CoV-2 assays, defined by a ≥2-thermocycle delay in detection of the ORF1ab gene compared to that of the E-gene. We demonstrate that pOGTF is 98.6% sensitive and 99.9% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may affect transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly, increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.


Subject(s)
COVID-19 , SARS-CoV-2 , Base Sequence , Humans , Mutation , SARS-CoV-2/genetics
18.
bioRxiv ; 2022 May 02.
Article in English | MEDLINE | ID: mdl-35547847

ABSTRACT

The stem-loop II motif (s2m) is an RNA element present in viruses from divergent viral families, including astroviruses and coronaviruses, but its functional significance is unknown. We created deletions or substitutions of the s2m in astrovirus VA1 (VA1), classic human astrovirus 1 (HAstV1) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). For VA1, recombinant virus could not be rescued upon partial deletion of the s2m or substitutions of G-C base pairs. Compensatory substitutions that restored the G-C base-pair enabled recovery of VA1. For HAstV1, a partial deletion of the s2m resulted in decreased viral titers compared to wild-type virus, and reduced activity in a replicon system. In contrast, deletion or mutation of the SARS-CoV-2 s2m had no effect on the ability to rescue the virus, growth in vitro , or growth in Syrian hamsters. Our study demonstrates the importance of the s2m is virus-dependent.

19.
medRxiv ; 2022 Apr 28.
Article in English | MEDLINE | ID: mdl-35547854

ABSTRACT

Mutations in the viral genome of SARS-CoV-2 can impact the performance of molecular diagnostic assays. In some cases, such as S gene target failure, the impact can serve as a unique indicator of a particular SARS-CoV-2 variant and provide a method for rapid detection. Here we describe partial ORF1ab gene target failure (pOGTF) on the cobas ® SARS-CoV-2 assays, defined by a ≥2 thermocycles delay in detection of the ORF1ab gene compared to the E gene. We demonstrate that pOGTF is 97% sensitive and 99% specific for SARS-CoV-2 lineage BA.2.12.1, an emerging variant in the United States with spike L452Q and S704L mutations that may impact transmission, infectivity, and/or immune evasion. Increasing rates of pOGTF closely mirrored rates of BA.2.12.1 sequences uploaded to public databases, and, importantly increasing local rates of pOGTF also mirrored increasing overall test positivity. Use of pOGTF as a proxy for BA.2.12.1 provides faster tracking of the variant than whole-genome sequencing and can benefit laboratories without sequencing capabilities.

20.
Case Rep Womens Health ; 34: e00401, 2022 Apr.
Article in English | MEDLINE | ID: mdl-35242600

ABSTRACT

This is a case report of a 39-year-old patient, G5P1031, with monochorionic diamniotic twins at 30 weeks and 1 day of gestation, who developed mirror syndrome without twin-to-twin transfusion syndrome (TTTS) with a unique presentation of maternal and neonatal hyponatremia. Coinciding with severe hyponatremia were maternal symptoms of edema, nausea and vomiting, hypoalbuminemia, elevated uric acid, as well as fetal selective growth restriction, polyhydramnios, umbilical artery absent end diastolic flow and prolonged bradycardia of twin B. Given the poor status of twin B and the risks to twin A, the patient underwent emergent cesarean delivery. Hyponatremia in all three patients resolved in the following 48-72 h. Mirror syndrome is associated with significant maternal and fetal morbidity and mortality. In this case, severe hyponatremia posed additional risks. Therefore, electrolyte monitoring should be considered in both mother and neonate(s).

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