Jointly modeling deep mutational scans identifies shifted mutational effects among SARS-CoV-2 spike homologs (preprint)

Deep mutational scanning (DMS) is a high-throughput experimental technique that measures the effects of thousands of mutations to a protein. These experiments can be performed on multiple homologs of a protein or on the same protein selected under multiple conditions. It is often of biological interest to identify mutations with shifted effects across homologs or conditions. However, it is challenging to determine if observed shifts arise from biological signal or experimental noise. Here, we describe a method for jointly inferring mutational effects across multiple DMS experiments while also identifying mutations that have shifted in their effects among experiments. A key aspect of our method is to regularize the inferred shifts, so that they are nonzero only when strongly supported by the data. We apply this method to DMS experiments that measure how mutations to spike proteins from SARS-CoV-2 variants (Delta, Omicron BA.1, and Omicron BA.2) affect cell entry. Most mutational effects are conserved between these spike homologs, but a fraction have markedly shifted. We experimentally validate a subset of the mutations inferred to have shifted effects, and confirm differences of >1,000-fold in the impact of the same mutation on spike-mediated viral infection across spikes from different SARS-CoV-2 variants. Overall, our work establishes a general approach for comparing sets of DMS experiments to identify biologically important shifts in mutational effects.

Acute Necrotizing Encephalopathy Post SARS-CoV-2 Infection in an Adult Patient: Case Report (preprint)

Purpose Show the MRI findings in a rare case of Acute Necrotizing Encephalopathy Post SARS-CoV-2 Infection in an Adult PatientIntroduction Acute necrotizing encephalopathy is a rare condition characterized by the presence of symmetrical multifocal lesions with predominantly thalamic involvement, as well as involvement of the brainstem, white matter of the brain, and cerebellum.Case Presentation We describe a case of a 26-year-old male, with a medical history of medulloblastoma that was disease-free after treatment, and who tested positive in a PCR for SARS-CoV-2 in cerebrospinal fluid. Upon evaluation at the emergency department one week later, the patient was found to be awake, oriented, and focused, and could maintain attention for periods. Mixed dysarthria persisted, characterized by being flaccid and hypokinetic. On magnetic resonance imaging, there were multiple hemorrhagic lesions with surrounding edema in the right thalamus with an extension to the posterior arm of the internal capsule, a smaller one, in the left thalamus, and another expanded to the ipsilateral peduncle.Conclusion Acute necrotizing encephalopathy presents a great clinical and diagnostic challenge, Close clinical and radiological follow-up is essential, and magnetic susceptibility sequences (T2 or SWI) should be included in the diagnosis protocol.

The BioVisualSpeech Serious Game with Voice Exercises for People with Parkinson's Disease with Hypokinetic Dysarthria.

People with Parkinson's disease (PD) can have dysarthria, a voice disorder that affects speech intelligibility. To fight this disorder people may resort to speech and language therapy. Unfortunately, weekly speech therapy sessions may not be enough, because to achieve and maintain good voice quality, intensive training is required. Additionally, the COVID-19 pandemic brought attention to the need for alternative speech therapy treatments that complement face-to-face appointments. Here, we propose a serious therapy game to improve voice loudness that can be used for intensive therapy or when face-to-face appointments are not possible. The game integrates three voice exercises used in speech therapy sessions for people with PD and aims to provide motivation for patients to perform the exercises on a daily basis. This application evaluates the vocal intensity, vocal frequency and maximum phonation time, offering real-time visual feedback. It also allows pathologists to customize the exercises difficulty to the needs of each patient.

Deep mutational scanning identifies SARS-CoV-2 Nucleocapsid escape mutations of currently available rapid antigen tests (preprint)

Widespread and frequent testing is critical to prevent the spread of COVID-19, and rapid antigen tests are the diagnostic tool of choice in many settings. With new viral variants continuously emerging and spreading rapidly, the effect of mutations on antigen test performance is a major concern. In response to the spread of variants the National Institutes of Health’s Rapid Acceleration of Diagnostics (RADx®) initiative created a Variant Task Force to assess the impact of emerging SARS-CoV-2 variants on in vitro diagnostic testing. To evaluate the impact of mutations on rapid antigen tests we developed a lentivirus-mediated mammalian surface-display platform for the SARS-CoV-2 Nucleocapsid protein, the target of the majority of rapid antigen tests. We employed deep mutational scanning (DMS) to directly measure the effect of all possible Nucleocapsid point mutations on antibody binding by 17 diagnostic antibodies used in 11 commercially available antigen tests with FDA emergency use authorization (EUA). The results provide a complete map of the antibodies’ epitopes and their susceptibility to mutational escape. This approach identifies linear epitopes, conformational epitopes, as well as allosteric escape mutations in any region of the Nucleocapsid protein. All 17 antibodies tested exhibit distinct escape mutation profiles, even among antibodies recognizing the same folded domain. Our data predict no vulnerabilities of rapid antigen tests for detection of mutations found in currently and previously dominant variants of concern and interest. We confirm this using the commercial tests and sequence-confirmed COVID-19 patient samples. The antibody escape mutation profiles generated here serve as a valuable resource for predicting the performance of rapid antigen tests against past, current, as well as any possible future variants of SARS-CoV-2, establishing the direct clinical and public health utility of our system. Further, our mammalian surface-display platform combined with DMS is a generalizable platform for complete mapping of protein-protein interactions.

Obtaining Objective Clinical Measures During Telehealth Evaluations of Dysarthria.

Purpose COVID-19 has shifted models of health care delivery, requiring the rapid adoption of telehealth, despite limited evidence and few resources to guide speech-language pathologists. Management of dysarthria presents specific challenges in the telehealth modality. Evaluations of dysarthria typically rely heavily on perceptual judgments, which are difficult to obtain via telehealth given a variety of technological factors such as inconsistencies in mouth-to-microphone distance, changes to acoustic properties based on device settings, and possible interruptions in connection that may cause video freezing. These factors limit the validity, reliability, and clinicians' certainty of perceptual speech ratings via telehealth. Thus, objective measures to supplement the assessment of dysarthria are essential. Method This tutorial outlines how to obtain objective measures in real time and from recordings of motor speech evaluations to support traditional perceptual ratings in telehealth evaluations of dysarthria. Objective measures include pause patterns, utterance length, speech rate, diadochokinetic rates, and overall speech severity. We demonstrate, through clinical case vignettes, how these measures were completed following three clinical telehealth evaluations of dysarthria conducted via Zoom during the COVID-19 pandemic. This tutorial describes how each of these objective measures were utilized, in combination with subjective perceptual analysis, to determine deviant speech characteristics and their etiology, develop a patient-specific treatment plan, and track change over time. Conclusion Utilizing objective measures as an adjunct to perceptual ratings for telehealth dysarthria evaluations is feasible under real-world pandemic conditions and can be used to enhance the quality and utility of these evaluations.

Dysphagia, Dysphonia, and Dysarthria Outcomes Among Adults Hospitalized With COVID-19 Across Ireland.

OBJECTIVE: To investigate the presence, degree, predictors, and trajectory of dysphagia, dysphonia, and dysarthria among adults hospitalized with COVID-19 across the Republic of Ireland (ROI) during the first wave of the pandemic. STUDY DESIGN: Prospective observational cohort study. METHODS: Adults with confirmed COVID-19 who were admitted into 14 participating acute hospitals across ROI and referred to speech and language therapy between March 1st and June 30th, 2020 were recruited. Outcomes obtained at initial SLT evaluation and at discharge were oral intake status (Functional Oral Intake Scale), perceptual voice quality (GRBAS), and global dysarthria rating (Dysarthria Severity Scale). RESULTS: Data from 315 adults were analyzed. At initial SLT assessment, 84% required modified oral diets, and 31% required tube feeding. There were high rates of dysphonia (42%) and dysarthria (23%). History of intubation (OR 19.959, 95% CI 6.272, 63.513; P = .000), COVID-19 neurological manifestations (OR 3.592, 95% CI 1.733, 7.445; P = .001), and age (OR 1.034; 95% CI 1.002, 1.066; P = .036) were predictive of oral intake status. History of intubation was predictive of voice quality (OR 4.250, 95% CI 1.838, 9.827; P = .001) and COVID-19 neurological manifestations were predictive of dysarthria (OR 2.275; 95% CI 1.162, 4.456; P = .017). At discharge, there were significant improvements in oral intake (Z = -7.971; P = .000), voice quality (Z = -5.971; P = .000), and dysarthria severity (Z = -2.619; P = .009), although need for modified oral intake (59%), dysphonia (23%), and dysarthria (14%) persisted. CONCLUSION: Dysphagia, dysphonia, and dysarthria were widespread among adults hospitalized with COVID-19 and they persisted for many at discharge. Prompt SLT evaluation is required to minimize complications. LEVEL OF EVIDENCE: 3 Laryngoscope, 132:1251-1259, 2022.

Myocardial Perfusion Spect Findings In Postcovid Period (preprint)

Purpose: To investigate if i) the risk of ischemia on Myocardial Perfusion Scan (MPS) ii) number of coronary angiographies (CAG) performed iii) necessity for invasive (stent implantation or coronary artery by-pass grefting (CABG)) or medical treatment increased in patients infected with COVID-19. Methods: : Patients who were referred to MPS between August 2020-April 2021 with a history of active symptomatic Covid-19 infection (confirmed by PCR positivity) in the last 6 months were involved in the study group. Age-and gender matched control group was composed of randomly chosen patients who attended for MPS between January 2019 – September 2019, before pandemic. Frequency of ischemia, CAG, invasive or medical treatments were compared between groups. Results: : Ischemia was reported more frequently in the study group (p<0.001). In clinical evaluation, regardless of the MPS results, the necessity for invasive evaluation with CAG and treatment (either medical therapy or invasive interventions), was higher in the study group (p=0.006 and p=0.015). It was also true for patients with abnormal MPS results (p=0.008 and p=0.024) but not for the patients with ischemia (p=0.29 and p=0.06). Conclusion: There exists a significant increase in the frequency of ischemia on MPS, undergoing CAG, stent implantation or CABG and initiation of medical therapy in patients with a history of Covid-19 infection in the last 6 months. MPS is a reliable method in patients who present with cardiovascular symptoms in the late COVID period.

An Expectation-Based Network Scan Statistic for a COVID-19 Early Warning System (preprint)

One of the Greater London Authority's (GLA) response to the COVID-19 pandemic brings together multiple large-scale and heterogeneous datasets capturing mobility, transportation and traffic activity over the city of London to better understand 'busyness' and enable targeted interventions and effective policy-making. As part of Project Odysseus we describe an early-warning system and introduce an expectation-based scan statistic for networks to help the GLA and Transport for London, understand the extent to which populations are following government COVID-19 guidelines. We explicitly treat the case of geographically fixed time-series data located on a (road) network and primarily focus on monitoring the dynamics across large regions of the capital. Additionally, we also focus on the detection and reporting of significant spatio-temporal regions. Our approach is extending the Network Based Scan Statistic (NBSS) by making it expectation-based (EBP) and by using stochastic processes for time-series forecasting, which enables us to quantify metric uncertainty in both the EBP and NBSS frameworks. We introduce a variant of the metric used in the EBP model which focuses on identifying space-time regions in which activity is quieter than expected.

Common Carotid Artery Occlusion in a Young Patient: Can Large-Vessel Stroke Be the Initial Clinical Manifestation of Coronavirus Disease 2019?

BACKGROUND: The occurrence of large-vessel occlusion in young patients with coronavirus disease 2019 (COVID-19) infection has been exceedingly rare. An extensive review of reported studies revealed a few reported cases. In the present report, we have described the clinical presentation, radiological findings, and outcome of large-vessel occlusion in a young patient with COVID-19 and reviewed the pertinent reported data on this condition. CASE DESCRIPTION: A 31-year-old woman was in her usual state of health until she had presented with a 3-day history of right-sided weakness, slurred speech, and decreased vision. The patient had been taken to several hospitals where she had been treated conservatively with analgesics and discharged. Shortly thereafter, her weakness had become progressive. She had become severely dysarthric and unresponsive. On arrival to the emergency department, her physical examination revealed that she was stuporous, with a Glasgow coma scale of 10 (eye response, 3; verbal response, 2; motor response, 5). The National Institutes of Health Stroke Scale score was 19 on presentation. Brain computed tomography and computed tomography venography revealed an occluded left internal carotid artery and left middle cerebral artery with subacute left middle cerebral artery territory infarction and midline shift. Computed tomography angiography revealed complete occlusion of the left common carotid artery. An emergent decompressive craniectomy was successfully performed. The patient was shifted to the intensive care unit. She was later found to be positive for COVID-19. CONCLUSIONS: Although rare, patients with COVID-19 can present with large-vessel occlusion. Prompt identification of COVID-19-related coagulopathy is essential to assess young patients with clinical manifestations of infarction.

The clinical spectrum of encephalitis in COVID-19 disease: the ENCOVID multicentre study (preprint)

Background: Several preclinical and clinical investigations have argued for nervous system involvement in SARS-CoV-2 infection. Some sparse case reports have described various forms of encephalitis in COVID-19 disease, but very few data have focused on clinical presentations, clinical course, response to treatment and outcomes yet. Objective: to describe the clinical phenotype, laboratory and neuroimaging findings of encephalitis associated with SARS-CoV-2 infection, their relationship with respiratory function and inflammatory parameters and their clinical course and response to treatment. Design: The ENCOVID multicentre study was carried out in 13 centres in northern Italy between February 20th and May 31st, 2020. Only patients with altered mental status and at least two supportive criteria for encephalitis with full infectious screening, CSF, EEG, MRI data and a confirmed diagnosis of SARS-CoV-2 infection were included. Clinical presentation and laboratory markers, severity of COVID-19 disease, response to treatment and outcomes were recorded. Results: Out of 45 cases screened, twenty-five cases of encephalitis positive for SARS-CoV-2 infection with full available data were included. The most common symptoms at onset were delirium (68%), aphasia/dysarthria (24%) and seizures (24%). CSF showed hyperproteinorrachia and/or pleocytosis in 68% of cases whereas SARS-CoV-2 RNA by RT-PCR resulted negative. Based on MRI, cases were classified as ADEM (n=3), limbic encephalitis (LE, n=2), encephalitis with normal imaging (n=13) and encephalitis with MRI alterations (n=7). ADEM and LE cases showed a delayed onset compared to the other encephalitis (p=0.001) and were associated with previous more severe COVID-19 respiratory involvement. Patients with MRI alterations exhibited worse response to treatment and final outcomes compared to other encephalitis. Conclusions and relevance: We found a wide clinical spectrum of encephalitis associated with COVID19 infection, underlying different pathophysiological mechanisms. Response to treatment and final outcome strongly depended on specific CNS-manifestations.

The 2019 novel coronavirus disease with secondary ischemic stroke: two cases report (preprint)

Background: The 2019 novel coronavirus disease is an outbreak of respiratory illness first detected in Wuhan, China in the end of Dec, 2019. The older patients complicated with underlying diseases are reported more likely to have clinical symptoms. But its secondary lesion is rarely reported. Case presentation We reported two cases of coronavirus infected pneumonia with acute ischemic stroke in patients at their middle-age. In both 2019 coronavirus diseases cases, neurological physical examination are normal before infection. Lymphocytopenia and high expression of cytokines and D-dimer were found from serum clinical laboratory test at admission. The dysarthria and limb muscle weakness are initial manifestations in one week after 2019 novel coronavirus infection. The head CT and head/neck arterial CTA showed small-vessel occlusion. The patients were diagnosed with coronavirus diseases with secondary acute ischemic stroke. They were treated with tirofiban and followed up with daily aspirin and atorvastatin. Conclusion: The present cases suggested that secondary ischemic stroke, which mainly manifested as small-vessel occlusion, should be considered for coronavirus disease patients with prompt diagnosis and treatment.