Sudden Acute Respiratory Syndrome Coronavirus Research Articles

Research trends on causes of Kawasaki disease in the COVID-19 era: focus on viral infections.

Despite studies on the etiology of Kawasaki disease (KD) ongoing for half a century since its discovery, its cause has not yet been clearly identified. Although the clinical, epidemiological, and pathophysiological characteristics of KD are presumed to be closely related to infectious diseases, studies of various pathogens to identify its etiology have been actively conducted. To date, bacteria, fungi, and viruses have been investigated to determine the relationship between KD and infection, among which viruses have attracted the most attention. In particular, during the coronavirus disease 2019 pandemic, there were many reports in Europe of a sharp increase in cases of Kawasaki-like disease (KLD), while conflicting reports that the prevalence of KD decreased due to thorough "social distancing" or "wearing mask" in Asian countries drew more attention regarding the association between KD and viral infection. Therefore, the differential diagnosis of KD from KLD with these similar spectra has become a very important issue; simultaneously, research to solve questions about the association between KD and viral infections, including sudden acute respiratory syndrome coronavirus 2, is drawing attention again. Moreover, a new concept has emerged that immune responses occurring in patients with KD can be caused by the pathogen itself as well as host cells damaged by infection. This paper summarizes the research trends into KD etiology and related pathophysiology, especially its association with viral infections, and present future research tasks to increase our understanding of KD.

Combination of cycle threshold time, absolute lymphocyte count and neutrophil:lymphocyte ratio is predictive of hypoxia in patients with SARS-CoV-2 infection.

BackgroundThere is currently no clinically validated biomarker to predict respiratory compromise in sudden acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Cycle threshold time (Ct), absolute lymphocyte count (AL) and neutrophil:lymphocyte ratio (NLR) have been previously evaluated for this purpose. We hypothesized that the combination of these parameters at presentation may be predictive of hypoxia (oxygen saturation <92%).MethodsData were collected on 118 patients with SARS-CoV-2 infection between May 2020 and April 2021. Demographics, clinical parameters and laboratory and radiological investigation results were recorded. Respiratory compromise (RC) was defined based on symptoms and signs, hypoxia and chest X-ray abnormalities.ResultsRC occurred in 61 (51.7%) of patients. The Ct, AL and NLR at median day 3 of illness were significantly different between patients with and without RC (Ct, RC vs not: 19.46±2.64 vs 22.62±3.37, p=0.0001; AL, RC vs not: 531.49±289.09 vs 764.69±481.79, p=0.0001; NLR, RC vs not: 3.42±0.75 vs 2.59±0.55, p=0.0001). Receiver operating characteristics analysis showed that a Ct <19.9, AL <630.8×103/μL and NLR >3.12 at median day 3 of symptoms was predictive of hypoxia on day 7 of illness (area under the curve 0.805, sensitivity 96.7%, specificity 69.1%). The predictive value for the parameters combined was significantly superior to their individual predictive power.ConclusionsCt, AL and NLR used in combination on day 3 of symptoms are predictive of hypoxia on day 7 of SARS-CoV-2 illness.

High-Throughput CRISPR-Cas13 SARS-CoV-2 Test.

The ability to control the spread of COVID-19 continues to be hampered by a lack of rapid, scalable, and easily deployable diagnostic solutions. We developed a diagnostic method based on CRISPR (clustered regularly interspaced short palindromic repeats) that can deliver sensitive, specific, and high-throughput detection of Sudden Acute Respiratory Syndrome-Coronavirus-2 (SARS-CoV-2). The assay utilizes SHERLOCK (Specific High-sensitivity Enzymatic Reporter unLOCKing) for the qualitative detection of SARS-CoV-2 RNA and may be performed directly on a swab or saliva sample without nucleic acid extraction. The assay uses a 384-well format and provides results in <1 hour. Assay performance was evaluated with 105 (55 negative, 50 positive) remnant SARS-CoV-2 specimens previously tested using Food and Drug Administration emergency use authorized assays and retested with a modified version of the Centers for Disease Control and Prevention (CDC) quantitative PCR with reverse transcription (RT-qPCR) assay. When combined with magnetic bead-based extraction, the high-throughput SHERLOCK SARS-CoV-2 assay was 100% concordant (n = 60) with the CDC RT-qPCR. When used with direct sample addition the high-throughput assay was also 100% concordant with the CDC RT-qPCR direct method (n = 45). With direct saliva sample addition, the negative and positive percentage agreements were 100% (15/15, 95% CI: 81.8-100%) and 88% (15/17, 95% CI: 63.6-98.5%), respectively, compared with results from a collaborating clinical laboratory. This high-throughput assay identifies SARS-CoV-2 from patient samples with or without nucleic acid extraction with high concordance to RT-qPCR methods. This test enables high complexity laboratories to rapidly increase their testing capacities with simple equipment.

Diminished and waning immunity to COVID-19 vaccination among hemodialysis patients in Israel: the case for a third vaccine dose.

ABSTRACTBackgroundHumoral responses to coronavirus disease 2019 (COVID-19) vaccines in hemodialysis (HD) patients can direct vaccination policy.MethodsWe compared 409 COVID-19-naïve HD patients from 13 HD units in Israel to 148 non-dialysis-dependent COVID-19-naïve controls. Twenty-four previously infected (antinucleocapsid positive) HD patients were analysed separately. Blood samples were obtained ≥14 days post-vaccination (BNT162b2, Pfizer/BioNTech) to assess seroconversion rates and titers of anti-spike (anti-S) and neutralizing antibodies.ResultsThe median time from vaccination to blood sample collection was 82 days [interquartile range (IAR) 64–87] and 89 days (IQR 68–96) for HD patients and controls, respectively. Seroconversion rates were lower in HD patients compared with controls for both anti-S and neutralizing antibodies (89% and 77% versus 99.3%, respectively; P < 0.0001). Antibody titers were also significantly lower in HD patients compared with controls {median 69.6 [IQR 33.2–120] versus 196.5 [IQR 118.5–246], P < 0.0001; geometric mean titer [GMT] 23.3 [95% confidence interval (CI) 18.7–29.1] versus 222.7 [95% CI 174–284], P < 0.0001, for anti-S and neutralizing antibodies, respectively}. Multivariate analysis demonstrated dialysis dependence to be strongly associated with lower antibody responses and antibody titers waning with time. Age, low serum albumin and low lymphocyte count were also associated with lower seroconversion rates and antibody titers. HD patients previously infected with sudden acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had no difference in their seroconversion rates or antibody titers compared with COVID-19-naïve patients.ConclusionThis study demonstrates diminished and waning humoral responses following COVID-19 vaccination in a large and diverse cohort of HD patients, including those previously infected with SARS-CoV-2. Considering these results and reduced vaccine effectiveness against variants of concern, in addition to continued social distancing precautions, a third booster dose should be considered in this population.

Viral load and rebound in children with coronavirus disease 2019 during the first outbreak in Daegu city.

BackgroundViral load and shedding duration are highly associated with the transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection. However, limited studies have reported on viral load or shedding in children and adolescents infected with sudden acute respiratory syndrome coronavirus 2 (SARS-CoV-2).PurposeThis study aimed to investigate the natural course of viral load in asymptomatic or mild pediatric cases.MethodsThirty-one children (<18 years) with confirmed SARS-CoV-2 infection were hospitalized and enrolled in this study. Viral loads were evaluated in nasopharyngeal swab samples using real-time reverse transcription polymerase chain reaction (E, RdRp, N genes). cycle threshold (Ct) values were measured when patients met the clinical criteria to be released from quarantine.ResultsThe mean age of the patients was 9.8 years, 18 (58%) had mild disease, and 13 (42%) were asymptomatic. Most children were infected by adult family members, most commonly by their mothers. The most common symptoms were fever and sputum (26%), followed by cough and runny nose. Nine patients (29%) had a high or intermediate viral load (Ct value≤30) when they had no clinical symptoms. Viral load showed no difference between symptomatic and asymptomatic patients. Viral rebounds were found in 15 cases (48%), which contributed to prolonged viral detection. The mean duration of viral detection was 25.6 days. Viral loads were significantly lower in patients with viral rebounds than in those with no rebound (E, P=0.003; RdRp, P=0.01; N, P=0.02).ConclusionOur study showed that many pediatric patients with coronavirus disease 2019 (COVID-19) experienced viral rebound and showed viral detection for more than 3 weeks. Further studies are needed to investigate the relationship between viral rebound and infectiousness in COVID-19.

Differentiation of immortalized human multi-lineage progenitor to alveolar type 2-like cells: angiotensin-converting enzyme 2 expression and binding of severe acute respiratory syndrome coronavirus 2 spike and spike 1 proteins

Along with the nasal epithelium, the lung epithelium is a portal of entry for sudden acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and many other respiratory viruses. In the case of SARS-CoV-2, the virus surface spike proteins bind to the angiotensin-converting enzyme 2 (ACE-2) receptor to facilitate entry into the respiratory epithelium. Alveolar type 2 (AT2) cells are committed respiratory progenitor cells responsible for the integrity and regeneration of the respiratory epithelium and production of respiratory surfactant proteins. AT2 cells express high levels of surface ACE-2 and thus are a leading target for primary infection by SARS-CoV-2. This study describes a method for directly differentiating telomerase reverse transcriptase-immortalized human cord blood-derived multi-lineage progenitor cells (MLPCs) to AT2-like cells for the purpose of generating an in vitro cellular platform for viral studies. Differentiation was confirmed with the acquisition of AT2 and absence of alveolar type 1 (AT1) specific markers by confocal microscopy. Expression of the ACE-2 receptor was confirmed by immunofluorescence antibody staining, quantitative reverse transcription polymerase chain reaction and binding of biotinylated SARS-CoV-2 spike and spike 1 proteins. The binding of biotinylated spike proteins was specifically blocked by unlabeled spike proteins and neutralizing antibodies. Additionally, it was demonstrated that the spike protein was internalized after binding to the surface membrane of the cells. The authors defined the culture conditions that enabled AT2-like cells to be repeatedly passaged and cryopreserved without further differentiation to AT1. The authors’ method provides a stable and renewable source of AT2 cells for respiratory viral binding, blocking and uptake studies.

Humoral response to a third injection of BNT162b2 vaccine in patients on maintenance haemodialysis.

BackgroundHumoral response against sudden acute respiratory syndrome coronavirus 2 (SARS-CoV-2) after two doses of BNT162b2 (Pfizer-BioNTech) has been proven to be less intense in maintenance dialysis patients as compared with healthy subjects, leading the French authorities to recommend a third injection in this population. Here we investigated the response to the third injection in two cohorts of haemodialysis (HD) patients.MethodsData from two prospective observational cohorts were collected. In the first (‘systematic’) cohort, patients from two HD centres (n = 66) received a third injection of BNT162b2, regardless of the response after two injections. In the second (‘conditional’) cohort, the injection was only prescribed to patients (n = 34) with no or low response to the previous two doses. In both cohorts, the third dose was injected 1–2 months after the second dose. Serology was performed after the second and third doses to assess anti-Spike immunoglobulin G (S IgG) antibody titre.ResultsIn the systematic cohort, anti-S IgG was found in 83.3 and 92.4% of patients after the second and third doses of BNT162b2, respectively. In this cohort, 6/11 (54.5%) and 20/21 (95.2%) patients switched from non-responder to low responder and from low responder to high responder, respectively. In low and high responders to two doses, 50/55 (90.9%) at least doubled their anti-S IgG titre. Similar trends were observed in the conditional cohort.ConclusionsIn maintenance HD patients, humoral response against SARS-CoV-2 was boosted after a third dose of BNT162b2, allowing seroconversion in more than half of non-responders. These data may support an intensified vaccination protocol with a third dose of BNT162b2 in dialysis patients.

A rigorous evaluation of optimal peptide targets for MS-based clinical diagnostics of Coronavirus Disease 2019 (COVID-19)

BackgroundThe Coronavirus Disease 2019 (COVID-19) global pandemic has had a profound, lasting impact on the world's population. A key aspect to providing care for those with COVID-19 and checking its further spread is early and accurate diagnosis of infection, which has been generally done via methods for amplifying and detecting viral RNA molecules. Detection and quantitation of peptides using targeted mass spectrometry-based strategies has been proposed as an alternative diagnostic tool due to direct detection of molecular indicators from non-invasively collected samples as well as the potential for high-throughput analysis in a clinical setting; many studies have revealed the presence of viral peptides within easily accessed patient samples. However, evidence suggests that some viral peptides could serve as better indicators of COVID-19 infection status than others, due to potential misidentification of peptides derived from human host proteins, poor spectral quality, high limits of detection etc.MethodsIn this study we have compiled a list of 636 peptides identified from Sudden Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) samples, including from in vitro and clinical sources. These datasets were rigorously analyzed using automated, Galaxy-based workflows containing tools such as PepQuery, BLAST-P, and the Multi-omic Visualization Platform as well as the open-source tools MetaTryp and Proteomics Data Viewer (PDV).ResultsUsing PepQuery for confirming peptide spectrum matches, we were able to narrow down the 639-peptide possibilities to 87 peptides that were most robustly detected and specific to the SARS-CoV-2 virus. The specificity of these sequences to coronavirus taxa was confirmed using Unipept and BLAST-P. Through stringent p-value cutoff combined with manual verification of peptide spectrum match quality, 4 peptides derived from the nucleocapsid phosphoprotein and membrane protein were found to be most robustly detected across all cell culture and clinical samples, including those collected non-invasively.ConclusionWe propose that these peptides would be of the most value for clinical proteomics applications seeking to detect COVID-19 from patient samples. We also contend that samples harvested from the upper respiratory tract and oral cavity have the highest potential for diagnosis of SARS-CoV-2 infection from easily collected patient samples using mass spectrometry-based proteomics assays.

OUP accepted manuscript

BackgroundThe first serosurvey conducted in Chennai, India in July 2020 reported sudden acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prevalence of 18.4%. The aim of this study was to estimate the seroprevalence in the month of October 2020.MethodsWe conducted a survey in 153 streets covering 51 wards and all 15 zones of the city and enrolled from each street 40 individuals ≥10 y of age. We collected 3–5 ml of venous blood and tested for anti-nucleocapsid (N) immunoglobulin (IgG) antibodies using a SARS-CoV-2 IgG assay. We estimated the weighted seroprevalence of SARS-CoV-2 infection and adjusted for test characteristics.ResultsOf the 6366 sera tested, 2052 were positive for anti-N IgG antibodies. The weighted seroprevalence after adjusting for test characteristics was 30.1% (95% confidence interval [CI] 24.7 to 36.1). There was wide variation in the seroprevalence between wards, ranging from 11.0% (95% CI 5.6 to 16.4) to 48.1% (95% CI 39.5 to 56.7).ConclusionsThe seroprevalence of SARS-CoV-2 infection in Chennai nearly doubled between July and October 2020.

RT-qPCR half-reaction optimization for the detection of SARS-CoV-2.

INTRODUCTION: The main laboratory test for the diagnosis of coronavirus disease 2019 (COVID-19) is the reverse transcription real-time polymerase chain reaction (RT-qPCR). However, RT-qPCR is expensive because of the number of tests required. This study aimed to evaluate an alternative to the RT-qPCR approach for the detection of sudden acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that is half of the total volume currently recommended by the US Centers for Disease Control and Prevention. METHODS: The analytical limit of detection (LoD) and the reaction efficiency using half volumes of the RT-qPCR assay were evaluated for the N1 and N2 regions using a synthetic control RNA. A panel of 76 SARS-CoV-2-positive and 26 SARS-CoV-2-negative clinical samples was evaluated to establish clinical sensitivity and specificity. RESULTS: The RT-qPCR assay efficiency was 105% for the half and standard reactions considering the N2 target and 84% (standard) and 101% (half) for N1. The RT-qPCR half-reaction LoD for N1 and N2 were 20 and 80 copies/µL, respectively. The clinical sensitivity and specificity were 100%. The half reaction presented a decrease of up to 5.5 cycle thresholds compared with standard RT-qPCR. CONCLUSIONS: The use of the RT-qPCR half-reaction proved feasible and economic for the detection of SARS-CoV-2 RNA.

NIH Workshop Report: sensory nutrition and disease

In November 2019, the NIH held the “Sensory Nutrition and Disease” workshop to challenge multidisciplinary researchers working at the interface of sensory science, food science, psychology, neuroscience, nutrition, and health sciences to explore how chemosensation influences dietary choice and health. This report summarizes deliberations of the workshop, as well as follow-up discussion in the wake of the current pandemic. Three topics were addressed: A) the need to optimize human chemosensory testing and assessment, B) the plasticity of chemosensory systems, and C) the interplay of chemosensory signals, cognitive signals, dietary intake, and metabolism. Several ways to advance sensory nutrition research emerged from the workshop: 1) refining methods to measure chemosensation in large cohort studies and validating measures that reflect perception of complex chemosensations relevant to dietary choice; 2) characterizing interindividual differences in chemosensory function and how they affect ingestive behaviors, health, and disease risk; 3) defining circuit-level organization and function that link and interact with gustatory, olfactory, homeostatic, visceral, and cognitive systems; and 4) discovering new ligands for chemosensory receptors (e.g., those produced by the microbiome) and cataloging cell types expressing these receptors. Several of these priorities were made more urgent by the current pandemic because infection with sudden acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the ensuing coronavirus disease of 2019 has direct short- and perhaps long-term effects on flavor perception. There is increasing evidence of functional interactions between the chemosensory and nutritional sciences. Better characterization of this interface is expected to yield insights to promote health, mitigate disease risk, and guide nutrition policy.

The probability of the 6-week lockdown in Victoria (commencing 9 July 2020) achieving elimination of community transmission of SARS-CoV-2.

The probability of the 6-week lockdown in Victoria (commencing 9 July 2020) achieving elimination of community transmission of SARS-CoV-2.

COVID-19: Why Has the Mortality Rate Declined?

This article explains how the mortality rate of an illness such as Coronavirus Disease 2019 (COVID-19) is calculated as well as how the definition of what is a "case" has changed from the earliest days of the pandemic to now. Many factors were not known about The Sudden Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) which causes COVID-19 at the beginning of the pandemic because it is a novel human pathogen. One key factor that was not known in the earliest days of the pandemic was that many patients are either asymptomatic or have symptoms so mild that they may not seek medical attention and hence these patients would not be identified as a "case" if that term is defined as being sufficiently symptomatic to be seeking medical attention. Cases in the earliest days of the pandemic were defined as based on having symptoms (eg, fever, cough, respiratory distress) after ruling out other possible causes. Cases now are defined by tests confirming that the person is shedding the SARS-CoV-2 (ie, a laboratory vs. a symptomatic diagnosis). The mortality rate of this virus dropped as a function of this change. On the basis of the results of an unintended, naturalistic experiment on an expeditionary cruise in March of 2020, there was more than a 5-fold drop in the calculated mortality rate due to this definitional change in what constituted a case. This column explains this issue and discusses its implications for effectively dealing with the SARS-CoV-2 (or COVID-19) pandemic.

Childhood detention during COVID-19 in Italy: building momentum for a comprehensive child protection agenda.

Childhood detention represents an integral part of the public health response to the COVID-19 emergency. Prison conditions in Italy put detained minors at grave risk of contracting sudden acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. To date (29 April 2020), the Italian penitentiary system is housing 161 minors (147 males), most of them in pre-trial custody, as well as 50 children <3 y of age residing with their mothers in detention. Furthermore, the government reported 5265 unaccompanied minor migrants, mainly from Gambia and Egypt. The fundamental approach to be followed in childhood detention during COVID-19 is prevention of the introduction of infectious agents into detention facilities, limiting the spread within the prison and reducing the possibility of spread from the prison to the outside community. This appears challenging in countries like Italy with intense SARS-CoV-2 transmission. The current COVID-19 pandemic shows the need to provide a comprehensive childhood protection agenda, as the provision of healthcare for people in prisons and other places of detention is a state responsibility.

Assessment of Sensitivity and Specificity of Patient-Collected Lower Nasal Specimens for Sudden Acute Respiratory Syndrome Coronavirus 2 Testing

This prognostic study compares the diagnostic equivalence of patient-collected lower nasal specimens with that of health care worker–collected oropharyngeal specimens for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing.

Furin Protease: From SARS CoV-2 to Anthrax, Diabetes, and Hypertension.

Furin is a protease that is ubiquitous in mammalian metabolism. One of the innovations that make sudden acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) more infectious than its ancestor viruses is the addition of a furin cleavage site. Conditions associated with elevated furin levels, including diabetes, obesity, and hypertension, overlap greatly with vulnerability to the severe form of coronavirus disease 2019 (COVID-19). We suggest that diet and lifestyle modifications that reduce the associated comorbidities may prevent the development of severe COVID-19 by, in part, lowering circulating furin levels. Likewise, natural and pharmaceutical inhibitors of furin may be candidate prophylactic interventions or, if used early in the COVID-19, may prevent the development of critical symptoms.