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1.
Skinmed ; 20(3): 197-204, 2022.
Article in English | MEDLINE | ID: covidwho-1918934

ABSTRACT

Falls in non-COVID-19-related hospital admissions during the pandemic affected the reasons for dermatology consultation and mode of consultation delivery. In order to assess the impact of the pandemic and the effects of telehealth on the inpatient dermatology service, we compared consultations completed between March 17, 2020 and October 31, 2020 with the same period of 2019. Dermatology received fewer consultations for management assistance during the pandemic, possibly due to patients with chronic dermatoses not meeting admission criteria or avoiding hospitalization. Consultations were also less likely to require laboratory work, imaging, and biopsies in 2020, potentially due to frequent consultation of benign conditions enabled by telehealth and stricter enforcement of only completing the biopsies necessary for acute inpatient management. Despite the shift toward remote consultations in 2020, the impact on diagnosis and management remained unchanged compared to 2019. Providers were less likely to document clinical improvement in 2020, potentially attributable to inferior communication regarding management recommendations or an increase in diagnoses not expected to improve. While remote consultations allowed dermatologists to provide comparable care during the pandemic, further research on clinical outcomes of remote consultations is required to maximize its benefits to patients and the healthcare system. (SKINmed. 2022;20:197-204).


Subject(s)
COVID-19 , Telemedicine , COVID-19/epidemiology , Humans , Inpatients , Referral and Consultation , Retrospective Studies
2.
Emerg Infect Dis ; 28(7): 1442-1445, 2022 07.
Article in English | MEDLINE | ID: covidwho-1917186

ABSTRACT

To detect new and changing SARS-CoV-2 variants, we investigated candidate Delta-Omicron recombinant genomes from Centers for Disease Control and Prevention national genomic surveillance. Laboratory and bioinformatic investigations identified and validated 9 genetically related SARS-CoV-2 viruses with a hybrid Delta-Omicron spike protein.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Computational Biology , Humans , SARS-CoV-2/genetics , United States/epidemiology
3.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-330917

ABSTRACT

Recombination between SARS-CoV-2 virus variants can result in different viral properties (e.g., infectiousness or pathogenicity). In this report, we describe viruses with recombinant genomes containing signature mutations from Delta and Omicron variants. These genomes are the first evidence for a Delta-Omicron hybrid Spike protein in the United States.

4.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-320180

ABSTRACT

Capabilities in continuous monitoring of key physiological parameters of disease have never been more important than in the context of the global COVID-19 pandemic. Soft, skin-mounted electronics that incorporate high-bandwidth, miniaturized motion sensors represent a powerful class of technology for digital, wireless measurements of mechano-acoustic (MA) signatures of both core vital signs (heart rate, respiratory rate, and temperature) and underexplored biomarkers (coughing count) with high fidelity and immunity to ambient noises. Here, we introduce an effort that integrates such an MA sensor, a cloud data infrastructure and data analytics approaches based on digital filtering and convolutional neural networks for comprehensive monitoring of COVID-19 infections in sick and healthy individuals in a population, both in the hospital and the home. This hardware/software system extracts diverse signatures of health status in an automated fashion from a single device and time series data stream. Unique features are in quantitative measurements of coughing and other vocal events, as indicators of both disease and infectiousness. Systematic imaging studies demonstrate direct correlations between the time and intensity of coughing, speaking and laughing and the total droplet production, as an approximate indicator of the probability for disease spread. The sensors, deployed on COVID-19 patients along with healthy controls in both inpatient and home settings, record coughing frequency and intensity continuously, along with a comprehensive collection of other biometrics, with recording times for individuals of more than a month after disease diagnosis. These pilot studies include 3,111 hours of data spanning 363 days from 37 COVID-19 patients (20 females, 17 males) with 27,651 coughs detected in total along with continuous measurements of heart rate, respiratory rate, physical activity, and skin temperature. Manual labeling of randomly sampled 10,258 vocal events from 11 COVID-19 patients (6 females, 5 males) suggests a sensitivity of 85% and a specificity of 96% in cough detection using automated algorithms. The collective results indicate a decaying trend of coughing frequency and intensity through the course of disease recovery, but with wide variations across patient populations. The methodology also opens opportunities to study patterns in biometrics across individuals and among different demographic groups.

5.
Nat Med ; 28(5): 1083-1094, 2022 05.
Article in English | MEDLINE | ID: covidwho-1671607

ABSTRACT

The coronavirus disease 2019 (COVID-19) pandemic has demonstrated a clear need for high-throughput, multiplexed and sensitive assays for detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses and their emerging variants. Here, we present a cost-effective virus and variant detection platform, called microfluidic Combinatorial Arrayed Reactions for Multiplexed Evaluation of Nucleic acids (mCARMEN), which combines CRISPR-based diagnostics and microfluidics with a streamlined workflow for clinical use. We developed the mCARMEN respiratory virus panel to test for up to 21 viruses, including SARS-CoV-2, other coronaviruses and both influenza strains, and demonstrated its diagnostic-grade performance on 525 patient specimens in an academic setting and 166 specimens in a clinical setting. We further developed an mCARMEN panel to enable the identification of 6 SARS-CoV-2 variant lineages, including Delta and Omicron, and evaluated it on 2,088 patient specimens with near-perfect concordance to sequencing-based variant classification. Lastly, we implemented a combined Cas13 and Cas12 approach that enables quantitative measurement of SARS-CoV-2 and influenza A viral copies in samples. The mCARMEN platform enables high-throughput surveillance of multiple viruses and variants simultaneously, enabling rapid detection of SARS-CoV-2 variants.


Subject(s)
COVID-19 , Influenza, Human , COVID-19/diagnosis , Humans , Microfluidics , SARS-CoV-2/genetics
7.
Am J Emerg Med ; 53: 286.e5-286.e7, 2022 03.
Article in English | MEDLINE | ID: covidwho-1432723

ABSTRACT

INTRODUCTION: The World Health Organization (WHO) declared severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) a pandemic in March 2020. Theoretically, homeless patients could have disproportionately worse outcomes from COVID-19, but little research has corroborated this claim. This study aimed to examine the demographics and incidence of COVID-19 in homeless vs non-homeless emergency department (ED) patients. METHODS: This is a retrospective study of all patients seen in the University of Louisville Hospital Emergency Department (ULH ED) from March 2019 to December 2020, excluding January and February 2020. Data was collected from the Kentucky Homeless Management Information System (HMIS) and ULH electronic health records. RESULTS: A total of 51,532 unique patients had 87,869 visits during the study period. There was a 18.1% decrease in homeless patient visits over the time period, which was similar to the decrease in non-homeless patient visits (19.2%). In the total population, 9471 individuals had known COVID-19 testing results, with a total of 610 positive (6.4% positivity rate). Of the 712 homeless ED patients, 39 tested positive (5.5% positivity rate). After adjusting for age, gender identity, race, and insurance, there was no statistically significant difference in test positivity between homeless and non-homeless patients, OR 1.23 (0.88, 1.73). Homeless patients were less likely to be admitted to either the intensive care unit (ICU) or hospital (OR = 0.55, 95% CI: OR 0.51, 0.60) as they were more likely to be discharged (OR = 1.65, 95% CI: 1.52, 1.79). CONCLUSION: Previous literature has indicated that higher disease burden, lack of access to social distancing, and poor hygiene would increase the risk of homeless individuals contracting COVID-19 and experiencing serious morbidity. However, this study found that homelessness was not an independent risk factor for COVID-19 infection.


Subject(s)
COVID-19/diagnosis , Emergency Service, Hospital/statistics & numerical data , Homeless Persons/statistics & numerical data , Adult , COVID-19/epidemiology , COVID-19 Testing/methods , COVID-19 Testing/statistics & numerical data , Emergency Service, Hospital/organization & administration , Female , Humans , Incidence , Kentucky/epidemiology , Male , Middle Aged , Retrospective Studies
8.
PLoS One ; 16(8): e0256352, 2021.
Article in English | MEDLINE | ID: covidwho-1360648

ABSTRACT

Rapid tests for SARS-COV-2 infection are important tools for pandemic control, but current rapid tests are based on proprietary designs and reagents. We report clinical validation results of an open-access lateral flow assay (OA-LFA) design using commercially available materials and reagents, along with RT-qPCR and commercially available comparators (BinaxNOW® and Sofia®). Adult patients with suspected COVID-19 based on clinical signs and symptoms, and with symptoms ≤7 days duration, underwent anterior nares (AN) sampling for the OA-LFA, Sofia®, BinaxNOW ™, and RT-qPCR, along with nasopharyngeal (NP) RT-qPCR. Results indicate a positive predictive agreement with NP sampling as 69% (60% -78%) OA-LFA, 74% (64% - 82%) Sofia®, and 82% (73% - 88%) BinaxNOW™. The implication for these results is that we provide an open-access LFA design that meets the minimum WHO target product profile for a rapid test, that virtually any diagnostic manufacturer could produce.


Subject(s)
Antigens, Viral/analysis , COVID-19/diagnosis , Immunoassay , SARS-CoV-2/metabolism , Area Under Curve , COVID-19/virology , Humans , Nasopharynx/virology , Point-of-Care Systems , RNA, Viral/analysis , RNA, Viral/metabolism , ROC Curve , Real-Time Polymerase Chain Reaction , SARS-CoV-2/isolation & purification , Sensitivity and Specificity
9.
Emerg Infect Dis ; 27(7): 1821-1830, 2021.
Article in English | MEDLINE | ID: covidwho-1278363

ABSTRACT

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in late 2019, and the outbreak rapidly evolved into the current coronavirus disease pandemic. SARS-CoV-2 is a respiratory virus that causes symptoms similar to those caused by influenza A and B viruses. On July 2, 2020, the US Food and Drug Administration granted emergency use authorization for in vitro diagnostic use of the Influenza SARS-CoV-2 Multiplex Assay. This assay detects influenza A virus at 102.0, influenza B virus at 102.2, and SARS-CoV-2 at 100.3 50% tissue culture or egg infectious dose, or as few as 5 RNA copies/reaction. The simultaneous detection and differentiation of these 3 major pathogens increases overall testing capacity, conserves resources, identifies co-infections, and enables efficient surveillance of influenza viruses and SARS-CoV-2.


Subject(s)
COVID-19 , Influenza A virus , Humans , Influenza A virus/genetics , Influenza B virus/genetics , Multiplex Polymerase Chain Reaction , Reverse Transcription , SARS-CoV-2
10.
Proc Natl Acad Sci U S A ; 118(19)2021 05 11.
Article in English | MEDLINE | ID: covidwho-1203480

ABSTRACT

Capabilities in continuous monitoring of key physiological parameters of disease have never been more important than in the context of the global COVID-19 pandemic. Soft, skin-mounted electronics that incorporate high-bandwidth, miniaturized motion sensors enable digital, wireless measurements of mechanoacoustic (MA) signatures of both core vital signs (heart rate, respiratory rate, and temperature) and underexplored biomarkers (coughing count) with high fidelity and immunity to ambient noises. This paper summarizes an effort that integrates such MA sensors with a cloud data infrastructure and a set of analytics approaches based on digital filtering and convolutional neural networks for monitoring of COVID-19 infections in sick and healthy individuals in the hospital and the home. Unique features are in quantitative measurements of coughing and other vocal events, as indicators of both disease and infectiousness. Systematic imaging studies demonstrate correlations between the time and intensity of coughing, speaking, and laughing and the total droplet production, as an approximate indicator of the probability for disease spread. The sensors, deployed on COVID-19 patients along with healthy controls in both inpatient and home settings, record coughing frequency and intensity continuously, along with a collection of other biometrics. The results indicate a decaying trend of coughing frequency and intensity through the course of disease recovery, but with wide variations across patient populations. The methodology creates opportunities to study patterns in biometrics across individuals and among different demographic groups.


Subject(s)
COVID-19/physiopathology , Heart Rate , Respiratory Rate , Respiratory Sounds , SARS-CoV-2 , Wireless Technology , Biomarkers , Humans , Monitoring, Physiologic
11.
Nature ; 592(7852): 122-127, 2021 04.
Article in English | MEDLINE | ID: covidwho-1104508

ABSTRACT

During the evolution of SARS-CoV-2 in humans, a D614G substitution in the spike glycoprotein (S) has emerged; virus containing this substitution has become the predominant circulating variant in the COVID-19 pandemic1. However, whether the increasing prevalence of this variant reflects a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains unknown. Here we use isogenic SARS-CoV-2 variants to demonstrate that the variant that contains S(D614G) has enhanced binding to the human cell-surface receptor angiotensin-converting enzyme 2 (ACE2), increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a human ACE2 knock-in mouse model, and markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Our data show that the D614G substitution in S results in subtle increases in binding and replication in vitro, and provides a real competitive advantage in vivo-particularly during the transmission bottleneck. Our data therefore provide an explanation for the global predominance of the variant that contains S(D614G) among the SARS-CoV-2 viruses that are currently circulating.


Subject(s)
COVID-19/transmission , COVID-19/virology , Mutation , SARS-CoV-2/genetics , SARS-CoV-2/physiology , Spike Glycoprotein, Coronavirus/genetics , Virus Replication/genetics , Angiotensin-Converting Enzyme 2/genetics , Angiotensin-Converting Enzyme 2/metabolism , Animals , Bronchi/cytology , Bronchi/virology , COVID-19/epidemiology , Cell Line , Cells, Cultured , Cricetinae , Disease Models, Animal , Epithelial Cells/virology , Female , Ferrets/virology , Founder Effect , Gene Knock-In Techniques , Genetic Fitness , Humans , Male , Mesocricetus , Mice , Nasal Mucosa/cytology , Nasal Mucosa/virology , Protein Binding , RNA, Viral/analysis , Receptors, Coronavirus/metabolism , SARS-CoV-2/metabolism , SARS-CoV-2/pathogenicity
12.
bioRxiv ; 2020 Oct 27.
Article in English | MEDLINE | ID: covidwho-915978

ABSTRACT

During the evolution of SARS-CoV-2 in humans a D614G substitution in the spike (S) protein emerged and became the predominant circulating variant (S-614G) of the COVID-19 pandemic 1 . However, whether the increasing prevalence of the S-614G variant represents a fitness advantage that improves replication and/or transmission in humans or is merely due to founder effects remains elusive. Here, we generated isogenic SARS-CoV-2 variants and demonstrate that the S-614G variant has (i) enhanced binding to human ACE2, (ii) increased replication in primary human bronchial and nasal airway epithelial cultures as well as in a novel human ACE2 knock-in mouse model, and (iii) markedly increased replication and transmissibility in hamster and ferret models of SARS-CoV-2 infection. Collectively, our data show that while the S-614G substitution results in subtle increases in binding and replication in vitro , it provides a real competitive advantage in vivo , particularly during the transmission bottle neck, providing an explanation for the global predominance of S-614G variant among the SARS-CoV-2 viruses currently circulating.

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