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2.
Front Immunol ; 13: 844749, 2022.
Article in English | MEDLINE | ID: covidwho-1809396

ABSTRACT

SARS-CoV-2 (severe acute respiratory syndrome coronavirus-2), a member of the coronavirus family, appeared in 2019 and has caused the largest global public health and economic emergency in recent history, affecting almost all sectors of society. SARS-CoV-2 is a single-stranded positive-sense RNA virus that relies on RNA-dependent RNA polymerase (RdRp) activity in viral transcription and replication. Due to its high sequence and structural conservation in coronavirus and new SARS-CoV-2 variants, RdRp has been recognized as the key therapeutic target to design novel antiviral strategies. Nucleotide analogs (NAs), such as remdesivir, is the most promising class of RdRp inhibitors to be used in the treatment of COVID-19. However, the presence of exonucleases in SARS-CoV-2 caused a great challenge to NAs; the excision of incorporated NAs will lead to viral resistance to this group of inhibitors. Here, we expressed active RdRp protein in both a eukaryotic expression system of baculovirus-infected insect cells and a prokaryotic expression system of Escherichia coli cells. Nsp7 and nsp8 of the functional RdRp holoenzyme were generated in E. coli. An in vitro RdRp activity assay has been established with a reconstituted nsp12/nsp7/nsp8 complex and biotin-labeled self-priming RNAs, and the activity of the RdRp complex was determined by detecting binding and extension of RNAs. Moreover, to meet the needs of high-throughput drug screening, we developed a fluorometric approach based on dsRNA quantification to assess the catalytic activity of the RdRp complex, which is also suitable for testing in 96-well plates. We demonstrated that the active triphosphate form of remdesivir (RTP) and several reported non-nucleotide analog viral polymerase inhibitors blocked the RdRp in the in vitro RdRp activity assay and high-throughput screening model. This high-throughput screening model has been applied to a custom synthetic chemical and natural product library of thousands of compounds for screening SARS-CoV-2 RdRp inhibitors. Our efficient RdRp inhibitor discovery system provides a powerful platform for the screening, validation, and evaluation of novel antiviral molecules targeting SARS-CoV-2 RdRp, particularly for non-nucleotide antivirals drugs (NNAs).


Subject(s)
COVID-19 , SARS-CoV-2 , Antiviral Agents/chemistry , Antiviral Agents/pharmacology , COVID-19/drug therapy , Escherichia coli/genetics , Humans , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/genetics
3.
J Korean Med Sci ; 37(16): e126, 2022 Apr 25.
Article in English | MEDLINE | ID: covidwho-1809347

ABSTRACT

BACKGROUND: The relationship between changes in anxiety levels and personal protective equipment (PPE) use is yet to be evaluated. The present study assessed this relationship among healthcare workers (HCWs) involved in the care of patients with coronavirus disease 2019 (COVID-19). METHODS: An online survey was conducted in a municipal hospital with 195 nationally designated negative pressure isolation units in Korea. Anxiety level was measured using the self-rating anxiety scale (SAS), and changes in anxiety levels were assessed based on the time when COVID-19 vaccine was introduced in March 2021 in Korea. Monthly PPE usage between June 2020 and May 2021 was investigated. RESULTS: The mean SAS score (33.25 ± 5.97) was within normal range and was lower than those reported in previous studies conducted before COVID-19 vaccination became available. Among the 93 HCWs who participated, 64 (68.8%) answered that their fear of contracting COVID-19 decreased after vaccination. The number of coveralls used per patient decreased from 33.6 to 0. However, a demand for more PPE than necessary was observed in situations where HCWs were exposed to body fluids and secretions (n = 38, 40.9%). Excessive demand for PPE was not related to age, working experience, or SAS score. CONCLUSION: Anxiety in HCWs exposed to COVID-19 was lower than it was during the early period of the pandemic, and the period before vaccination was introduced. The number of coveralls used per patient also decreased although an excessive demand for PPE was observed.


Subject(s)
COVID-19 , Personal Protective Equipment , Anxiety/epidemiology , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19 Vaccines , Health Personnel , Humans , SARS-CoV-2
5.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315888

ABSTRACT

Background: The re-emerging outbreak of COVID-19 in Beijing China in summer of 2020 was originated from a contaminated super food wholesale market. The transmission mechanism was analyzed. Methods: We hypothesized that the Xinfadi outbreak was associated with activities of food-trade. Therefore, all the confirmed cases were divided into groups of sellers, buyer, seller transmitted and buyer transmitted. Data for each case were georeferenced and aggregated to the 500m-spaced hexagon grids using geodata and base maps, road networks, urban points of interest from OpenStreetMap. The Xinfadi-related trade activity data were derived using Python crawling scripts. The spatial association of the outbreak was studied with Moran’s I statistic method and a Susceptible-Infected-Recovered (SIR) coupled Agent-Based Model (ABM). Findings: Of 335 cases reported, 177 (45·3%) were sellers who worked for the Market, 83 (23·7%) were buyers who visited the Market, and 74 were transmitted by either of the infected buyers or sellers. The Market was the outbreak center, which were spreading along the urban rapid transit lines. The areas with a high incidence were concentrated across neighborhoods in the southwest of Beijing's Fifth Ring Road and the west section of the Fourth Ring of southwestern Beijing, and the west portion of Fuxing Road. The highest number of seller transmission hubs were located in Market neighborhood, however the buyer transmission hubs extended to cover more than three different districts. Our SIR-ABM model analysis suggested that the trade-distancing strategy effectively reduced the R0. The retail shops closure strategy reduced nearly half number of visitors to market. The Buy-local policy option reduced more than 70% infection in total. Interpretation: The Xinfadi outbreak was associated contaminated super food market by people's movements for food-trade, including their interactions in related activities. Therefore, the retails closures and buy-local policy could reduce size of the outbreak and prevent possible outbreak in future.Funding Statement: Ministry of Science and Technology China (Grant number 2018ZX10712001-017 and 2018ZX10712001-018), Chinese Academy of Medical Sciences (2018RU010), Chinese Academy (2020-XZ-37) and the National Natural Science Foundation of China (71603253 and 72074209).Declaration of Interests: All authors declare no competing interests.

6.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-315595

ABSTRACT

Background: Since the first public genome of SARS-CoV-2, over 170,000 genome sequences of the virus have been shared by researchers world-wide (till November 1st 2020). Multiplex PCR targeting SARS-CoV-2 followed by massively parallel sequencing (MPS) and/or nanopore sequencing is a widely used strategy to recover the genome from primary samples. However, the bias of amplification among different amplicons should not be ignored, which might lead to uneven sequencing coverage on the viral genome.MethodsWe aim to develop a novel multiplex PCR panel to achieve an improved coverage evenness of SARS-CoV-2. We adapt long amplicons (~1000-bp) for the panel and thus reduced the number of primer pairs. The panel was validated with clinical samples and sequenced via MPS sequencing systems and a portable nanopore sequencing device MinION. We evaluated the full-genome coverage evenness and its dependence on viral loads of the long amplicon panel;we then compared it with a 98-plex panel provided by the ARTIC network. The accuracy to identify viral genomic variations based on the panel and sequencing with MinION was assessed.ResultsWe developed a two-pool 36-plex panel for full-genome sequencing of SARS-CoV-2, whose amplicon size ranged from 880 to 1027 bp. For samples with a <30 C t value, >90% viral genome could be recovered with a high sequencing depth (>0.2 mean depth) by using the long-amplicon panel (n = 36), compared with 79-88% highly covered genome region for the ARTIC panel (n = 5). The coverage evenness of the long-amplicon panel was also less affected by low viral titers and not dependent on sequencing data amount. With MinION sequencing, the consensus viral genomes could be reliably recovered. However, a high false positive rate was observed to identify sub-clonal genomic variations with a <0.6 frequency.ConclusionA novel multiplex PCR panel for full-genome sequencing of SARS-CoV-2 with improved coverage evenness and low requirement of data throughput was validated with clinical samples. Amplification of SARS-CoV-2 with the panel followed by MinION sequencing could generate reliable consensus genome sequences, but the detection of non-dominating viral populations within host is error-prone.

7.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-313588

ABSTRACT

Objectives: Few studies have investigated the contamination of personal protective equipment (PPE) during the management of patients with severe to critical coronavirus disease (COVID-19). This study aimed to determine the necessity of coveralls and foot cover for body protection during the management of patients with COVID-19. Methods PPE samples were collected from physicians exiting a room after the management of a patient with severe to critical COVID-19 who was within 14 days after symptom onset. The PPE sites were categorized into coverall-only parts (the frontal surface of the head, anterior neck, dorsal surface of the foot cover, and back and hip) and gown-covered parts (the anterior side of the forearm and the abdomen). Environmental sampling was performed in patient rooms. We tried to identify significant differences in contamination with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between the coverall-only and gown-covered parts. Results A total of 105 swabs from PPE and 28 swabs from patient rooms were collected. Of the PPE swabs, only three (2.8 %) swabs from gown-covered parts were contaminated by SARS-CoV-2. However, 23 of the total 28 sites (82.1%) from patient rooms were contaminated. There was significant difference in the contamination of PPE between coverall-only and gown-covered parts (0.0 vs 6.7%, p = 0.022). Conclusions Coverall contamination rarely occurred while managing severe to critical COVID-19 patients residing in negative pressure rooms in the early stages of the illness. Long-sleeved gowns may be used safely in the management of COVID-19 patients.

8.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-313360

ABSTRACT

The resurgence of coronavirus disease 2019 (COVID-19) has been seen in many counties where outbreaks appear to be leveling off. While China experienced a dramatic decline of COVID-19 at the outset of 2020, regional outbreaks continuously emerged in recent months. In Guangzhou, a small outbreak emerged in March and April involving less than 100 residents, and a comprehensive and near-real-time genomic surveillance of SARS-CoV-2 was conducted. When confirmed cases among overseas travelers increased, public health authorities enhanced measures as shifting self-quarantine to central quarantine and SARS-CoV-2 testing for all overseas travelers. From 109 imported cases we found diverse viral variants distributing in the global viral phylogeny, which were usually shared within households but not among passengers on the same flight. Nonetheless, local transmission was predominately attributed to two specific variants imported from Africa, including the local cases who reported no direct/indirect contact with imported cases. The introducing events of the virus were identified or deduced before enhanced measures were taken. These results show that the interventions are effective in containing the spread of SARS-CoV-2, and also rule out the possibility of cryptic transmission of viral variants from the first wave in January and February. Moreover, we found that intra-host viral diversity was usually different between close contacts, implying a transmission bottleneck of SARS-CoV-2. Our study provides evidence and emphasizes the importance of controls for oversea travelers in the context of the pandemic, and exemplifies how viral genomic data facilitates COVID-19 surveillance and prevention.Funding: This study was supported by National Natural Science Foundation of China (31870079, 91953122, 31871326), National Science and Technology Major Project of the Ministry of Science and Technology of China (2017ZX10103011, 2018ZX10305410, 2018ZX10201001), Guangdong Provincial Novel Coronavirus Scientific and Technological Project (2020111107001), Guangdong Basic and Applied Basic Research Foundation (2020A1515010776 and 2020B1515020057) and the Beijing Nova Program (Z181100006218114 and Z181100006218110) to M.N. and P.L..Conflict of Interest: The authors declare no competing interests.Ethical Approval: This study was approved by the ethics committee of the Center for Disease Control and Prevention (CDC) of Guangzhou (GZCDC-ECHR-2020P0002). Written informed consent was obtained from patients about the surveillance and data related to disease control and further analysis. All information regarding individual persons has been anonymized in this study.

9.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-325219

ABSTRACT

In the middle of March, the World Health Organization declared the outbreak of COVID-19 caused by SARS-CoV-2 infection a global pandemic. While China experienced a dramatic decline in daily growth rate of COVID-19, multiple importations of new cases from other countries and their related local infections caused a rapid rise. Between March 12 and April 15, we collected nasopharyngeal samples from 109 imported cases from 25 countries and 69 local cases in Guangzhou, China. In order to characterize the transmission patterns and genetic evolution of this virus among different populations, we sequenced the genome of SARS-CoV-2. The imported viral strains were assigned to lineages distributed in Europe (33.0%), America (17.4%), Africa (25.7%), or Southeast/West Asia (23.9%). Importantly, 10 imported cases from Africa formed two novel sub-lineages not identified in global tree previously. A detailed analysis showed that the imported viral strains from Philippines and Pakistan were closely related and within the same sub-lineage, whereas Ethiopia had varied lineages in the African phylogenetic tree. In spite of the diversity of imported SARS-CoV-2, 60 of 69 local infections could be traced back to two specific small lineages imported from Africa. A combined genetic and epidemiological analysis revealed a high-resolution transmission network of the imported SARS-CoV-2 in local communities, which might help inform the public health response and genomic surveillance in other cities and regions. Finally, we observed in-frame deletions on seven loci of SARS-CoV-2 genome, some of which were intra-host mutations, and they exhibited no enrichment on the S protein. Our findings provide new insight into the viral phylodynamics of SARS-CoV-2 and beta coronavirus.

10.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-323632

ABSTRACT

Background: Early warnings of emerging infectious disease are crucial to prevent epidemics. However, in the early stage of the COVID-19 pandemic, traditional infectious disease surveillance failed to deliver a warning alert. The aim of this work is to develop search-engine-based surveillance methods for the early warning and prediction of COVID-19 outbreaks. Methods: By using more than 444 million Baidu search queries from China as training set, we collected 32 keywords from the Baidu Search Index that may related to COVID-19 outbreak from 18 December 2019 to 11 February 2020. The Beijing Xinfadi outbreak from 30 May 2020 to 30 July 2020 was used as independent test set. A multiple linear regression was applied to model the relationship between the daily query frequencies of keywords and the daily new cases. Findings: Our results show that 11 keywords in search queries were highly correlated to the daily numbers of confirmed cases (r =0.96, P <0.01). An abnormal initial peak (1.46 times the normal volume) in queries appeared on 31 December 2019, which could have served as an early warning signal for an outbreak. Of particular concern, on this day, the volume of the query “Wuhan Seafood Market” increased by over 240 times (from 10 to 2410), the volume of the query “Wuhan outbreak” increased by over 622 times (from 7 to 4359), and 17.5% of China’s query volume originated from Hubei Province, 51.15% of which was from Wuhan city. The quantitative model using four keywords (“Epidemic”, “Masks”, “Coronavirus” and “Clustered pneumonia”) successfully predicted the daily numbers of cases for the next two days, and detected an early signal during the Beijing Xinfadi outbreak (R2 =0.80). Interpretation: Our study demonstrates the ability of search engine query data to detect COVID-19 outbreaks, and suggests that abnormalities in query volume can serve as early warning signals.

11.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-321830

ABSTRACT

Background: During the COVID-19 pandemic, people have been required to follow preventive measures such as government policy including the closure of exercise facilities and movement restriction, can lead to an unhealthy lifestyle. We investigated the effect of these preventive measures on metabolic parameters in individuals with cardiometabolic disorders. Methods: In the current retrospective observational study of patients who visited the hospital at least twice a year for the past 4 years, changes in cardiometabolic factors from the COVID-19 pandemic (2019–2020) were compared with changes in the same cohort at the same annual time points during the previous seasons of 2016–2019. Results: A total of 1,485 individuals with a mean age of 61.8 ± 11.7 years were included in the analysis. During the COVID-19 pandemic, the number of patients whose metabolic syndrome worsened increased significantly by 21% compared with the 2018–2019 season. The body mass index increased by 0.09 ± 1.16 kg/m2 in the 2019–2020 pandemic period, whereas it decreased by –0.39 ± 3.03 kg/m2 in 2018–2019 and by –0.34 ± 2.18 kg/m2 in 2017–2018 (both p < 0.05). Systolic blood pressure increased by 2.6 ± 18.2 mmHg in the COVID-19 pandemic period, while it decreased in the three antecedent seasons (all p < 0.05). The lipid profiles worsened in the pandemic period compared with the previous years. The Framingham coronary heart disease risk score also increased significantly. Conclusions: With preventive procedures during the contagious disease pandemic, nationwide strategies to maintain cardiometabolic health are necessary.

12.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-320007

ABSTRACT

Memory T-cell responses have been demonstrated after recovery from SARS-CoV-2 infection, but the phenotypes of SARS-CoV-2-specific T cells have not been comprehensively investigated ex vivo. We detected SARS-CoV-2-specific CD8+ T cells by MHC-I multimer staining and examined their phenotypes in relation to their functional capacity in acute and convalescent COVID-19. In the convalescent phase, multimer+ cells exhibited early differentiated effector-memory phenotypes. The frequency of CD127+KLRG1- memory precursor effector cells among multimer+ cells was significantly lower in convalescent individuals with severe disease than those with mild disease. Cytokine-secretion assays combined with MHC-I multimer staining revealed that the proportion of IFN-γ-producing cells was significantly lower among SARS-CoV-2-specific CD8+ T cells than those specific to other viruses. Importantly, the proportion of IFN-γ-producing cells was significantly higher in PD-1+ cells than PD-1- cells among multimer+ cells in both the acute and convalescence phases, indicating that PD-1-expressing, SARS-CoV-2-specific CD8+ T cells are not exhausted, but functional. Our findings provide insights for effective vaccine development.

13.
Journal of Virology ; 96(1):1-23, 2022.
Article in English | A9H | ID: covidwho-1647636

ABSTRACT

The replication of coronaviruses, including severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERSCoV), and the recently emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is closely associated with the endoplasmic reticulum (ER) of infected cells. The unfolded protein response (UPR), which is mediated by ER stress (ERS), is a typical outcome in coronavirus-infected cells and is closely associated with the characteristics of coronaviruses. However, the interaction between virus-induced ERS and coronavirus replication is poorly understood. Here, we demonstrate that infection with the betacoronavirus porcine hemagglutinating encephalomyelitis virus (PHEV) induced ERS and triggered all three branches of the UPR signaling pathway both in vitro and in vivo. In addition, ERS suppressed PHEV replication in mouse neuro-2a (N2a) cells primarily by activating the protein kinase R-like ER kinase (PERK)-eukaryotic initiation factor 2α (eIF2α) axis of the UPR. Moreover, another eIF2a phosphorylation kinase, interferon (IFN)-induced double-stranded RNA-dependent protein kinase (PKR), was also activated and acted cooperatively with PERK to decrease PHEV replication. Furthermore, we demonstrate that the PERK/PKR-eIF2a pathways negatively regulated PHEV replication by attenuating global protein translation. Phosphorylated eIF2a also promoted the formation of stress granules (SGs), which in turn repressed PHEV replication. In summary, our study presents a vital aspect of the host innate response to invading pathogens and reveals attractive host targets (e.g., PERK, PKR, and eIF2a) for antiviral drugs. [ FROM AUTHOR] Copyright of Journal of Virology is the property of American Society for Microbiology and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full . (Copyright applies to all s.)

14.
J Korean Med Sci ; 36(50): e343, 2021 Dec 27.
Article in English | MEDLINE | ID: covidwho-1594418

ABSTRACT

As hospitals cater to elderly and vulnerable patients, a high mortality rate is expected if a coronavirus disease 2019 (COVID-19) outbreak occurs. Consequently, policies to prevent the spread of COVID-19 in hospital settings are essential. This study was conducted to investigate how effectively national and international guidelines provide recommendations for infection control issues in hospitals. After selecting important issues in infection control, we performed a systematic review and analysis of recommendations and guidelines for preventing COVID-19 transmission within medical institutions at national and international levels. We analyzed guidelines from the World Health Organization, Centers for Disease Control and Prevention, European Centre for Disease Prevention and Control, and Korea Disease Control and Prevention Agency. Recent guidelines do not provide specific solutions to infection control issues. Therefore, efforts need to be made to devise consistent advice and guidelines for COVID-19 control.


Subject(s)
COVID-19/prevention & control , Infection Control/methods , Practice Guidelines as Topic , SARS-CoV-2 , Health Personnel , Humans
16.
Open forum infectious diseases ; 8(Suppl 1):S316-S317, 2021.
Article in English | EuropePMC | ID: covidwho-1564302

ABSTRACT

Background Infection control measures against the coronavirus disease 2019 (COVID-19) within a hospital often rely on expert experience and intuition due to the lack of clear guidelines. This study surveyed current strategies for the prevention of the spread of COVID-19 in medical institutions. Methods Upon systematic review of the guidelines at the national level, 14 key topics were selected. Six hospitals were provided an open survey that assessed their responses to these topics between August 11 and 25, 2020. Using these data, an online questionnaire was developed and sent to the infection control teams of 46 hospitals in South Korea. The survey was conducted between January 31, 2021, and February 20, 2021. Results All 46 hospitals responded to the survey, and 24 hospitals (52.2%) had treated 100 or more cases of COVID-19. All hospitals operated screening clinics, and the criteria were respiratory symptoms (100%), fever (97.8%), and epidemiological association (93.5%). It was found that 89.1% (41/46) of hospitals allowed symptomatic patients to visit their general outpatient clinics if fever or respiratory symptoms were not associated with COVID-19. Most hospitals (87.2%;34/39) conducted polymerase chain reaction (PCR) tests for all hospitalized patients. Moreover, 76.1% (35/46) of hospitals implemented preemptive isolation policies for hospitalized patients, of which 97.1% (34/35) were released from isolation after a single negative PCR test. A little over half of the hospitals (58.7%;27/46) treated patients that met the national criteria for release from isolation but consistently had positive PCR results. Of these hospitals, 63% (17/27) used N95/KF94 masks, and 40.7% (11/27) used surgical masks without other personal protective equipment for treating them. Most hospitals (76.9%;20/26) accommodated them in shared rooms when the cycle threshold value of the PCR test was more than a certain value (34.6%;9/26), or after a certain period that satisfied the national criteria (26.9%;7/26). Finally, 76.1% (35/46) of hospitals performed emergency procedures or operations on suspected patients. Table 1. Screening and selective treatment policy to prevent COVID-19 patients from entering the hospital Note Values are presented as number (%) Abbreviations: COVID-19, coronavirus disease 2019;PCR, polymerase chain reaction 1 This question requested the respondent to select multiple items. 2 Suspected cases of COVID-19 include fever, respiratory symptoms, and epidemiological associations with COVID-19 patients. Note Values are presented as number (%) Abbreviations: COVID-19, coronavirus disease 2019;PCR, polymerase chain reaction;PAPR, powered air-purifying respirator;Ct, cycle threshold 1 This question requested the respondent to select multiple items. 2 It includes infectious diseases, pulmonology, and the infection control and prevention office. 3 One hospital that wrote a non-categorical answer for the question was excluded. The hospital made a decision after discussing it with an infectious diseases specialist. Conclusion Various guidelines were being applied by each medical institution, but there was a lack of an explicit set of national guidelines to support them. Disclosures All Authors: No reported disclosures

17.
Antimicrob Resist Infect Control ; 10(1): 164, 2021 11 27.
Article in English | MEDLINE | ID: covidwho-1538091

ABSTRACT

OBJECTIVES: Few studies have investigated the contamination of personal protective equipment (PPE) during the management of patients with severe-to-critical coronavirus disease (COVID-19). This study aimed to determine the necessity of coveralls and foot covers for body protection during the management of COVID-19 patients. METHODS: PPE samples were collected from the coveralls of physicians exiting a room after the management of a patient with severe-to-critical COVID-19 within 14 days after the patient's symptom onset. The surface of coveralls was categorized into coverall-only parts (frontal surface of the head, anterior neck, dorsal surface of the foot cover, and back and hip) and gown-covered parts (the anterior side of the forearm and the abdomen). Sampling of the high-contact surfaces in the patient's environment was performed. We attempted to identify significant differences in contamination with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) between the coverall-only and gown-covered parts. RESULTS: A total of 105 swabs from PPEs and 28 swabs from patient rooms were collected. Of the PPE swabs, only three (2.8%) swabs from the gown-covered parts were contaminated with SARS-CoV-2. However, 23 of the 28 sites (82.1%) from patient rooms were contaminated. There was a significant difference in the contamination of PPE between the coverall-only and gown-covered parts (0.0 vs 10.0%, p = 0.022). CONCLUSIONS: Coverall contamination rarely occurred while managing severe-to-critical COVID-19 patients housed in negative pressure rooms in the early stages of the illness. Long-sleeved gowns may be used in the management of COVID-19 patients.


Subject(s)
COVID-19/prevention & control , Infection Control/instrumentation , Infectious Disease Transmission, Patient-to-Professional/prevention & control , Protective Clothing , Humans , Patient Isolation , Patients' Rooms , Physicians
18.
Microbiol Spectr ; 9(3): e0067221, 2021 12 22.
Article in English | MEDLINE | ID: covidwho-1532977

ABSTRACT

Here, we aimed to investigate the diagnostic value of a serological assay using the nucleocapsid protein developed for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection and evaluated its performance using three commercial enzyme-linked immunosorbent assays (ELISAs), namely, Standard E 2019 novel coronavirus disease (COVID-19) total antibody (Ab) ELISA (SD Biosensor), and EDI novel coronavirus COVID-19 IgG and IgM ELISA. A recombinant nucleocapsid protein (rNP) was expressed from plants and Escherichia coli for the detection of serum total Ab. We prospectively collected 141 serum samples from 32 patients with reverse transcription-PCR (RT-PCR)-confirmed COVID-19 and determined the sensitivity and dynamics of their total Ab response. Specificity was evaluated using 158 prepandemic samples. To validate the assays, we evaluated the performance using two different cutoff values. The sensitivity and specificity for each assay were as follows: 92.91% and 94.30% (plant-rNP), 83.69% and 98.73% (SD Biosensor), 75.89% and 98.10% (E. coli-rNP), 76.47% and 100% (EDI-IgG), and 80.39% and 80% (EDI-IgM). The plant-based rNP showed the highest sensitivity and area under the receiver operating characteristic (ROC) curve (0.980) among all the assays (P < 0.05). The seroconversion rate for total Ab increased sequentially with disease progression, with a sensitivity of 100% after 10 to 12 days of post-symptom onset (PSO) for both rNP-plant-based and SD Biosensor ELISAs. After 2 weeks of PSO, the seroconversion rates were >80% and 100% for EDI-IgM and EDI-IgG ELISA, respectively. Seroconversion occurred earlier with rNP plant-based ELISA (5 days PSO) compared with E. coli-based (7 days PSO) and SD Biosensor (8 days PSO) ELISA. We determined that rNP produced in plants enables the robust detection of SARS-CoV-2 total Abs. The assay can be used for serosurvey and complementary diagnosis of COVID-19. IMPORTANCE At present, the principal diagnostic methods for COVID-19 comprise the identification of viral nucleic acid by genetic approaches, including PCR-based techniques or next-generation sequencing. However, there is an urgent need for validated serological assays which are crucial for the understanding of immune responses against SARS-CoV-2. In this study, a highly sensitive and specific serological antibody assay was developed for the detection of SARS-CoV-2 with an overall accuracy of 93.56% using a recombinant nucleoprotein expressed from plants.


Subject(s)
Antibodies, Viral/blood , COVID-19 Testing/methods , COVID-19/diagnosis , Enzyme-Linked Immunosorbent Assay/methods , Nucleocapsid Proteins/immunology , Plant Proteins/immunology , Escherichia coli/genetics , Humans , Immunoglobulin G , Immunoglobulin M , Nucleocapsid , Plant Proteins/genetics , Recombinant Proteins/genetics , Recombinant Proteins/immunology , SARS-CoV-2/isolation & purification , Sensitivity and Specificity , Seroconversion , Tobacco/genetics
19.
Comput Math Methods Med ; 2021: 6636396, 2021.
Article in English | MEDLINE | ID: covidwho-1476878

ABSTRACT

Group testing (or pool testing), for example, Dorfman's method or grid method, has been validated for COVID-19 RT-PCR tests and implemented widely by most laboratories in many countries. These methods take advantages since they reduce resources, time, and overall costs required for a large number of samples. However, these methods could have more false negative cases and lower sensitivity. In order to maintain both accuracy and efficiency for different prevalence, we provide a novel pooling strategy based on the grid method with an extra pool set and an optimized rule inspired by the idea of error-correcting codes. The mathematical analysis shows that (i) the proposed method has the best sensitivity among all the methods we compared, if the false negative rate (FNR) of an individual test is in the range [1%, 20%] and the FNR of a pool test is closed to that of an individual test, and (ii) the proposed method is efficient when the prevalence is below 10%. Numerical simulations are also performed to confirm the theoretical derivations. In summary, the proposed method is shown to be felicitous under the above conditions in the epidemic.


Subject(s)
COVID-19 Testing/methods , COVID-19 Testing/standards , COVID-19/diagnosis , Algorithms , Computer Simulation , False Negative Reactions , Humans , Laboratories/standards , Models, Theoretical , Prevalence , Probability , Reproducibility of Results
20.
Nat Commun ; 12(1): 5975, 2021 10 13.
Article in English | MEDLINE | ID: covidwho-1467103

ABSTRACT

Acquired somatic mutations in hematopoietic stem and progenitor cells (clonal hematopoiesis or CH) are associated with advanced age, increased risk of cardiovascular and malignant diseases, and decreased overall survival. These adverse sequelae may be mediated by altered inflammatory profiles observed in patients with CH. A pro-inflammatory immunologic profile is also associated with worse outcomes of certain infections, including SARS-CoV-2 and its associated disease Covid-19. Whether CH predisposes to severe Covid-19 or other infections is unknown. Among 525 individuals with Covid-19 from Memorial Sloan Kettering (MSK) and the Korean Clonal Hematopoiesis (KoCH) consortia, we show that CH is associated with severe Covid-19 outcomes (OR = 1.85, 95%=1.15-2.99, p = 0.01), in particular CH characterized by non-cancer driver mutations (OR = 2.01, 95% CI = 1.15-3.50, p = 0.01). We further explore the relationship between CH and risk of other infections in 14,211 solid tumor patients at MSK. CH is significantly associated with risk of Clostridium Difficile (HR = 2.01, 95% CI: 1.22-3.30, p = 6×10-3) and Streptococcus/Enterococcus infections (HR = 1.56, 95% CI = 1.15-2.13, p = 5×10-3). These findings suggest a relationship between CH and risk of severe infections that warrants further investigation.


Subject(s)
COVID-19/etiology , COVID-19/pathology , Clonal Hematopoiesis/genetics , Hematopoietic Stem Cells/virology , Adolescent , Adult , Aged , Aged, 80 and over , COVID-19/immunology , Child , Child, Preschool , Clonal Hematopoiesis/immunology , Cohort Studies , Female , Humans , Infant , Infant, Newborn , Male , Middle Aged , Mutation/immunology , Neoplasms/genetics , Risk Factors , SARS-CoV-2 , Severity of Illness Index
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