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1.
Antibiotics (Basel) ; 11(4)2022 Mar 27.
Article in English | MEDLINE | ID: covidwho-1809656

ABSTRACT

Multidrug resistant organisms (MDRO) are commonly isolated in respiratory specimens taken from mechanically ventilated patients. The purpose of this narrative review is to discuss the approach to antimicrobial prescription in ventilated patients who have grown a new MDRO isolate in their respiratory specimen. A MEDLINE and PubMed literature search using keywords "multidrug resistant organisms", "ventilator-associated pneumonia" and "decision making", "treatment" or "strategy" was used to identify 329 references as background for this review. Lack of universally accepted diagnostic criteria for ventilator-associated pneumonia, or ventilator-associated tracheobronchitis complicates treatment decisions. Consideration of the clinical context including signs of respiratory infection or deterioration in respiratory or other organ function is essential. The higher the quality of respiratory specimens or the presence of bacteremia would suggest the MDRO is a true pathogen, rather than colonization, and warrants antimicrobial therapy. A patient with higher severity of illness has lower safety margins and may require initiation of antimicrobial therapy until an alternative diagnosis is established. A structured approach to the decision to treat with antimicrobial therapy is proposed.

2.
Microbiol Spectr ; 10(2): e0018222, 2022 04 27.
Article in English | MEDLINE | ID: covidwho-1752768

ABSTRACT

SARS-CoV-2 transcribes a set of subgenomic RNAs (sgRNAs) essential for the translation of structural and accessory proteins to sustain its life cycle. We applied RNA-seq on 375 respiratory samples from individual COVID-19 patients and revealed that the majority of the sgRNAs were canonical transcripts with N being the most abundant (36.2%), followed by S (11.6%), open reading frame 7a (ORF7a; 10.3%), M (8.4%), ORF3a (7.9%), ORF8 (6.0%), E (4.6%), ORF6 (2.5%), and ORF7b (0.3%); but ORF10 was not detected. The profile of most sgRNAs, except N, showed an independent association with viral load, time of specimen collection after onset, age of the patient, and S-614D/G variant with ORF7b and then ORF6 being the most sensitive to changes in these characteristics. Monitoring of 124 serial samples from 10 patients using sgRNA-specific real-time RT-PCR revealed a potential of adopting sgRNA as a marker of viral activity. Respiratory samples harboring a full set of canonical sgRNAs were mainly collected early within 1 to 2 weeks from onset, and most of the stool samples (90%) were negative for sgRNAs despite testing positive by diagnostic PCR targeting genomic RNA. ORF7b was the first to become undetectable and again being the most sensitive surrogate marker for a full set of canonical sgRNAs in clinical samples. The potential of using sgRNA to monitor viral activity and progression of SARS-CoV-2 infection, and hence as one of the objective indicators to triage patients for isolation and treatment should be considered. IMPORTANCE Attempts to use subgenomic RNAs (sgRNAs) of SARS-CoV-2 to identify active infection of COVID-19 have produced diverse results. In this work, we applied next-generation sequencing and RT-PCR to profile the full spectrum of SARS-CoV-2 sgRNAs in a large cohort of respiratory and stool samples collected throughout infection. Numerous known and novel discontinuous transcription events potentially encoding full-length, deleted and frameshift proteins were observed. In particular, the expression profile of canonical sgRNAs was associated with genomic RNA level and clinical characteristics. Our study found sgRNAs as potential biomarkers for monitoring infectivity and progression of SARS-CoV-2 infection, which provides an alternative target for the management and treatment of COVID-19 patients.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/diagnosis , Humans , Open Reading Frames , RNA, Viral/genetics , SARS-CoV-2/genetics , Viral Load
3.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-312879

ABSTRACT

Rationale: Unprecedented public health measures have been used during this coronavirus 2019 (COVID-19) pandemic but with a cost to economic and social disruption. It is a challenge to implement timely and appropriate public health interventions. Objectives: This study evaluates the timing and intensity of public health policies in each country and territory in the COVID-19 pandemic, and whether machine learning can help them to find better global health strategies. Methods: : Population and COVID-19 epidemiological data between 21st January 2020 to 7th April 2020 from 183 countries and 78 territories were included with the implemented public health interventions. We used deep reinforcement learning, and the model was trained to try to find the optimal public health strategies with maximizing total reward on controlling spread of COVID-19. The results proposed by the model were analyzed against the actual timing and intensity of lockdown and travel restrictions. Measurements and Main Results: Early implementation of the actual lockdown and travel restriction policies were associated with gradually groups of less severe crisis severity, relative to local index case date in each country or territory, not to 31st December 2019. However, our model suggested to initiate at least minimal intensity of lockdown or travel restriction even before index cases in each country and territory. In addition, the model mostly recommended a combination of lockdown and travel restrictions and higher intensity policies than the implemented policies by government, but did not always encourage rapid full lockdown and full border closures. Conclusion: Compared to actual government implementation, our model mostly recommended earlier and higher intensity of lockdown and travel restrictions. Machine learning may be used as a decision support tool for implementation of public health interventions during COVID-19 and future pandemics.

4.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-325537

ABSTRACT

Background: Coronavirus Disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from faecal samples and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need. Methods: : We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had faecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial faecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the faecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters. Results: : Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in faecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Faecal virome in SARS-CoV-2 infection harboured more stress-, inflammation- and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, Pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age;5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects. Conclusions: Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19.

5.
BMJ Open ; 11(12): e052462, 2021 12 30.
Article in English | MEDLINE | ID: covidwho-1599280

ABSTRACT

OBJECTIVES: Determine 90-day mortality of mechanically ventilated ward patients outside the intensive care unit (ICU) and its association with organisational factors. DESIGN: Multicentre prospective observational study of mechanically ventilated ward patients. Modified Poisson regression was used to assess association between nurse to patient ratio (NPR) and 90-day mortality, adjusted for designated medical team, Society of Critical Care Medicine (SCCM) triage priority and centre effect. NPR was divided into low (1:9.6 to 1:10), medium (1:6 to 1:8) and high (1:2.6). Sensitivity analysis was conducted for pneumonia with or without acute respiratory distress syndrome (ARDS) to assess magnitude of association. SETTING: 7 acute public hospitals in Hong Kong. PARTICIPANTS: All 485 mechanically ventilated patients in wards from participating hospitals between 18 January 2016 and 17 April 2016 were recruited. Three hundred patients were included after excluding patients with limitation of therapy within 24 hours of intubation. MAIN OUTCOMES: 90-day mortality, Mortality Prediction Model III Standardised mortality ratio (MPMIII0 SMR). RESULTS: 201 patients died within 90 days after intubation (67.0%, 95% CI 61.5% to 72.1%), with MPMIII0 SMR 1.88, 95% CI 1.63 to 2.17. Compared with high NPR, medium and low NPRs were associated with higher risk of 90-day mortality (adjusted relative risk (RRadj) 1.84, 95% CI 1.70 to 1.99 and 1.64, 95% CI 1.47 to 1.83, respectively). For 114 patients with pneumonia with or without ARDS, low to medium NPR, too sick to benefit from ICU (SCCM priority 4b), no ICU consultation and designated medical team were associated with risk of 90-day mortality (RRadj 1.49, 95% CI 1.40 to 1.58; RRadj 1.60, 95% CI 1.49 to 1.72; RRadj 1.34, 95% CI 1.27 to 1.40; RRadj 0.85, 95% CI 0.78 to 0.93, respectively). CONCLUSION: The 90-day mortality rates of mechanically ventilated ward patients were high. NPR was an independent predictor of survival for mechanically ventilated ward patients.


Subject(s)
Respiration, Artificial , Respiratory Distress Syndrome , Hospital Mortality , Hospitals , Humans , Intensive Care Units , Prospective Studies , Respiratory Distress Syndrome/therapy
6.
Front Immunol ; 12: 763292, 2021.
Article in English | MEDLINE | ID: covidwho-1581338

ABSTRACT

The cytokine release syndrome has been proposed as the driver of inflammation in coronavirus disease 2019 (COVID-19). However, studies on longitudinal cytokine profiles in patients across the whole severity spectrum of COVID-19 are lacking. In this prospective observational study on adult COVID-19 patients admitted to two Hong Kong public hospitals, cytokine profiling was performed on blood samples taken during early phase (within 7 days of symptom onset) and late phase (8 to 12 days of symptom onset). The primary objective was to evaluate the difference in early and late cytokine profiles among patient groups with different disease severity. The secondary objective was to assess the associations between cytokines and clinical endpoints in critically ill patients. A total of 40 adult patients (mild = 8, moderate = 15, severe/critical = 17) hospitalized with COVID-19 were included in this study. We found 22 cytokines which were correlated with disease severity, as proinflammatory Th1-related cytokines (interleukin (IL)-18, interferon-induced protein-10 (IP-10), monokine-induced by gamma interferon (MIG), and IL-10) and ARDS-associated cytokines (IL-6, monocyte chemoattractant protein-1 (MCP-1), interleukin-1 receptor antagonist (IL-1RA), and IL-8) were progressively elevated with increasing disease severity. Furthermore, 11 cytokines were consistently different in both early and late phases, including seven (growth-regulated oncogene-alpha (GRO-α), IL-1RA, IL-6, IL-8, IL-10, IP-10, and MIG) that increased and four (FGF-2, IL-5, macrophage-derived chemokine (MDC), and MIP-1α) that decreased from mild to severe/critical patients. IL-8, followed by IP-10 and MDC were the best performing early biomarkers to predict disease severity. Among critically ill patients, MCP-1 predicted the duration of mechanical ventilation, highest norepinephrine dose administered, and length of intensive care stay.


Subject(s)
Biomarkers/blood , COVID-19/immunology , Cytokines/blood , Adult , Aged , COVID-19/blood , Cytokines/immunology , Female , Hong Kong , Humans , Male , Middle Aged , Prospective Studies , SARS-CoV-2 , Severity of Illness Index
7.
J Intensive Care ; 9(1): 60, 2021 Oct 07.
Article in English | MEDLINE | ID: covidwho-1456012

ABSTRACT

BACKGROUND: Asia has more critically ill people than any other part of our planet. The aim of this article is to review the development of critical care as a specialty, critical care societies and education and research, the epidemiology of critical illness as well as epidemics and pandemics, accessibility and cost and quality of critical care, culture and end-of-life care, and future directions for critical care in Asia. MAIN BODY: Although the first Asian intensive care units (ICUs) surfaced in the 1960s and the 1970s and specialisation started in the 1990s, multiple challenges still exist, including the lack of intensivists, critical care nurses, and respiratory therapists in many countries. This is aggravated by the brain drain of skilled ICU staff to high-income countries. Critical care societies have been integral to the development of the discipline and have increasingly contributed to critical care education, although critical care research is only just starting to take off through collaboration across groups. Sepsis, increasingly aggravated by multidrug resistance, contributes to a significant burden of critical illness, while epidemics and pandemics continue to haunt the continent intermittently. In particular, the coronavirus disease 2019 (COVID-19) has highlighted the central role of critical care in pandemic response. Accessibility to critical care is affected by lack of ICU beds and high costs, and quality of critical care is affected by limited capability for investigations and treatment in low- and middle-income countries. Meanwhile, there are clear cultural differences across countries, with considerable variations in end-of-life care. Demand for critical care will rise across the continent due to ageing populations and rising comorbidity burdens. Even as countries respond by increasing critical care capacity, the critical care community must continue to focus on training for ICU healthcare workers, processes anchored on evidence-based medicine, technology guided by feasibility and impact, research applicable to Asian and local settings, and rallying of governments for support for the specialty. CONCLUSIONS: Critical care in Asia has progressed through the years, but multiple challenges remain. These challenges should be addressed through a collaborative approach across disciplines, ICUs, hospitals, societies, governments, and countries.

8.
R Soc Open Sci ; 8(9): 201867, 2021 Sep.
Article in English | MEDLINE | ID: covidwho-1429382

ABSTRACT

The novel coronavirus disease 2019 (COVID-19) has spread worldwide and threatened human life. Diagnosis is crucial to contain the spread of SARS-CoV-2 infections and save lives. Diagnostic tests for COVID-19 have varying sensitivity and specificity, and the false-negative results would have substantial consequences to patient treatment and pandemic control. To detect all suspected infections, multiple testing is widely used. However, it may be challenging to build an assertion when the testing results are inconsistent. Considering the situation where there is more than one diagnostic outcome for each subject, we proposed a Bayesian probabilistic framework based on the sensitivity and specificity of each diagnostic method to synthesize a posterior probability of being infected by SARS-CoV-2. We demonstrated that the synthesized posterior outcome outperformed each individual testing outcome. A user-friendly web application was developed to implement our analytic framework with free access via http://www2.ccrb.cuhk.edu.hk/statgene/COVID_19/. The web application enables the real-time display of the integrated outcome incorporating two or more tests and calculated based on Bayesian posterior probability. A simulation-based assessment demonstrated higher accuracy and precision of the Bayesian probabilistic model compared with a single-test outcome. The online tool developed in this study can assist physicians in making clinical evaluations by effectively integrating multiple COVID-19 tests.

9.
J Intensive Care ; 9(1): 55, 2021 Sep 10.
Article in English | MEDLINE | ID: covidwho-1403264

ABSTRACT

The effect of changes to cardiopulmonary resuscitation (CPR) procedures in response to Coronavirus disease 2019 (COVID-19) on in-hospital cardiac arrest (IHCA) management and outcomes are unreported. In this multicenter retrospective study, we showed that median time to arrival of resuscitation team has increased and proportion of patients receiving first-responder CPR has lowered during this pandemic. IHCA during the pandemic was independently associated with lower return of spontaneous circulation OR 0.63 (95% CI 0.43-0.91), despite adjustment for lowered patient comorbidity and increased time to resuscitation team arrival. Changes to resuscitation practice in this pandemic had effects on IHCA outcomes, even in patients without COVID-19.

10.
PLoS One ; 16(5): e0251550, 2021.
Article in English | MEDLINE | ID: covidwho-1226900

ABSTRACT

BACKGROUND: Unprecedented public health measures have been used during this coronavirus 2019 (COVID-19) pandemic to control the spread of SARS-CoV-2 virus. It is a challenge to implement timely and appropriate public health interventions. METHODS AND FINDINGS: Population and COVID-19 epidemiological data between 21st January 2020 to 15th November 2020 from 216 countries and territories were included with the implemented public health interventions. We used deep reinforcement learning, and the algorithm was trained to enable agents to try to find optimal public health strategies that maximized total reward on controlling the spread of COVID-19. The results suggested by the algorithm were analyzed against the actual timing and intensity of lockdown and travel restrictions. Early implementations of the actual lockdown and travel restriction policies, usually at the time of local index case were associated with less burden of COVID-19. In contrast, our agent suggested to initiate at least minimal intensity of lockdown or travel restriction even before or on the day of the index case in each country and territory. In addition, the agent mostly recommended a combination of lockdown and travel restrictions and higher intensity policies than the policies implemented by governments, but did not always encourage rapid full lockdown and full border closures. The limitation of this study was that it was done with incomplete data due to the emerging COVID-19 epidemic, inconsistent testing and reporting. In addition, our research focuses only on population health benefits by controlling the spread of COVID-19 without balancing the negative impacts of economic and social consequences. INTERPRETATION: Compared to actual government implementation, our algorithm mostly recommended earlier intensity of lockdown and travel restrictions. Reinforcement learning may be used as a decision support tool for implementation of public health interventions during COVID-19 and future pandemics.


Subject(s)
COVID-19/prevention & control , Communicable Disease Control , Public Health , COVID-19/epidemiology , Deep Learning , Global Health , Humans , Pandemics , SARS-CoV-2/isolation & purification
11.
Microbiome ; 9(1): 91, 2021 04 14.
Article in English | MEDLINE | ID: covidwho-1183579

ABSTRACT

BACKGROUND: Coronavirus disease 2019 (COVID-19) caused by the enveloped RNA virus SARS-CoV-2 primarily affects the respiratory and gastrointestinal tracts. SARS-CoV-2 was isolated from fecal samples, and active viral replication was reported in human intestinal cells. The human gut also harbors an enormous amount of resident viruses (collectively known as the virome) that play a role in regulating host immunity and disease pathophysiology. Understanding gut virome perturbation that underlies SARS-CoV-2 infection and severity is an unmet need. METHODS: We enrolled 98 COVID-19 patients with varying disease severity (3 asymptomatic, 53 mild, 34 moderate, 5 severe, 3 critical) and 78 non-COVID-19 controls matched for gender and co-morbidities. All subjects had fecal specimens sampled at inclusion. Blood specimens were collected for COVID-19 patients at admission to test for inflammatory markers and white cell counts. Among COVID-19 cases, 37 (38%) patients had serial fecal samples collected 2 to 3 times per week from time of hospitalization until after discharge. Using shotgun metagenomics sequencing, we sequenced and profiled the fecal RNA and DNA virome. We investigated alterations and longitudinal dynamics of the gut virome in association with disease severity and blood parameters. RESULTS: Patients with COVID-19 showed underrepresentation of Pepper mild mottle virus (RNA virus) and multiple bacteriophage lineages (DNA viruses) and enrichment of environment-derived eukaryotic DNA viruses in fecal samples, compared to non-COVID-19 subjects. Such gut virome alterations persisted up to 30 days after disease resolution. Fecal virome in SARS-CoV-2 infection harbored more stress-, inflammation-, and virulence-associated gene encoding capacities including those pertaining to bacteriophage integration, DNA repair, and metabolism and virulence associated with their bacterial host. Baseline fecal abundance of 10 virus species (1 RNA virus, pepper chlorotic spot virus, and 9 DNA virus species) inversely correlated with disease COVID-19 severity. These viruses inversely correlated with blood levels of pro-inflammatory proteins, white cells, and neutrophils. Among the 10 COVID-19 severity-associated DNA virus species, 4 showed inverse correlation with age; 5 showed persistent lower abundance both during disease course and after disease resolution relative to non-COVID-19 subjects. CONCLUSIONS: Both enteric RNA and DNA virome in COVID-19 patients were different from non-COVID-19 subjects, which persisted after disease resolution of COVID-19. Gut virome may calibrate host immunity and regulate severity to SARS-CoV-2 infection. Our observation that gut viruses inversely correlated with both severity of COVID-19 and host age may partly explain that older subjects are prone to severe and worse COVID-19 outcomes. Altogether, our data highlight the importance of human gut virome in severity and potentially therapeutics of COVID-19. Video Abstract.


Subject(s)
COVID-19 , Gastrointestinal Microbiome , Child, Preschool , DNA , Gastrointestinal Microbiome/genetics , Humans , RNA , SARS-CoV-2 , Virome
12.
Gut ; 70(4): 698-706, 2021 04.
Article in English | MEDLINE | ID: covidwho-1024254

ABSTRACT

OBJECTIVE: Although COVID-19 is primarily a respiratory illness, there is mounting evidence suggesting that the GI tract is involved in this disease. We investigated whether the gut microbiome is linked to disease severity in patients with COVID-19, and whether perturbations in microbiome composition, if any, resolve with clearance of the SARS-CoV-2 virus. METHODS: In this two-hospital cohort study, we obtained blood, stool and patient records from 100 patients with laboratory-confirmed SARS-CoV-2 infection. Serial stool samples were collected from 27 of the 100 patients up to 30 days after clearance of SARS-CoV-2. Gut microbiome compositions were characterised by shotgun sequencing total DNA extracted from stools. Concentrations of inflammatory cytokines and blood markers were measured from plasma. RESULTS: Gut microbiome composition was significantly altered in patients with COVID-19 compared with non-COVID-19 individuals irrespective of whether patients had received medication (p<0.01). Several gut commensals with known immunomodulatory potential such as Faecalibacterium prausnitzii, Eubacterium rectale and bifidobacteria were underrepresented in patients and remained low in samples collected up to 30 days after disease resolution. Moreover, this perturbed composition exhibited stratification with disease severity concordant with elevated concentrations of inflammatory cytokines and blood markers such as C reactive protein, lactate dehydrogenase, aspartate aminotransferase and gamma-glutamyl transferase. CONCLUSION: Associations between gut microbiota composition, levels of cytokines and inflammatory markers in patients with COVID-19 suggest that the gut microbiome is involved in the magnitude of COVID-19 severity possibly via modulating host immune responses. Furthermore, the gut microbiota dysbiosis after disease resolution could contribute to persistent symptoms, highlighting a need to understand how gut microorganisms are involved in inflammation and COVID-19.


Subject(s)
Bacteria , COVID-19 , Dysbiosis , Gastrointestinal Microbiome/immunology , Gastrointestinal Tract , Immunity , SARS-CoV-2 , Adult , Bacteria/genetics , Bacteria/immunology , Bacteria/isolation & purification , C-Reactive Protein/analysis , COVID-19/blood , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/immunology , Cytokines/analysis , DNA, Bacterial/isolation & purification , Dysbiosis/epidemiology , Dysbiosis/etiology , Dysbiosis/immunology , Dysbiosis/virology , Female , Gastrointestinal Tract/immunology , Gastrointestinal Tract/microbiology , Gastrointestinal Tract/virology , Hong Kong , Humans , Male , SARS-CoV-2/immunology , SARS-CoV-2/isolation & purification , Severity of Illness Index , Transferases/analysis
13.
Nature ; 591(7848): 92-98, 2021 03.
Article in English | MEDLINE | ID: covidwho-971937

ABSTRACT

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice.


Subject(s)
COVID-19/genetics , COVID-19/physiopathology , Critical Illness , 2',5'-Oligoadenylate Synthetase/genetics , COVID-19/pathology , Chromosomes, Human, Pair 12/genetics , Chromosomes, Human, Pair 19/genetics , Chromosomes, Human, Pair 21/genetics , Critical Care , Dipeptidyl-Peptidases and Tripeptidyl-Peptidases/genetics , Drug Repositioning , Female , Genome-Wide Association Study , Humans , Inflammation/genetics , Inflammation/pathology , Inflammation/physiopathology , Lung/pathology , Lung/physiopathology , Lung/virology , Male , Multigene Family/genetics , Receptor, Interferon alpha-beta/genetics , Receptors, CCR2/genetics , TYK2 Kinase/genetics , United Kingdom
14.
J Infect Dis ; 222(10): 1612-1619, 2020 10 13.
Article in English | MEDLINE | ID: covidwho-863294

ABSTRACT

BACKGROUND: Self-collected specimens have been advocated to avoid infectious exposure to healthcare workers. Self-induced sputum in those with a productive cough and saliva in those without a productive cough have been proposed, but sensitivity remains uncertain. METHODS: We performed a prospective study in 2 regional hospitals in Hong Kong. RESULTS: We prospectively examined 563 serial samples collected during the virus shedding periods of 50 patients: 150 deep throat saliva (DTS), 309 pooled-nasopharyngeal (NP) and throat swabs, and 104 sputum. Deep throat saliva had the lowest overall reverse-transcriptase polymerase chain reaction (RT-PCR)-positive rate (68.7% vs 89.4% [sputum] and 80.9% [pooled NP and throat swabs]) and the lowest viral ribonucleic acid (RNA) concentration (mean log copy/mL 3.54 vs 5.03 [sputum] and 4.63 [pooled NP and throat swabs]). Analyses with respect to time from symptom onset and severity also revealed similar results. Virus yields of DTS correlated with that of sputum (Pearson correlation index 0.76; 95% confidence interval, 0.62-0.86). We estimated that the overall false-negative rate of DTS could be as high as 31.3% and increased 2.7 times among patients without sputum. CONCLUSIONS: Deep throat saliva produced the lowest viral RNA concentration and RT-PCR-positive rate compared with conventional respiratory specimens in all phases of illness. Self-collected sputum should be the choice for patients with sputum.


Subject(s)
Betacoronavirus/genetics , Clinical Laboratory Techniques , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Nasopharynx/virology , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , Saliva/virology , Sputum/virology , Adolescent , Adult , Aged , COVID-19 , COVID-19 Testing , COVID-19 Vaccines , Clinical Laboratory Techniques/methods , Coronavirus Infections/virology , Female , Hong Kong/epidemiology , Humans , Male , Middle Aged , Pandemics , Pneumonia, Viral/virology , Prospective Studies , RNA, Viral/genetics , Real-Time Polymerase Chain Reaction , Reverse Transcriptase Polymerase Chain Reaction , SARS-CoV-2 , Specimen Handling/methods , Young Adult
16.
Gastroenterology ; 159(3): 944-955.e8, 2020 09.
Article in English | MEDLINE | ID: covidwho-324569

ABSTRACT

BACKGROUND & AIMS: Although severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects gastrointestinal tissues, little is known about the roles of gut commensal microbes in susceptibility to and severity of infection. We investigated changes in fecal microbiomes of patients with SARS-CoV-2 infection during hospitalization and associations with severity and fecal shedding of virus. METHODS: We performed shotgun metagenomic sequencing analyses of fecal samples from 15 patients with Coronavirus Disease 2019 (COVID-19) in Hong Kong, from February 5 through March 17, 2020. Fecal samples were collected 2 or 3 times per week from time of hospitalization until discharge; disease was categorized as mild (no radiographic evidence of pneumonia), moderate (pneumonia was present), severe (respiratory rate ≥30/min, or oxygen saturation ≤93% when breathing ambient air), or critical (respiratory failure requiring mechanical ventilation, shock, or organ failure requiring intensive care). We compared microbiome data with those from 6 subjects with community-acquired pneumonia and 15 healthy individuals (controls). We assessed gut microbiome profiles in association with disease severity and changes in fecal shedding of SARS-CoV-2. RESULTS: Patients with COVID-19 had significant alterations in fecal microbiomes compared with controls, characterized by enrichment of opportunistic pathogens and depletion of beneficial commensals, at time of hospitalization and at all timepoints during hospitalization. Depleted symbionts and gut dysbiosis persisted even after clearance of SARS-CoV-2 (determined from throat swabs) and resolution of respiratory symptoms. The baseline abundance of Coprobacillus, Clostridium ramosum, and Clostridium hathewayi correlated with COVID-19 severity; there was an inverse correlation between abundance of Faecalibacterium prausnitzii (an anti-inflammatory bacterium) and disease severity. Over the course of hospitalization, Bacteroides dorei, Bacteroides thetaiotaomicron, Bacteroides massiliensis, and Bacteroides ovatus, which downregulate expression of angiotensin-converting enzyme 2 (ACE2) in murine gut, correlated inversely with SARS-CoV-2 load in fecal samples from patients. CONCLUSIONS: In a pilot study of 15 patients with COVID-19, we found persistent alterations in the fecal microbiome during the time of hospitalization, compared with controls. Fecal microbiota alterations were associated with fecal levels of SARS-CoV-2 and COVID-19 severity. Strategies to alter the intestinal microbiota might reduce disease severity.


Subject(s)
Betacoronavirus , Coronavirus Infections/microbiology , Dysbiosis/virology , Feces/microbiology , Gastrointestinal Microbiome/genetics , Pneumonia, Viral/microbiology , Adult , Aged , COVID-19 , Female , Gastrointestinal Tract/microbiology , Hong Kong/epidemiology , Hospitalization/statistics & numerical data , Humans , Male , Middle Aged , Pandemics , Pilot Projects , SARS-CoV-2
18.
Critical care and resuscitation : journal of the Australasian Academy of Critical Care Medicine ; 2020.
Article | WHO COVID | ID: covidwho-34896

ABSTRACT

OBJECTIVE: To report the first eight cases of critically ill patients with coronavirus disease 2019 (COVID-19) in Hong Kong, describing the treatments and supportive care they received and their 28-day outcomes. DESIGN: Multicentre retrospective observational cohort study. SETTING: Three multidisciplinary intensive care units (ICUs) in Hong Kong. PARTICIPANTS: All adult critically ill patients with confirmed COVID-19 admitted to ICUs in Hong Kong between 22 January and 11 February 2020. MAIN OUTCOME MEASURE: 28-day mortality. RESULTS: Eight out of 49 patients with COVID-19 (16%) were admitted to Hong Kong ICUs during the study period. The median age was 64.5 years (range, 42–70) with a median admission Sequential Organ Failure Assessment (SOFA) score of 6 (IQR, 4–7). Six patients (75%) required mechanical ventilation, six patients (75%) required vasopressors and two (25%) required renal replacement therapy. None of the patients required prone ventilation, nitric oxide or extracorporeal membrane oxygenation. The median times to shock reversal and extubation were 9 and 11 days respectively. At 28 days, one patient (12%) had died and the remaining seven (88%) all survived to ICU discharge. Only one of the survivors (14%) still required oxygen at 28 days. CONCLUSION: Critically ill patients with COVID-19 often require a moderate duration of mechanical ventilation and vasopressor support. Most of these patients recover and survive to ICU discharge with supportive care using lung protective ventilation strategies, avoiding excess fluids, screening and treating bacterial co-infection, and timely intubation. Lower rather than upper respiratory tract viral burden correlates with clinical severity of illness.

19.
Lancet Respir Med ; 8(5): 506-517, 2020 05.
Article in English | MEDLINE | ID: covidwho-35108

ABSTRACT

As coronavirus disease 2019 (COVID-19) spreads across the world, the intensive care unit (ICU) community must prepare for the challenges associated with this pandemic. Streamlining of workflows for rapid diagnosis and isolation, clinical management, and infection prevention will matter not only to patients with COVID-19, but also to health-care workers and other patients who are at risk from nosocomial transmission. Management of acute respiratory failure and haemodynamics is key. ICU practitioners, hospital administrators, governments, and policy makers must prepare for a substantial increase in critical care bed capacity, with a focus not just on infrastructure and supplies, but also on staff management. Critical care triage to allow the rationing of scarce ICU resources might be needed. Researchers must address unanswered questions, including the role of repurposed and experimental therapies. Collaboration at the local, regional, national, and international level offers the best chance of survival for the critically ill.


Subject(s)
Coronavirus Infections/therapy , Pneumonia, Viral/therapy , Betacoronavirus/isolation & purification , COVID-19 , Coronavirus Infections/diagnosis , Coronavirus Infections/drug therapy , Coronavirus Infections/epidemiology , Critical Care/methods , Humans , Pandemics , Pneumonia, Viral/diagnosis , Pneumonia, Viral/drug therapy , Pneumonia, Viral/epidemiology , Randomized Controlled Trials as Topic , SARS-CoV-2
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