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1.
Front Med (Lausanne) ; 9: 912367, 2022.
Article in English | MEDLINE | ID: covidwho-1865456

ABSTRACT

Background: Currently, as the omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) surges amid the coronavirus disease 2019 (COVID-19) pandemic, its clinical characteristics with intrinsic severity and the protection from vaccination have been understudied. Methods: We reported 169 COVID-19 patients that were infected with the omicron variant of SARS-CoV-2 and hospitalized in Suzhou, China, from February to March 2022, with their demographic information, medical/immunization history, clinical symptom, and hematological profile. At the same time, patients with none/partial (one-dose), full (two-dose) and three-dose vaccination were also compared to assess the vaccine effectiveness. Findings: For the omicron COVID-19 patients included in this study, their median age was 33.0 [interquartile range (IQR): 24.0-45.5], 53.3% were male and the median duration from illness onset to hospitalization was 2 days. Hypertension, bronchitis, and diabetes were the leading comorbidities among patients. While the common clinical symptoms included cough, fever, expectoration, and fatigue, etc., asymptomatic patients took up a significant portion (46.7%). For hematological parameters, most values revealed the alleviated pathogenicity induced by the omicron variant infection. No critically ill or deceased patients due to COVID-19 infection were reported in this study. Interpretation: Our results supported that the viremic effect of the omicron variant became milder than the previous circulating variants, while full vaccination or booster shot was greatly desired for an effective protection against clinical severity.

2.
World J Clin Cases ; 10(7): 2253-2260, 2022 Mar 06.
Article in English | MEDLINE | ID: covidwho-1737393

ABSTRACT

BACKGROUND: Plexiform fibromyxoma (PF) is a rare mesenchymal tumor, with limited case reports worldwide. Common clinical symptoms are abdominal discomfort and bleeding signs, which frequently present slow-onset in reported cases. Herein, we report a case of gastric PF presenting as acute onset and with pyemia accom-panying tumor rupture. We resected the tumor as well as the distal gastric, bulbus duodeni and gallbladder for treatment in emergency surgery. Notably, before the onset of the disease, the patient received coronavirus disease 2019 (COVID-19) vaccines. CASE SUMMARY: A 26-year-old man was admitted to our hospital, due to abdominal pain and fever after having received COVID-19 vaccines. Laboratory examination indicated severe sepsis. Computed tomography scan revealed a large mass in the abdomen. Deformation of the gastrointestinal tract was seen during gastroscopy. After failure of anti-infective treatment and symptoms of shock developed, he received an emergency surgery. We found a huge and partly ruptured mass, with thick purulence. Microscopically, the mass was composed of spindle cells with clarified cytoplasm, accompanied by myxoid stroma and arborizing blood vessels. Immunohistochemistry showed the tumor cells as positive for smooth muscle actin and succinate dehydrogenase subunit B but negative for DOG-1 and CD117. Finally, the patient was diagnosed with gastric PF and discharged from the hospital. CONCLUSION: Gastric PF manifesting as tumor rupture combined with pyemia is rare. Timely surgery is critical for optimal prognosis.

3.
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.
Ren Fail ; 43(1): 1329-1337, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1493366

ABSTRACT

BACKGROUND: This study sought to investigate incidence and risk factors for acute kidney injury (AKI) in hospitalized COVID-19. METHODS: In this retrospective study, we enrolled 823 COVID-19 patients with at least two evaluations of renal function during hospitalization from four hospitals in Wuhan, China between February 2020 and April 2020. Clinical and laboratory parameters at the time of admission and follow-up data were recorded. Systemic renal tubular dysfunction was evaluated via 24-h urine collections in a subgroup of 55 patients. RESULTS: In total, 823 patients were enrolled (50.5% male) with a mean age of 60.9 ± 14.9 years. AKI occurred in 38 (40.9%) ICU cases but only 6 (0.8%) non-ICU cases. Using forward stepwise Cox regression analysis, we found eight independent risk factors for AKI including decreased platelet level, lower albumin level, lower phosphorus level, higher level of lactate dehydrogenase (LDH), procalcitonin, C-reactive protein (CRP), urea, and prothrombin time (PT) on admission. For every 0.1 mmol/L decreases in serum phosphorus level, patients had a 1.34-fold (95% CI 1.14-1.58) increased risk of AKI. Patients with hypophosphatemia were likely to be older and with lower lymphocyte count, lower serum albumin level, lower uric acid, higher LDH, and higher CRP. Furthermore, serum phosphorus level was positively correlated with phosphate tubular maximum per volume of filtrate (TmP/GFR) (Pearson r = 0.66, p < .001) in subgroup analysis, indicating renal phosphate loss via proximal renal tubular dysfunction. CONCLUSION: The AKI incidence was very low in non-ICU patients as compared to ICU patients. Hypophosphatemia is an independent risk factor for AKI in patients hospitalized for COVID-19 infection.


Subject(s)
Acute Kidney Injury/etiology , COVID-19/complications , Hypophosphatemia/complications , Pneumonia, Viral/complications , Acute Kidney Injury/epidemiology , COVID-19/epidemiology , China/epidemiology , Female , Hospitalization , Humans , Hypophosphatemia/epidemiology , Incidence , Intensive Care Units , Kidney Function Tests , Male , Middle Aged , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Retrospective Studies , Risk Factors , SARS-CoV-2
6.
Int J Mol Sci ; 22(19)2021 Sep 26.
Article in English | MEDLINE | ID: covidwho-1463703

ABSTRACT

Exosomes are associated with cancer progression, pregnancy, cardiovascular diseases, central nervous system-related diseases, immune responses and viral pathogenicity. However, study on the role of exosomes in the immune response of teleost fish, especially antiviral immunity, is limited. Herein, serum-derived exosomes from mandarin fish were used to investigate the antiviral effect on the exosomes of teleost fish. Exosomes isolated from mandarin fish serum by ultra-centrifugation were internalized by mandarin fish fry cells and were able to inhibit Infectious spleen and kidney necrosis virus (ISKNV) infection. To further investigate the underlying mechanisms of exosomes in inhibiting ISKNV infection, the protein composition of serum-derived exosomes was analyzed by mass spectrometry. It was found that myxovirus resistance 1 (Mx1) was incorporated by exosomes. Furthermore, the mandarin fish Mx1 protein was proven to be transferred into the recipient cells though exosomes. Our results showed that the serum-derived exosomes from mandarin fish could inhibit ISKNV replication, which suggested an underlying mechanism of the exosome antivirus in that it incorporates Mx1 protein and delivery into recipient cells. This study provided evidence for the important antiviral role of exosomes in the immune system of teleost fish.


Subject(s)
DNA Virus Infections , Exosomes , Fish Diseases , Fish Proteins , Fishes , Iridoviridae , Myxovirus Resistance Proteins , Animals , Cell Line , DNA Virus Infections/blood , DNA Virus Infections/immunology , DNA Virus Infections/veterinary , Exosomes/immunology , Exosomes/metabolism , Fish Diseases/blood , Fish Diseases/immunology , Fish Proteins/blood , Fish Proteins/immunology , Fishes/blood , Fishes/immunology , Fishes/virology , Iridoviridae/immunology , Iridoviridae/metabolism , Myxovirus Resistance Proteins/blood , Myxovirus Resistance Proteins/immunology
7.
Atmospheric Pollution Research ; : 101209, 2021.
Article in English | ScienceDirect | ID: covidwho-1415195

ABSTRACT

Knowing the contribution rates and sharing rate of local source emissions to the atmospheric environmental capacity (AEC) is of great significance to the formulation of regional air pollution source control measures. Based on WRF-CALPUFF coupling models and the second pollution source survey data, Wuhan was taken as the research area, and the contribution rates of point and area source emissions to the SO2, NO2 and PM2.5 concentration in national pollutant control points (abbreviated as "national control points"), the AEC and its source emission sharing rate of each region were calculated. The results showed that WRF-CALPUFF had better reproducibility, the contribution rates of different pollution source emissions to the SO2, NO2 and PM2.5 concentration in national control points had obvious spatial distribution characteristics, and the contribution rates of key point sources to the SO2 concentration of each national control point exceeded 40%, while the contribution rates of the main urban area source to the NO2 and PM2.5 concentrations exceed 60%;the AEC of SO2, NO2 and PM2.5 in different regions had obvious seasonal and spatial changes, and the source emissions of NO2 and PM2.5 in the main urban area were 8.7 times and 3 times of its AEC, respectively. The calculation results from source sharing rate of regional AEC showed that the AEC of SO2 was mainly shared by point sources, and the AEC of NO2 and PM2.5 was mainly shared by area sources, but the sharing rate of SO2, NO2 and PM2.5 AEC from different regional source emissions showed different characteristics. The analysis of air quality improvement during the 7th Military World Games in 2019 and the COVID-19 pandemic in 2020 shows that the calculation formula about regional source sharing rate of AEC proposed in this paper is reasonable and the implementation of refined control to regional source emissions with the source sharing rate of regional AEC plays an important role on the continued improvement of Wuhan air quality.

8.
NPJ Climate and Atmospheric Science ; 4(1), 2021.
Article in English | ProQuest Central | ID: covidwho-1317819

ABSTRACT

The less improvement of ambient visibility suspects the government’s efforts on alleviating PM2.5 pollution. The COVID-19 lockdown reduced PM2.5 and increased visibility in Wuhan. Compared to pre-lockdown period, the PM2.5 concentration decreased by 39.0 μg m−3, dominated by NH4NO3 mass reduction (24.8 μg m−3) during lockdown period. The PM2.5 threshold corresponding to visibility of 10 km (PTV10) varied in 54–175 μg m−3 and an hourly PM2.5 of 54 μg m−3 was recommended to prevent haze occurrence. The lockdown measures elevated PTV10 by 9–58 μg m−3 as the decreases in PM2.5 mass scattering efficiency and optical hygroscopicity. The visibility increased by 107%, resulted from NH4NO3 extinction reduction. The NH4NO3 mass reduction weakened its mutual promotion with aerosol water and increased PM2.5 deliquescence humidity. Controlling TNO3 (HNO3 + NO3−) was more effective to reduce PM2.5 and improve visibility than NHx (NH3 + NH4+) unless the NHx reduction exceeded 11.7–17.5 μg m−3.

9.
Ren Fail ; 43(1): 1115-1123, 2021 Dec.
Article in English | MEDLINE | ID: covidwho-1301248

ABSTRACT

INTRODUCTION: Acute kidney injury (AKI) in coronavirus disease 2019 (COVID-19) patients is associated with poor prognosis. Early prediction and intervention of AKI are vital for improving clinical outcome of COVID-19 patients. As lack of tools for early AKI detection in COVID-19 patients, this study aimed to validate the USCD-Mayo risk score in predicting hospital-acquired AKI in an extended multi-center COVID-19 cohort. METHODS: Five hundred seventy-two COVID-19 patients from Wuhan Tongji Hospital Guanggu Branch, Wuhan Leishenshan Hospital, and Wuhan No. Ninth Hospital was enrolled for this study. Patients who developed AKI or reached an outcome of recovery or death during the study period were included. Predictors were evaluated according to data extracted from medical records. RESULTS: Of all patients, a total of 44 (8%) developed AKI. The UCSD-Mayo risk score achieved excellent discrimination in predicting AKI with the C-statistic of 0.88 (95%CI: 0.84-0.91). Next, we determined the UCSD-Mayo risk score had good overall performance (Nagelkerke R2 = 0.32) and calibration in our cohort. Further analysis showed that the UCSD-Mayo risk score performed well in subgroups defined by gender, age, and several chronic comorbidities. However, the discrimination of the UCSD-Mayo risk score in ICU patients and patients with mechanical ventilation was not good which might be resulted from different risk factors of these patients. CONCLUSIONS: We validated the performance of UCSD-Mayo risk score in predicting hospital-acquired AKI in COVID-19 patients was excellent except for patients from ICU or patients with mechanical ventilation.


Subject(s)
Acute Kidney Injury/diagnosis , Acute Kidney Injury/etiology , COVID-19/complications , Severity of Illness Index , Acute Kidney Injury/mortality , Adult , Aged , COVID-19/mortality , China/epidemiology , Female , Hospital Mortality , Humans , Male , Middle Aged , Prognosis , Regression Analysis , Retrospective Studies , Risk Factors , SARS-CoV-2
10.
Am J Clin Oncol ; 44(8): 409-412, 2021 08 01.
Article in English | MEDLINE | ID: covidwho-1262256

ABSTRACT

OBJECTIVES: Current coronavirus disease 2019 (COVID-19) guidelines recommend delaying clinical care for all affected cancer patients, including incidentally diagnosed asymptomatic infections. This retrospective study conducted in a safety-net hospital in Houston examines the care delivery of asymptomatic COVID-19 cancer patients and how their diagnosis affected their care. METHODS: A retrospective chart review was conducted on cancer patients with a documented positive SARS-CoV-2 laboratory result in the Harris Health System in Houston, Texas. Patient demographics, treatment delays, and patient outcomes were analyzed. RESULTS: Thirteen percent (n=24) of all patients with cancer and COVID-19 diagnosis (n=181) were asymptomatic and 96% had a solid organ malignancy. Among asymptomatic patients, 44% (n=11) of them experienced a median treatment delay of 33 days and 21% (n=5) transitioned to hospice. No patients had progression of disease at first evaluation after recovering from COVID-19 diagnosis. Asymptomatic patients were more likely to have a worse ECOG performance status, metastatic disease, and charity insurance as compared with symptomatic patients. CONCLUSIONS: This study supports the safety of our current isolation guidelines for all COVID-19 asymptomatic cancer patients. While treatment delays occurred, they did not appear to significantly impact overall care. Differences in care delivery and health care usage patterns between symptomatic and asymptomatic patients demonstrate the need for continued studies in vulnerable populations.


Subject(s)
COVID-19/etiology , Delivery of Health Care/methods , Neoplasms/therapy , Neoplasms/virology , Adult , Aged , Aged, 80 and over , Asymptomatic Infections/epidemiology , COVID-19/epidemiology , COVID-19 Testing , Delivery of Health Care/organization & administration , Female , Humans , Male , Middle Aged , Patient Safety , Safety-net Providers , Tertiary Care Centers , Texas/epidemiology , Time-to-Treatment
11.
Sci Total Environ ; 791: 148226, 2021 Oct 15.
Article in English | MEDLINE | ID: covidwho-1253611

ABSTRACT

Absorbing carbonaceous aerosols, i.e. black and brown carbon (BC and BrC), affected heavily on climate change, regional air quality and human health. The nationwide lockdown measures in 2020 were performed to against the COVID-19 outbreak, which could provide an important opportunity to understand their variations on light absorption, concentrations, sources and formation mechanism of carbonaceous aerosols. The BC concentration in Wuhan megacity (WH) was 1.9 µg m-3 during lockdown, which was 24% lower than those in the medium-sized cities and 26% higher than those in small city; in addition, 39% and 16-23% reductions occurred compared with the same periods in 2019 in WH and other cities, respectively. Fossil fuels from vehicles and industries were the major contributors to BC; and compared with other periods, minimum contribution (64-86%) mainly from fossil fuel to BC occurred during the lockdown in all cities. Secondary BrC (BrCsec) played a major role in the BrC light absorption, accounting for 65-77% in WH during different periods. BrCsec was promoted under high humidity, and decreased through the photobleaching of chromophores under higher Ox. Generally, the lockdown measures reduced the BC concentrations significantly; however, the variation of BrCsec was slight.


Subject(s)
COVID-19 , Soot/analysis , Carbon/analysis , China , Cities , Communicable Disease Control , Environmental Monitoring , Humans , SARS-CoV-2
12.
Ann Transl Med ; 9(9): 811, 2021 May.
Article in English | MEDLINE | ID: covidwho-1257377

ABSTRACT

Since the outbreak of coronavirus disease in 2019, the controversy over the effectiveness, safety, and enforceability of masks used by the public has been prominent. This study aims to identify, describe, and organize the currently available high-quality design evidence concerning mask use during the spread of respiratory viruses and find evidence gaps. Databases including PubMed, Cochrane Library, Web of Science, EMBASE, WHO International Clinical Trials Registry Platform (ICTRP), clinical trial registry, gray literature database, and reference lists of articles were searched for relevant randomized controlled trials (RCTs) and systematic reviews (SRs) in April 2020. The quality of the studies was assessed using the risk of bias tool recommended by the Cochrane Handbook Version 5.1.0 and the Assessment of Multiple Systematic Reviews (AMSTAR 2) tool. A bubble plot was designed to display information in four dimensions. Finally, twenty-one RCTs and nine SRs met our inclusion criteria. Most studies were of "Low quality" and focused on healthcare workers. Six RCTs reported adverse effects, with one implying that the cloth masks reuse may increase the infection risk. When comparing masks with usual practice, over 70% RCTs and also SRs showed that masks were "beneficial" or "probably beneficial"; however, when comparing N95 respirators with medical masks, 75% of SRs showed "no effect", whereas 50% of RCTs showed "beneficial effect". Overall, the current evidence provided by high-quality designs may be insufficient to deal with a second impact of the pandemic. Masks may be effective in interrupting or reducing the spread of respiratory viruses; however, the effect of an N95 respirator or cloth masks versus medical masks is unclear. Additional high-quality studies determining the impact of prolonged mask use on vulnerable populations (such as children and pregnant women), the possible adverse effects (such as skin allergies and shortness of breath) and optimal settings and exposure circumstances for populations to use masks are needed.

13.
Proc Natl Acad Sci U S A ; 118(24)2021 06 15.
Article in English | MEDLINE | ID: covidwho-1246475

ABSTRACT

The COVID-19 pandemic is a global threat presenting health, economic, and social challenges that continue to escalate. Metapopulation epidemic modeling studies in the susceptible-exposed-infectious-removed (SEIR) style have played important roles in informing public health policy making to mitigate the spread of COVID-19. These models typically rely on a key assumption on the homogeneity of the population. This assumption certainly cannot be expected to hold true in real situations; various geographic, socioeconomic, and cultural environments affect the behaviors that drive the spread of COVID-19 in different communities. What's more, variation of intracounty environments creates spatial heterogeneity of transmission in different regions. To address this issue, we develop a human mobility flow-augmented stochastic SEIR-style epidemic modeling framework with the ability to distinguish different regions and their corresponding behaviors. This modeling framework is then combined with data assimilation and machine learning techniques to reconstruct the historical growth trajectories of COVID-19 confirmed cases in two counties in Wisconsin. The associations between the spread of COVID-19 and business foot traffic, race and ethnicity, and age structure are then investigated. The results reveal that, in a college town (Dane County), the most important heterogeneity is age structure, while, in a large city area (Milwaukee County), racial and ethnic heterogeneity becomes more apparent. Scenario studies further indicate a strong response of the spread rate to various reopening policies, which suggests that policy makers may need to take these heterogeneities into account very carefully when designing policies for mitigating the ongoing spread of COVID-19 and reopening.


Subject(s)
COVID-19/epidemiology , COVID-19/transmission , Human Migration , Models, Biological , Pandemics , SARS-CoV-2 , Cities/epidemiology , Humans , Wisconsin/epidemiology
14.
Asian J Psychiatr ; 60: 102656, 2021 Jun.
Article in English | MEDLINE | ID: covidwho-1184783

ABSTRACT

BACKGROUND AND AIM: Recently, the availability and usefulness of mobile self-help mental health applications have increased, but few applications deal with COVID-19-related psychological problems. This study explored the intervention efficacy of a mobile application on addressing psychological problems related to COVID-19. METHODS: A longitudinal control trial involving 129 Chinese participants with depression symptoms was conducted through the mobile application "Care for Your Mental Health and Sleep during COVID-19" (CMSC) based on WeChat. Participants were divided into two groups: mobile internet cognitive behavioral therapy (MiCBT) and wait-list. The primary outcome was improvement in depression symptoms. Secondary outcomes included improvement in anxiety and insomnia. The MiCBT group received three self-help CBT intervention sessions in one week via CMSC. RESULTS: The MiCBT group showed significant improvement in depression and insomnia (allP < 0.05) compared with the wait-list group. Although both groups showed significant improvement in anxiety at the intervention's end, compared with the wait-list group, the MiCBT group had no significant advantage. Correlation analysis showed that improvement in depression and anxiety had a significant positive association with education level. Changes in insomnia were significantly negatively correlated with anxiety of COVID-19 at the baseline. CMSC was considered helpful (n=68, 81.9 %) and enjoyable (n=54, 65.9 %) in relieving depression and insomnia during the COVID-19 outbreak. CONCLUSIONS: CMSC is verified to be effective and convenient for improving COVID-19-related depression and insomnia symptoms. A large study with sufficient evidence is required to determine its continuous effect on reducing mental health problems during the pandemic.


Subject(s)
Anxiety/therapy , COVID-19/psychology , Cognitive Behavioral Therapy/methods , Depression/therapy , Sleep Initiation and Maintenance Disorders/psychology , Sleep Initiation and Maintenance Disorders/therapy , Anxiety/psychology , COVID-19/epidemiology , Depression/psychology , Female , Humans , Male , Mental Health , Pandemics , SARS-CoV-2 , Sleep Initiation and Maintenance Disorders/diagnosis , Treatment Outcome
15.
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
16.
Sci Total Environ ; 739: 140000, 2020 Oct 15.
Article in English | MEDLINE | ID: covidwho-981143

ABSTRACT

Wuhan was the first city to adopt the lockdown measures to prevent COVID-19 spreading, which improved the air quality accordingly. This study investigated the variations in chemical compositions, source contributions, and regional transport of fine particles (PM2.5) during January 23-February 22 of 2020, compared with the same period in 2019. The average mass concentration of PM2.5 decreased from 72.9 µg m-3 (2019) to 45.9 µg m-3 (2020), by 27.0 µg m-3. It was predominantly contributed by the emission reduction (92.0%), retrieved from a random forest tree approach. The main chemical species of PM2.5 all decreased with the reductions ranging from 0.85 µg m-3 (chloride) to 9.86 µg m-3 (nitrate) (p < 0.01). Positive matrix factorization model indicated that the mass contributions of seven PM2.5 sources all decreased. However, their contribution percentages varied from -11.0% (industrial processes) to 8.70% (secondary inorganic aerosol). Source contributions of PM2.5 transported from potential geographical regions showed reductions with mean values ranging from 0.22 to 4.36 µg m-3. However, increased contributions of firework burning, secondary inorganic aerosol, road dust, and vehicle emissions from transboundary transport were observed. This study highlighted the complex and nonlinear response of chemical compositions and sources of PM2.5 to air pollution control measures, suggesting the importance of regional-joint control.


Subject(s)
Air Pollutants/analysis , Coronavirus Infections , Pandemics , Particulate Matter/analysis , Pneumonia, Viral , Betacoronavirus , COVID-19 , Cities , Environmental Monitoring , Humans , SARS-CoV-2 , Vehicle Emissions/analysis
17.
Artif Organs ; 45(7): 762-769, 2021 Jul.
Article in English | MEDLINE | ID: covidwho-978684

ABSTRACT

Our aim was to investigate the effect of artificial liver blood purification treatment on the survival of severe/critical patients with coronavirus disease 2019 (COVID-19). A total of 101 severe and critical patients with coronavirus SARS-CoV-2 infection were enrolled in this open, case-control, multicenter, prospective study. According to the patients' and their families' willingness, they were divided into two groups. One was named the treatment group, in which the patients received artificial liver therapy plus comprehensive treatment (n = 50), while the other was named the control group, in which the patients received only comprehensive treatment (n = 51). Clinical data and laboratory examinations, as well as the 28-day mortality rate, were collected and analyzed. Baseline data comparisons on average age, sex, pre-treatment morbidity, initial symptoms, vital signs, pneumonia severity index score, blood routine examination and biochemistry indices etc. showed no difference between the two groups. Cytokine storm was detected, with a significant increase of serum interleukin-6 (IL-6) level. The serum IL-6 level decreased from 119.94 to 20.49 pg/mL in the treatment group and increased from 40.42 to 50.81 pg/mL in the control group (P < .05), indicating that artificial liver therapy significantly decreased serum IL-6. The median duration of viral nucleic acid persistence was 19 days in the treatment group (ranging from 6 to 67 days) and 17 days in the control group (ranging from 3 to 68 days), no significant difference was observed (P = .36). As of 28-day follow-up,17 patients in the treatment group experienced a median weaning time of 24 days, while 11 patients in the control group experienced a median weaning time of 35 days, with no significant difference between the two groups (P = .33). The 28-day mortality rates were 16% (8/50) in the treatment group and 50.98% (26/51) in the control group, with a significant difference (z = 3.70, P < .001). Cytokine storm is a key factor in the intensification of COVID-19 pneumonia. The artificial liver therapy blocks the cytokine storm by clearing inflammatory mediators, thus preventing severe cases from progressing to critically ill stages and markedly reducing short-term mortality.


Subject(s)
COVID-19/therapy , Cytokine Release Syndrome/prevention & control , Liver, Artificial , Plasma Exchange/instrumentation , Aged , Biomarkers/blood , COVID-19/blood , COVID-19/mortality , COVID-19/virology , Case-Control Studies , Cytokine Release Syndrome/blood , Cytokine Release Syndrome/mortality , Cytokine Release Syndrome/virology , Cytokines/blood , Female , Hospital Mortality , Host-Pathogen Interactions , Humans , Male , Middle Aged , Plasma Exchange/adverse effects , Plasma Exchange/mortality , Prospective Studies , SARS-CoV-2/pathogenicity , Severity of Illness Index , Time Factors , Treatment Outcome , Viral Load
19.
Gastroenterology ; 159(4): 1302-1310.e5, 2020 Oct.
Article in English | MEDLINE | ID: covidwho-621434

ABSTRACT

BACKGROUND & AIMS: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infects intestinal cells, and might affect the intestinal microbiota. We investigated changes in the fecal fungal microbiomes (mycobiome) of patients with SARS-CoV-2 infection during hospitalization and on recovery. METHODS: We performed deep shotgun metagenomic sequencing analysis of fecal samples from 30 patients with coronavirus disease 2019 (COVID-19) in Hong Kong, from February 5 through May 12, 2020. Fecal samples were collected 2 to 3 times per week from time of hospitalization until discharge. We compared fecal mycobiome compositions of patients with COVID-19 with those from 9 subjects with community-acquired pneumonia and 30 healthy individuals (controls). We assessed fecal mycobiome profiles throughout time of hospitalization until clearance of SARS-CoV-2 from nasopharyngeal samples. RESULTS: Patients with COVID-19 had significant alterations in their fecal mycobiomes compared with controls, characterized by enrichment of Candia albicans and a highly heterogeneous mycobiome configuration, at time of hospitalization. Although fecal mycobiomes of 22 patients with COVID-19 did not differ significantly from those of controls during times of hospitalization, 8 of 30 patients with COVID-19 had continued significant differences in fecal mycobiome composition, through the last sample collected. The diversity of the fecal mycobiome of the last sample collected from patients with COVID-19 was 2.5-fold higher than that of controls (P < .05). Samples collected at all timepoints from patients with COVID-19 had increased proportions of opportunistic fungal pathogens, Candida albicans, Candida auris, and Aspergillus flavus compared with controls. Two respiratory-associated fungal pathogens, A. flavus and Aspergillus niger, were detected in fecal samples from a subset of patients with COVID-19, even after clearance of SARS-CoV-2 from nasopharyngeal samples and resolution of respiratory symptoms. CONCLUSIONS: In a pilot study, we found heterogeneous configurations of the fecal mycobiome, with enrichment of fungal pathogens from the genera Candida and Aspergillus, during hospitalization of 30 patients with COVID-19 compared with controls. Unstable gut mycobiomes and prolonged dysbiosis persisted in a subset of patients with COVID-19 up to 12 days after nasopharyngeal clearance of SARS-CoV-2. Studies are needed to determine whether alterations in intestinal fungi contribute to or result from SARS-CoV-2 infection, and the effects of these changes in disease progression.


Subject(s)
Coronavirus Infections/microbiology , Feces/microbiology , Fungi/isolation & purification , Gastrointestinal Microbiome , Mycobiome , Pneumonia, Viral/microbiology , Adult , Aged , Aspergillus flavus/genetics , Aspergillus flavus/isolation & purification , Aspergillus niger/genetics , Aspergillus niger/isolation & purification , Betacoronavirus , COVID-19 , Candida/genetics , Candida/isolation & purification , Candida albicans/genetics , Candida albicans/isolation & purification , Case-Control Studies , Community-Acquired Infections/microbiology , DNA, Fungal/analysis , Female , Fungi/genetics , Humans , Male , Metagenomics , Middle Aged , Nasopharynx/virology , Pandemics , Patient Discharge , Pneumonia/microbiology , SARS-CoV-2 , Time Factors , Young Adult
20.
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
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