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1.
PLoS Pathog ; 18(2): e1010259, 2022 Feb.
Article in English | MEDLINE | ID: covidwho-1690683

ABSTRACT

At the end of 2019 Wuhan witnessed an outbreak of "atypical pneumonia" that later developed into a global pandemic. Metagenomic sequencing rapidly revealed the causative agent of this outbreak to be a novel coronavirus denoted SARS-CoV-2. To provide a snapshot of the pathogens in pneumonia-associated respiratory samples from Wuhan prior to the emergence of SARS-CoV-2, we collected bronchoalveolar lavage fluid samples from 408 patients presenting with pneumonia and acute respiratory infections at the Central Hospital of Wuhan between 2016 and 2017. Unbiased total RNA sequencing was performed to reveal their "total infectome", including viruses, bacteria and fungi. We identified 35 pathogen species, comprising 13 RNA viruses, 3 DNA viruses, 16 bacteria and 3 fungi, often at high abundance and including multiple co-infections (13.5%). SARS-CoV-2 was not present. These data depict a stable core infectome comprising common respiratory pathogens such as rhinoviruses and influenza viruses, an atypical respiratory virus (EV-D68), and a single case of a sporadic zoonotic pathogen-Chlamydia psittaci. Samples from patients experiencing respiratory disease on average had higher pathogen abundance than healthy controls. Phylogenetic analyses of individual pathogens revealed multiple origins and global transmission histories, highlighting the connectedness of the Wuhan population. This study provides a comprehensive overview of the pathogens associated with acute respiratory infections and pneumonia, which were more diverse and complex than obtained using targeted PCR or qPCR approaches. These data also suggest that SARS-CoV-2 or closely related viruses were absent from Wuhan in 2016-2017.


Subject(s)
COVID-19/epidemiology , Disease Outbreaks , Pneumonia/epidemiology , Respiratory Tract Infections/epidemiology , SARS-CoV-2/isolation & purification , Acute Disease , Adolescent , Adult , Aged , Aged, 80 and over , Bronchoalveolar Lavage Fluid/microbiology , COVID-19/virology , China/epidemiology , Cohort Studies , Female , Gene Expression Profiling , Humans , Male , Metagenomics , Middle Aged , Phylogeny , Pneumonia/microbiology , Respiratory Tract Infections/microbiology , Young Adult
2.
EuropePMC; 2020.
Preprint in English | EuropePMC | ID: ppcovidwho-311721

ABSTRACT

Background: Pulmonary embolism is a severe condition prone to misdiagnosis given its nonspecific signs and symptoms. Previous studies on the pneumonia outbreak caused by coronavirus disease 2019 (COVID-19) showed a number of patients with elevated d-dimer, whether those patients combined with pulmonary embolism got our attention. Methods: Data on clinical manifestations, laboratory and radiological findings, treatment, and disease progression of 19 patients with laboratory-confirmed COVID-19 pneumonia,who completed computed tomographic pulmonary angiography (CTPA) during hospitalization in the Central Hospital of Wuhan from January 2 to March 26, 2020, were reviewed. Results: Of the 19 suspected pulmonary embolism and subjected to CTPA patients, six were diagnosed with pulmonary embolism. The Wells’ score of the six patients with pulmonary embolism was 0–1, which suggested a low risk of pulmonary embolism. The median level of d-dimers collected at the day before or on the day of CTPA completion in the patients with pulmonary embolism was 18.36 (interquartile range [IQR]: 6.69–61.46) µg/mL, which was much higher than that in the patients without pulmonary embolism (median 9.47 [IQR: 4.22–28.02] µg/mL). Of the 6 patients diagnosed with pulmonary embolism, all patients received anticoagulant therapy, 5 of which survived and were discharged and 1 died. Conclusion: A potential causal relationship exists between COVID-19 infection and pulmonary embolism, but whether this phenomenon is common remains uncertain. The clinical manifestations of COVID-19 patients who developed pulmonary embolism are similar to those of patients with increased d-dimer alone, prompting a significant challenge on differential diagnoses.

3.
Diabetes Care ; 44(4): 865-873, 2021 04.
Article in English | MEDLINE | ID: covidwho-1041481

ABSTRACT

OBJECTIVE: To investigate the association of in-hospital early-phase glycemic control with adverse outcomes among inpatients with coronavirus disease 2019 (COVID-19) in Wuhan, China. RESEARCH DESIGN AND METHODS: The study is a large case series, and data were obtained regarding consecutive patients hospitalized with COVID-19 in the Central Hospital of Wuhan between 2 January and 15 February 2020. All patients with definite outcomes (death or discharge) were included. Demographic, clinical, treatment, and laboratory information were extracted from electronic medical records. We collected daily fasting glucose data from standard morning fasting blood biochemistry to determine glycemic status and fluctuation (calculated as the square root of the variance of daily fasting glucose levels) during the 1st week of hospitalization. RESULTS: A total of 548 patients were included in the study (median age 57 years; 298 [54%] were women, and n = 99 had diabetes [18%]), 215 suffered acute respiratory distress syndrome (ARDS), 489 survived, and 59 died. Patients who had higher mean levels of glucose during their 1st week of hospitalization were older and more likely to have a comorbidity and abnormal laboratory markers, prolonged hospital stays, increased expenses, and greater risks of severe pneumonia, ARDS, and death. Compared with patients with the lowest quartile of glycemic fluctuation, those who had the highest quartile of fluctuation magnitude had an increased risk of ARDS (risk ratio 1.97 [95% CI 1.01, 4.04]) and mortality (hazard ratio 2.73 [95% CI 1.06, 7.73]). CONCLUSIONS: These results may have implications for optimizing glycemic control strategies in COVID-19 patients during the early phase of hospitalization.


Subject(s)
Blood Glucose/metabolism , COVID-19/blood , COVID-19/diagnosis , COVID-19/mortality , Hospitalization , Adult , Aged , COVID-19/pathology , China/epidemiology , Comorbidity , Diabetes Mellitus/blood , Diabetes Mellitus/epidemiology , Disease Progression , Female , Hospitalization/statistics & numerical data , Hospitals/statistics & numerical data , Humans , Male , Middle Aged , Prognosis , Retrospective Studies , SARS-CoV-2/physiology
4.
Nat Biomed Eng ; 4(12): 1188-1196, 2020 12.
Article in English | MEDLINE | ID: covidwho-894396

ABSTRACT

Accurate assays for the detection of antibodies to SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) are essential for the control of the COVID-19 (coronavirus disease 2019) pandemic. Here, we report antibody and antibody-avidity assays, relying on near-infrared-fluorescence amplification by nanostructured plasmonic gold substrates, for the simultaneous detection of antibodies to the S1 subunit of the spike protein and to the receptor binding domain of SARS-CoV-2 in human serum and saliva, and for quantifying immunoglobulin avidities against coronavirus antigens from SARS-CoV-2, SARS-CoV-1 and the common-cold viruses OC43, HKU1, NL63 and 229E. The antibody assay detected immunoglobulin M in 87% (52 of 60) COVID-19-positive serum samples collected 6 or more days after symptom onset (and the immunoglobulins M and G in all 33 samples collected at least 15 days after symptom onset), and correctly classified 456 out of the 457 COVID-19-negative serum samples tested (424 of them collected before the pandemic, including 73 that were positive for other viruses). We used the antibody-avidity assay to study antibody-maturation patterns, anamnestic responses, and cross-immunity to the common-cold coronaviruses.


Subject(s)
Antibodies, Viral/blood , Antibodies, Viral/immunology , COVID-19/immunology , SARS-CoV-2/immunology , Saliva/immunology , Aged , Antibody Affinity/immunology , Antigens, Viral/immunology , COVID-19/blood , COVID-19 Serological Testing/methods , Female , Humans , Immunoglobulin G/blood , Immunoglobulin G/immunology , Immunoglobulin M/blood , Immunoglobulin M/immunology , Pandemics/prevention & control
5.
SSRN; 2020.
Preprint | SSRN | ID: ppcovidwho-648

ABSTRACT

Background: Coronavirus disease 2019 is an emerging infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has an average

6.
Stroke ; 51(9): 2674-2682, 2020 09.
Article in English | MEDLINE | ID: covidwho-697017

ABSTRACT

BACKGROUND AND PURPOSE: No studies have reported the effect of the coronavirus disease 2019 (COVID-19) epidemic on patients with preexisting stroke. We aim to study the clinical course of COVID-19 patients with preexisting stroke and to investigate death-related risk factors. METHODS: We consecutively included 651 adult inpatients with COVID-19 from the Central Hospital of Wuhan between January 2 and February 15, 2020. Data on the demography, comorbidities, clinical manifestations, laboratory findings, treatments, complications, and outcomes (ie, discharged or death) of the participants were extracted from electronic medical records and compared between patients with and without preexisting stroke. The association between risk factors and mortality was estimated using a Cox proportional hazards regression model for stroke patients infected with severe acute respiratory syndrome coronavirus 2. RESULTS: Of the 651 patients with COVID-19, 49 with preexisting stroke tended to be elderly, male, had more underlying comorbidities and greater severity of illness, prolonged length of hospital stay, and greater hospitalization expenses than those without preexisting stroke. Cox regression analysis indicated that the patients with stroke had a higher risk of developing critical pneumonia (adjusted hazard ratio, 2.01 [95% CI, 1.27-3.16]) and subsequent mortality (adjusted hazard ratio, 1.73 [95% CI, 1.00-2.98]) than the patients without stroke. Among the 49 stroke patients, older age and higher score of Glasgow Coma Scale or Sequential Organ Failure Assessment were independent risk factors associated with in-hospital mortality. CONCLUSIONS: Preexisting stroke patients infected with severe acute respiratory syndrome coronavirus 2 were readily predisposed to death, providing an important message to individuals and health care workers that preventive measures must be implemented to protect and reduce transmission in stroke patients in this COVID-19 crisis.


Subject(s)
Coronavirus Infections/complications , Coronavirus Infections/mortality , Pneumonia, Viral/complications , Pneumonia, Viral/mortality , Stroke/complications , Stroke/mortality , Adult , Age Factors , Aged , Aged, 80 and over , COVID-19 , China/epidemiology , Comorbidity , Coronavirus Infections/therapy , Disease Progression , Electronic Health Records , Female , Glasgow Coma Scale , Hospital Mortality , Humans , Male , Middle Aged , Multiple Organ Failure/epidemiology , Multiple Organ Failure/etiology , Pandemics , Pneumonia/etiology , Pneumonia, Viral/therapy , Retrospective Studies , Risk Factors , Sex Factors , Stroke/therapy , Treatment Outcome
7.
Nature ; 580(7803): E7, 2020 04.
Article in English | MEDLINE | ID: covidwho-73543

ABSTRACT

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

8.
Platelets ; 31(4): 490-496, 2020 May 18.
Article in English | MEDLINE | ID: covidwho-66223

ABSTRACT

BACKGROUND: Thrombocytopenia has been implicated in patients infected with severe acute respiratory syndrome coronavirus 2, while the association of platelet count and changes with subsequent mortality remains unclear. METHODS: The clinical and laboratory data of 383 patients with the definite outcome by March 1, 2020 in the Central Hospital of Wuhan were reviewed. The association between platelet parameters and mortality risk was estimated by utilizing Cox proportional hazard regression models. RESULTS: Among the 383 patients, 334 (87.2%) were discharged and survived, and 49 (12.8%) died. Thrombocytopenia at admission was associated with mortality of almost three times as high as that for those without thrombocytopenia (P < 0.05). Cox regression analyses revealed that platelet count was an independent risk factor associated with in-hospital mortality in a dose-dependent manner. An increment of per 50 × 109/L in platelets was associated with a 40% decrease in mortality (hazard ratio: 0.60, 95%CI: 0.43, 0.84). Dynamic changes of platelets were also closely related to death during hospitalization. CONCLUSIONS: Baseline platelet levels and changes were associated with subsequent mortality. Monitoring platelets during hospitalization may be important in the prognosis of patients with coronavirus disease in 2019.


Subject(s)
Betacoronavirus , Coronavirus Infections , Pandemics , Pneumonia, Viral , Thrombocytopenia , Adult , Aged , COVID-19 , Cohort Studies , Coronavirus Infections/blood , Coronavirus Infections/complications , Coronavirus Infections/mortality , Female , Hospital Mortality , Humans , Male , Middle Aged , Platelet Count , Pneumonia, Viral/blood , Pneumonia, Viral/complications , Pneumonia, Viral/mortality , Prognosis , Retrospective Studies , Risk Factors , SARS-CoV-2 , Thrombocytopenia/etiology , Thrombocytopenia/mortality
9.
Nature ; 579(7798): 265-269, 2020 03.
Article in English | MEDLINE | ID: covidwho-258

ABSTRACT

Emerging infectious diseases, such as severe acute respiratory syndrome (SARS) and Zika virus disease, present a major threat to public health1-3. Despite intense research efforts, how, when and where new diseases appear are still a source of considerable uncertainty. A severe respiratory disease was recently reported in Wuhan, Hubei province, China. As of 25 January 2020, at least 1,975 cases had been reported since the first patient was hospitalized on 12 December 2019. Epidemiological investigations have suggested that the outbreak was associated with a seafood market in Wuhan. Here we study a single patient who was a worker at the market and who was admitted to the Central Hospital of Wuhan on 26 December 2019 while experiencing a severe respiratory syndrome that included fever, dizziness and a cough. Metagenomic RNA sequencing4 of a sample of bronchoalveolar lavage fluid from the patient identified a new RNA virus strain from the family Coronaviridae, which is designated here 'WH-Human 1' coronavirus (and has also been referred to as '2019-nCoV'). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that the virus was most closely related (89.1% nucleotide similarity) to a group of SARS-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) that had previously been found in bats in China5. This outbreak highlights the ongoing ability of viral spill-over from animals to cause severe disease in humans.


Subject(s)
Betacoronavirus/classification , Communicable Diseases, Emerging/complications , Communicable Diseases, Emerging/virology , Coronavirus Infections/complications , Coronavirus Infections/virology , Pneumonia, Viral/complications , Pneumonia, Viral/virology , Severe Acute Respiratory Syndrome/etiology , Severe Acute Respiratory Syndrome/virology , Adult , Betacoronavirus/genetics , COVID-19 , China , Communicable Diseases, Emerging/diagnostic imaging , Communicable Diseases, Emerging/pathology , Coronavirus Infections/diagnostic imaging , Coronavirus Infections/pathology , Genome, Viral/genetics , Humans , Lung/diagnostic imaging , Male , Phylogeny , Pneumonia, Viral/diagnostic imaging , Pneumonia, Viral/pathology , RNA, Viral/genetics , Recombination, Genetic/genetics , SARS-CoV-2 , Severe Acute Respiratory Syndrome/diagnostic imaging , Severe Acute Respiratory Syndrome/pathology , Tomography, X-Ray Computed , Whole Genome Sequencing
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