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Identification of coronavirus sequences in carp cDNA from Wuhan, China.

ABSTRACT: Severe acute respiratory syndrome (SARS)-like coronavirus sequences were identified in two separate complementary DNA (cDNA) pools. The first pool was from a Carassius auratus (crusian carp) cell line and the second was from Ctenopharyngodon idella (grass carp) head kidney tissue. BLAST analysis suggests that these sequences belong to SARS-like coronaviruses, and that they are not evolutionarily conserved in other species. Investigation of the submitting laboratories revealed that two laboratories from the Institute of Hydrobiology at the Chinese Academy of Sciences in Wuhan, China performed the research and submitted the cDNA libraries to GenBank. This institution is very close in proximity to the Wuhan South China Seafood Wholesale Market where SARS-CoV-2 first amplified in the human population. It is possible that these sequences are an artifact of the bioinformatics pipeline that was used. It is also possible that SARS-like coronaviruses are a common environmental pathogen in the region that may be in aquatic habitats.

SUBMITTER: Conway MJ

PROVIDER: S-EPMC7228230 | biostudies-literature | 2020 Sep

REPOSITORIES: biostudies-literature

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Identification of coronavirus sequences in carp cDNA from Wuhan, China.

Conway Michael J MJ

Journal of medical virology 20200316 9

Severe acute respiratory syndrome (SARS)-like coronavirus sequences were identified in two separate complementary DNA (cDNA) pools. The first pool was from a Carassius auratus (crusian carp) cell line and the second was from Ctenopharyngodon idella (grass carp) head kidney tissue. BLAST analysis suggests that these sequences belong to SARS-like coronaviruses, and that they are not evolutionarily conserved in other species. Investigation of the submitting laboratories revealed that two laboratori ...[more]

PMID: 32159234

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Project description:BackgroundA recent cluster of pneumonia cases in Wuhan, China, was caused by a novel betacoronavirus, the 2019 novel coronavirus (2019-nCoV). We report the epidemiological, clinical, laboratory, and radiological characteristics and treatment and clinical outcomes of these patients.MethodsAll patients with suspected 2019-nCoV were admitted to a designated hospital in Wuhan. We prospectively collected and analysed data on patients with laboratory-confirmed 2019-nCoV infection by real-time RT-PCR and next-generation sequencing. Data were obtained with standardised data collection forms shared by WHO and the International Severe Acute Respiratory and Emerging Infection Consortium from electronic medical records. Researchers also directly communicated with patients or their families to ascertain epidemiological and symptom data. Outcomes were also compared between patients who had been admitted to the intensive care unit (ICU) and those who had not.FindingsBy Jan 2, 2020, 41 admitted hospital patients had been identified as having laboratory-confirmed 2019-nCoV infection. Most of the infected patients were men (30 [73%] of 41); less than half had underlying diseases (13 [32%]), including diabetes (eight [20%]), hypertension (six [15%]), and cardiovascular disease (six [15%]). Median age was 49·0 years (IQR 41·0-58·0). 27 (66%) of 41 patients had been exposed to Huanan seafood market. One family cluster was found. Common symptoms at onset of illness were fever (40 [98%] of 41 patients), cough (31 [76%]), and myalgia or fatigue (18 [44%]); less common symptoms were sputum production (11 [28%] of 39), headache (three [8%] of 38), haemoptysis (two [5%] of 39), and diarrhoea (one [3%] of 38). Dyspnoea developed in 22 (55%) of 40 patients (median time from illness onset to dyspnoea 8·0 days [IQR 5·0-13·0]). 26 (63%) of 41 patients had lymphopenia. All 41 patients had pneumonia with abnormal findings on chest CT. Complications included acute respiratory distress syndrome (12 [29%]), RNAaemia (six [15%]), acute cardiac injury (five [12%]) and secondary infection (four [10%]). 13 (32%) patients were admitted to an ICU and six (15%) died. Compared with non-ICU patients, ICU patients had higher plasma levels of IL2, IL7, IL10, GSCF, IP10, MCP1, MIP1A, and TNFα.InterpretationThe 2019-nCoV infection caused clusters of severe respiratory illness similar to severe acute respiratory syndrome coronavirus and was associated with ICU admission and high mortality. Major gaps in our knowledge of the origin, epidemiology, duration of human transmission, and clinical spectrum of disease need fulfilment by future studies.FundingMinistry of Science and Technology, Chinese Academy of Medical Sciences, National Natural Science Foundation of China, and Beijing Municipal Science and Technology Commission.

Project description:ImportanceThe outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China, is serious and has the potential to become an epidemic worldwide. Several studies have described typical clinical manifestations including fever, cough, diarrhea, and fatigue. However, to our knowledge, it has not been reported that patients with COVID-19 had any neurologic manifestations.ObjectiveTo study the neurologic manifestations of patients with COVID-19.Design, setting, and participantsThis is a retrospective, observational case series. Data were collected from January 16, 2020, to February 19, 2020, at 3 designated special care centers for COVID-19 (Main District, West Branch, and Tumor Center) of the Union Hospital of Huazhong University of Science and Technology in Wuhan, China. The study included 214 consecutive hospitalized patients with laboratory-confirmed diagnosis of severe acute respiratory syndrome coronavirus 2 infection.Main outcomes and measuresClinical data were extracted from electronic medical records, and data of all neurologic symptoms were checked by 2 trained neurologists. Neurologic manifestations fell into 3 categories: central nervous system manifestations (dizziness, headache, impaired consciousness, acute cerebrovascular disease, ataxia, and seizure), peripheral nervous system manifestations (taste impairment, smell impairment, vision impairment, and nerve pain), and skeletal muscular injury manifestations.ResultsOf 214 patients (mean [SD] age, 52.7 [15.5] years; 87 men [40.7%]) with COVID-19, 126 patients (58.9%) had nonsevere infection and 88 patients (41.1%) had severe infection according to their respiratory status. Overall, 78 patients (36.4%) had neurologic manifestations. Compared with patients with nonsevere infection, patients with severe infection were older, had more underlying disorders, especially hypertension, and showed fewer typical symptoms of COVID-19, such as fever and cough. Patients with more severe infection had neurologic manifestations, such as acute cerebrovascular diseases (5 [5.7%] vs 1 [0.8%]), impaired consciousness (13 [14.8%] vs 3 [2.4%]), and skeletal muscle injury (17 [19.3%] vs 6 [4.8%]).Conclusions and relevancePatients with COVID-19 commonly have neurologic manifestations. During the epidemic period of COVID-19, when seeing patients with neurologic manifestations, clinicians should suspect severe acute respiratory syndrome coronavirus 2 infection as a differential diagnosis to avoid delayed diagnosis or misdiagnosis and lose the chance to treat and prevent further transmission.

Project description:Coronavirus disease 2019 (COVID-19) patients were classified into four clinical stages (uncomplicated illness, mild, severe and critical pneumonia) depending on disease severity. We aim to investigate the corresponding clinical, radiological and laboratory characteristics between different clinical stages. A retrospective, single-centre study of 101 confirmed patients with COVID-19 at Renmin Hospital of Wuhan University from 2 January to 28 January 2020 was enrolled; follow-up endpoint was on 8 February 2020. Clinical data were collected and compared during the course of illness. The median age of the 101 patients was 51.0 years and 33.6% were medical staff. Fever (68%), cough (50%) and fatigue (23%) are the most common symptoms. About 26% patients underwent the mechanical ventilation and 98% patients were treated with antibiotics. Thirty-seven per cent patients were cured and 11 died. On admission, the number of patients with uncomplicated illness, mild, severe and critical pneumonia were 2 [2%], 86 [85%], 11 [11%] and 2 [2%]. Forty-four of the 86 mild pneumonia progressed to severe illness within 4 days, with nine patients worsened due to critical pneumonia within 4 days. Two of the 11 severe patients improved to mild condition while three others deteriorated. Significant differences were observed among groups of different clinical stages in numbers of influenced pulmonary segments (6 vs. 12 vs. 17, P < 0.001). A significantly upward trend was witnessed in ground-glass opacities overlapped with striped shadows (33% vs. 42% vs. 55% vs. 80%, P < 0.001), while pure ground-glass opacities gradually decreased as disease progressed (45% vs. 35% vs. 24% vs. 13%, P < 0.001) within 12 days. Lymphocytes, prealbumin and albumin showed a downtrend as disease progressed from mild to severe or critical condition, an uptrend was found in white blood cells, C-reactive protein, neutrophils and lactate dehydrogenase. The proportions of serum amyloid A > 300 mg/l in mild, severe and critical conditions were 18%, 46% and 71%, respectively.

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Identification of coronavirus sequences in carp cDNA from Wuhan, China.

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Identification of coronavirus sequences in carp cDNA from Wuhan, China.

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