Laboratory diagnosis of emerging human coronavirus infections - the state of the art. 2020

Michael J Loeffelholz, and Yi-Wei Tang
Cepheid, Sunnyvale, CA, USA.

The three unprecedented outbreaks of emerging human coronavirus (HCoV) infections at the beginning of the twenty-first century have highlighted the necessity for readily available, accurate and fast diagnostic testing methods. The laboratory diagnostic methods for human coronavirus infections have evolved substantially, with the development of novel assays as well as the availability of updated tests for emerging ones. Newer laboratory methods are fast, highly sensitive and specific, and are gradually replacing the conventional gold standards. This presentation reviews the current laboratory methods available for testing coronaviruses by focusing on the coronavirus disease 2019 (COVID-19) outbreak going on in Wuhan. Viral pneumonias typically do not result in the production of purulent sputum. Thus, a nasopharyngeal swab is usually the collection method used to obtain a specimen for testing. Nasopharyngeal specimens may miss some infections; a deeper specimen may need to be obtained by bronchoscopy. Alternatively, repeated testing can be used because over time, the likelihood of the SARS-CoV-2 being present in the nasopharynx increases. Several integrated, random-access, point-of-care molecular devices are currently under development for fast and accurate diagnosis of SARS-CoV-2 infections. These assays are simple, fast and safe and can be used in the local hospitals and clinics bearing the burden of identifying and treating patients.

UI MeSH Term Description Entries
D011024 Pneumonia, Viral Inflammation of the lung parenchyma that is caused by a viral infection. Pneumonias, Viral,Viral Pneumonia,Viral Pneumonias
D004196 Disease Outbreaks Sudden increase in the incidence of a disease. The concept includes EPIDEMICS and PANDEMICS. Outbreaks,Infectious Disease Outbreaks,Disease Outbreak,Disease Outbreak, Infectious,Disease Outbreaks, Infectious,Infectious Disease Outbreak,Outbreak, Disease,Outbreak, Infectious Disease,Outbreaks, Disease,Outbreaks, Infectious Disease
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D000067716 Point-of-Care Testing Allows patient diagnoses in the physician’s office, in other ambulatory setting or at bedside. The results of care are timely, and allow rapid treatment to the patient. (from NIH Fact Sheet Point-of-Care Diagnostic Testing, 2010.) Bedside Testing,Point-Of-Care Diagnostic Testing,Point-Of-Care Diagnostic Tests,Point-Of-Care Diagnostics,Point-Of-Care Test,Point-Of-Care Tests,Point of Care Testing,Diagnostic Test, Point-Of-Care,Diagnostic Testing, Point-Of-Care,Diagnostic Tests, Point-Of-Care,Diagnostic, Point-Of-Care,Diagnostics, Point-Of-Care,Point Of Care Diagnostic Testing,Point Of Care Diagnostic Tests,Point Of Care Diagnostics,Point Of Care Test,Point Of Care Tests,Point-Of-Care Diagnostic,Point-Of-Care Diagnostic Test,Test, Point-Of-Care,Test, Point-Of-Care Diagnostic,Testing, Bedside,Testing, Point-Of-Care Diagnostic,Testing, Point-of-Care,Tests, Point-Of-Care,Tests, Point-Of-Care Diagnostic
D000073640 Betacoronavirus A genus of the family CORONAVIRIDAE which causes respiratory or gastrointestinal disease in a variety of mostly mammals. Human betacoronaviruses include HUMAN ENTERIC CORONAVIRUS; HUMAN CORONAVIRUS OC43; MERS VIRUS; and SEVERE ACUTE RESPIRATORY SYNDROME-RELATED CORONAVIRUS. Members have either core transcription regulatory sequences of 5’-CUAAAC-3’ or 5’-CUAAAC-3’ and mostly have no ORF downstream to the N protein gene. HCoV-HKU1,Human coronavirus HKU1,Pipistrellus bat coronavirus HKU5,Rousettus bat coronavirus HKU9,Tylonycteris bat coronavirus HKU4,Betacoronaviruses
D000086382 COVID-19 A viral disorder generally characterized by high FEVER; COUGH; DYSPNEA; CHILLS; PERSISTENT TREMOR; MUSCLE PAIN; HEADACHE; SORE THROAT; a new loss of taste and/or smell (see AGEUSIA and ANOSMIA) and other symptoms of a VIRAL PNEUMONIA. In severe cases, a myriad of coagulopathy associated symptoms often correlating with COVID-19 severity is seen (e.g., BLOOD COAGULATION; THROMBOSIS; ACUTE RESPIRATORY DISTRESS SYNDROME; SEIZURES; HEART ATTACK; STROKE; multiple CEREBRAL INFARCTIONS; KIDNEY FAILURE; catastrophic ANTIPHOSPHOLIPID ANTIBODY SYNDROME and/or DISSEMINATED INTRAVASCULAR COAGULATION). In younger patients, rare inflammatory syndromes are sometimes associated with COVID-19 (e.g., atypical KAWASAKI SYNDROME; TOXIC SHOCK SYNDROME; pediatric multisystem inflammatory disease; and CYTOKINE STORM SYNDROME). A coronavirus, SARS-CoV-2, in the genus BETACORONAVIRUS is the causative agent. 2019 Novel Coronavirus Disease,2019 Novel Coronavirus Infection,2019-nCoV Disease,2019-nCoV Infection,COVID-19 Pandemic,COVID-19 Pandemics,COVID-19 Virus Disease,COVID-19 Virus Infection,Coronavirus Disease 2019,Coronavirus Disease-19,SARS Coronavirus 2 Infection,SARS-CoV-2 Infection,Severe Acute Respiratory Syndrome Coronavirus 2 Infection,COVID19,2019 nCoV Disease,2019 nCoV Infection,2019-nCoV Diseases,2019-nCoV Infections,COVID 19,COVID 19 Pandemic,COVID 19 Virus Disease,COVID 19 Virus Infection,COVID-19 Virus Diseases,COVID-19 Virus Infections,Coronavirus Disease 19,Disease 2019, Coronavirus,Disease, 2019-nCoV,Disease, COVID-19 Virus,Infection, 2019-nCoV,Infection, COVID-19 Virus,Infection, SARS-CoV-2,Pandemic, COVID-19,SARS CoV 2 Infection,SARS-CoV-2 Infections,Virus Disease, COVID-19,Virus Infection, COVID-19
D000086402 SARS-CoV-2 A species of BETACORONAVIRUS causing atypical respiratory disease (COVID-19) in humans. The organism was first identified in 2019 in Wuhan, China. The natural host is the Chinese intermediate horseshoe bat, RHINOLOPHUS affinis. 2019 Novel Coronavirus,COVID-19 Virus,COVID19 Virus,Coronavirus Disease 2019 Virus,SARS Coronavirus 2,SARS-CoV-2 Virus,Severe Acute Respiratory Syndrome Coronavirus 2,Wuhan Coronavirus,Wuhan Seafood Market Pneumonia Virus,2019-nCoV,2019 Novel Coronaviruses,COVID 19 Virus,COVID-19 Viruses,COVID19 Viruses,Coronavirus 2, SARS,Coronavirus, 2019 Novel,Coronavirus, Wuhan,Novel Coronavirus, 2019,SARS CoV 2 Virus,SARS-CoV-2 Viruses,Virus, COVID-19,Virus, COVID19,Virus, SARS-CoV-2,Viruses, COVID19
D000086663 COVID-19 Vaccines Vaccines or candidate vaccines containing SARS-CoV-2 component antigens, genetic materials, or inactivated SARS-CoV-2 virus, and designed to prevent COVID-19. 2019 Novel Coronavirus Vaccine,2019 Novel Coronavirus Vaccines,2019-nCoV Vaccine,2019-nCoV Vaccines,COVID 19 Vaccine,COVID-19 Vaccine,COVID-19 Virus Vaccine,COVID-19 Virus Vaccines,COVID19 Vaccine,COVID19 Vaccines,COVID19 Virus Vaccine,COVID19 Virus Vaccines,Coronavirus Disease 2019 Vaccine,Coronavirus Disease 2019 Vaccines,Coronavirus Disease 2019 Virus Vaccine,Coronavirus Disease 2019 Virus Vaccines,Coronavirus Disease-19 Vaccine,Coronavirus Disease-19 Vaccines,SARS Coronavirus 2 Vaccines,SARS-CoV-2 Vaccine,SARS-CoV-2 Vaccines,SARS2 Vaccine,SARS2 Vaccines,2019 nCoV Vaccine,2019 nCoV Vaccines,COVID 19 Vaccines,COVID 19 Virus Vaccine,COVID 19 Virus Vaccines,Coronavirus Disease 19 Vaccine,Coronavirus Disease 19 Vaccines,SARS CoV 2 Vaccine,SARS CoV 2 Vaccines,Vaccine, 2019-nCoV,Vaccine, COVID 19,Vaccine, COVID-19,Vaccine, COVID-19 Virus,Vaccine, COVID19,Vaccine, COVID19 Virus,Vaccine, Coronavirus Disease-19,Vaccine, SARS-CoV-2,Vaccine, SARS2,Vaccines, 2019-nCoV,Vaccines, COVID-19,Vaccines, COVID-19 Virus,Vaccines, COVID19,Vaccines, COVID19 Virus,Vaccines, Coronavirus Disease-19,Vaccines, SARS-CoV-2,Vaccines, SARS2,Virus Vaccine, COVID-19,Virus Vaccine, COVID19,Virus Vaccines, COVID-19,Virus Vaccines, COVID19
D000086742 COVID-19 Testing Diagnosis of COVID-19 by assaying bodily fluids or tissues for the presence of COVID-19 antibodies, SARS-COV-2 antigens or the VIRAL RNA of SARS-COV-2. 2019 Novel Coronavirus Disease Testing,2019 Novel Coronavirus Testing,2019-nCoV Disease Testing,2019-nCoV Infection Testing,2019-nCoV Testing,COVID-19 Diagnostic Testing,COVID-19 Virus Testing,COVID19 Testing,COVID19 Virus Testing,Coronavirus Disease 2019 Testing,Coronavirus Disease-19 Testing,SARS Coronavirus 2 Testing,SARS-CoV-2 Testing,Severe Acute Respiratory Syndrome Coronavirus 2 Testing,2019 nCoV Disease Testing,2019 nCoV Infection Testing,2019 nCoV Testing,2019-nCoV Disease Testings,2019-nCoV Infection Testings,2019-nCoV Testings,COVID 19 Diagnostic Testing,COVID 19 Testing,COVID 19 Virus Testing,COVID-19 Diagnostic Testings,COVID-19 Testings,COVID-19 Virus Testings,COVID19 Testings,COVID19 Virus Testings,Coronavirus Disease 19 Testing,Coronavirus Disease-19 Testings,Diagnostic Testing, COVID-19,Disease Testing, 2019-nCoV,Infection Testing, 2019-nCoV,SARS CoV 2 Testing,SARS-CoV-2 Testings,Testing, 2019-nCoV,Testing, 2019-nCoV Disease,Testing, 2019-nCoV Infection,Testing, COVID-19,Testing, COVID-19 Virus,Testing, COVID19,Testing, COVID19 Virus,Testing, Coronavirus Disease-19,Testing, SARS-CoV-2,Virus Testing, COVID-19,Virus Testing, COVID19
D000956 Antigens, Viral Substances elaborated by viruses that have antigenic activity. Viral Antigen,Viral Antigens,Antigen, Viral

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