Severe acute respiratory syndrome-related coronavirus: The species and its viruses – a statement of the Coronavirus Study Group

AbstractThe present outbreak of lower respiratory tract infections, including respiratory distress syndrome, is the third spillover, in only two decades, of an animal coronavirus to humans resulting in a major epidemic. Here, the Coronavirus Study Group (CSG) of the International Committee on Taxonomy of Viruses, which is responsible for developing the official classification of viruses and taxa naming (taxonomy) of the Coronaviridae family, assessed the novelty of the human pathogen tentatively named 2019-nCoV. Based on phylogeny, taxonomy and established practice, the CSG formally recognizes this virus as a sister to severe acute respiratory syndrome coronaviruses (SARS-CoVs) of the species Severe acute respiratory syndrome-related coronavirus and designates it as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). To facilitate communication, the CSG further proposes to use the following naming convention for individual isolates: SARS-CoV-2/Isolate/Host/Date/Location. The spectrum of clinical manifestations associated with SARS-CoV-2 infections in humans remains to be determined. The independent zoonotic transmission of SARS-CoV and SARS-CoV-2 highlights the need for studying the entire (virus) species to complement research focused on individual pathogenic viruses of immediate significance. This research will improve our understanding of virus-host interactions in an ever-changing environment and enhance our preparedness for future outbreaks.

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The treatment of Covid tongue in an isolation unit

Dental Journal (Majalah Kedokteran Gigi) ◽

10.20473/j.djmkg.v54.i3.p155-159 ◽

2021 ◽

Vol 54 (3) ◽

pp. 155

Author(s):

Dwi Setianingtyas ◽

N. Nafiah ◽

Cane Lukisari ◽

Paulus Budi Teguh ◽

Felicia Eda Haryanto ◽

...

Keyword(s):

Health Care ◽

Oral Health ◽

Severe Acute Respiratory Syndrome ◽

Viral Disease ◽

International Committee ◽

Disease Spread ◽

Study Group ◽

Main Diagnosis ◽

Exfoliative Dermatitis ◽

Patient Cooperation

Background: In 2019, a viral disease spread from Wuhan, Hubei Province in China. The disease was caused by severe acute respiratory syndrome related to coronavirus 2 (SARS-CoV-2 virus), which was named by the Coronavirus Study Group of the International Committee on Taxonomy of Viruses. Purpose: This article reports the multi-discipline treatment of Covid tongue and exfoliative cheilitis with a main diagnosis of bilateral pneumonia caused by SARS-CoV-2 infection. Case: A female patient, 70 years old was referred with a diagnosis of bilateral pneumonia by a pulmonologist. She complained of painful wounds all over her mouth. An intraoral clinical examination revealed white-thick lesion and multiple ulcerations, whilst an extraoral exam for exfoliative dermatitis has not been described. The working diagnosis was Covid tongue mixed with exfoliative cheilitis. Case management: The procedure was performed by teledentistry and direct visits to implement oral health care by asepsis, debridement and the application of Oxygene gel. Conclusion: The lesion was treated successfully due to the multidisciplinary approaches by an internist and pulmonologist by implementing integrated knowledge and was supported hugely by patient cooperation.

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The human coronaviruses (HCoVs) and the molecular mechanisms of SARS-CoV-2 infection

Journal of Molecular Medicine ◽

10.1007/s00109-020-02012-8 ◽

2020 ◽

Vol 99 (1) ◽

pp. 93-106

Author(s):

Luigi Santacroce ◽

Ioannis A. Charitos ◽

Domenico M. Carretta ◽

Emanuele De Nitto ◽

Roberto Lovero

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Respiratory Tract ◽

Common Cold ◽

Molecular Mechanisms ◽

Middle Eastern ◽

International Committee ◽

Upper Respiratory Tract ◽

Human Coronaviruses ◽

The 1960S ◽

Tract Infections

AbstractIn humans, coronaviruses can cause infections of the respiratory system, with damage of varying severity depending on the virus examined: ranging from mild-to-moderate upper respiratory tract diseases, such as the common cold, pneumonia, severe acute respiratory syndrome, kidney failure, and even death. Human coronaviruses known to date, common throughout the world, are seven. The most common—and least harmful—ones were discovered in the 1960s and cause a common cold. Others, more dangerous, identified in the early 2000s and cause more severe respiratory tract infections. Among these the SARS-CoV, isolated in 2003 and responsible for the severe acute respiratory syndrome (the so-called SARS), which appeared in China in November 2002, the coronavirus 2012 (2012-nCoV) cause of the Middle Eastern respiratory syndrome (MERS) from coronavirus, which exploded in June 2012 in Saudi Arabia, and actually SARS-CoV-2. On December 31, 2019, a new coronavirus strain was reported in Wuhan, China, identified as a new coronavirus beta strain ß-CoV from group 2B, with a genetic similarity of approximately 70% to SARS-CoV, the virus responsible of SARS. In the first half of February, the International Committee on Taxonomy of Viruses (ICTV), in charge of the designation and naming of the viruses (i.e., species, genus, family, etc.), thus definitively named the new coronavirus as SARS-CoV-2. This article highlights the main knowledge we have about the biomolecular and pathophysiologic mechanisms of SARS-CoV-2.

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The Human Coronaviruses (HCoVs) and the Molecular Mechanisms of SARS-CoV-2 Infection

10.20944/preprints202010.0041.v1 ◽

2020 ◽

Author(s):

Luigi Santacroce ◽

Ioannis A. Charitos ◽

Domenico M. Carretta ◽

Emanuele De Nitto ◽

Roberto Lovero

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Respiratory Tract ◽

Common Cold ◽

Molecular Mechanisms ◽

Middle Eastern ◽

International Committee ◽

Upper Respiratory Tract ◽

Human Coronaviruses ◽

The 1960S ◽

Tract Infections

In humans, coronaviruses can cause infections of the respiratory system, with damage of varying severity depending on the virus examined: ranging from mild or moderate upper respiratory tract diseases, such as the common cold, to pneumonia, severe acute respiratory syndrome, kidney failure and even death. Human coronaviruses known to date, common throughout the world, are seven. The most common - and least harmful - ones were discovered in the 1960s and cause a common cold. Others, more dangerous, were identified in the early 2000s and cause more severe respiratory tract infections. Among these the SARS-CoV, isolated in 2003 and responsible for the Severe Acute Respiratory Syndrome (the so-called SARS), which appeared in China in November 2002, the Coronavirus 2012 (2012-nCoV) cause of the Middle Eastern Respiratory Syndrome from Coronavirus (MERS), which exploded in June 2012 in Saudi Arabia, and actually SARS-CoV-2. On December 31, 2019, a new Coronavirus strain was reported in Wuhan, China, identified as a new Coronavirus beta strain ß-CoV from Group 2B, with a genetic similarity of approximately 70% to SARS-CoV, the virus responsible. of SARS. In the first half of February, the International Committee on Taxonomy of Viruses (ICTV), in charge of the designation and naming of the viruses (i.e., species, genus, family, etc.), thus definitively named the new coronavirus as SARS-CoV-2. This article highlights the main knowledge we have about the biomolecular and pathophysiologic mechanisms of SARS-CoV-2.

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On Classification and Taxonomy of Coronaviruses (Riboviria, Nidovirales, Coronaviridae) with Special Focus on Severe Acute Respiratory Syndrome-Related Coronavirus 2 (SARS-CoV-2)

10.21203/rs.3.rs-282371/v1 ◽

2021 ◽

Author(s):

Evgeny Mavrodiev ◽

Melinda L Tursky ◽

Nicholas E Mavrodiev ◽

Malte C Ebach ◽

David M Williams ◽

...

Keyword(s):

Maximum Likelihood Method ◽

Cladistic Analysis ◽

Hierarchical Classification ◽

International Committee ◽

Likelihood Method ◽

Special Focus ◽

Virus Species ◽

Highly Pathogenic ◽

One Step

Abstract Coronaviruses are highly pathogenic and therefore important human and veterinary pathogens viruses worldwide. This study is the first that produced phylogenies based on all 39 species of Coronaviridae recognized by the Coronaviridae Study Group and International Committee on Taxonomy of Viruses and has, uniquely, used several methods of cladistic analysis in combination with the Maximum Likelihood method. Resultant trees were utilized to test for monophyly of all available non-monotypic genera and infrageneric taxa of Coronaviridae. Monophyly was confirmed, thereby validating they are representative of a nature hierarchy. This study therefore presents the first natural hierarchical classification of Coronaviridae and the most accurate taxonomic representation of Coronaviridae’s relationships to date. The authors additionally seek at add to the current discussion regarding the nomenclature of viruses, demonstrating and supporting a “one-step” solution to incorporate the principles of binary nomenclature into Coronaviridae, which will aid future recognition of numerous virus species, particularly in currently monotypic subgenus Sarbecovirus. Commenting on the nature of SARS-CoV-2, the authors emphasize that no member of the Sarbecovirus clade is an ancestor of this virus, and humans are the only natural known host.

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How SARS-CoV-2 (COVID-19) spreads within infected hosts — what we know so far

Emerging Topics in Life Sciences ◽

10.1042/etls20200165 ◽

2020 ◽

Vol 4 (4) ◽

pp. 383-390

Author(s):

Sumana Sanyal

Keyword(s):

Severe Acute Respiratory Syndrome ◽

Rational Design ◽

Vaccine Development ◽

Clinical Manifestations ◽

Converting Enzyme ◽

Angiotensin Converting Enzyme 2 ◽

Pathogenic Viruses ◽

Fundamental Biology ◽

Key Aspects ◽

Infectious Cycle

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the ongoing pandemic of coronavirus disease 2019 (COVID-19), belongs to the betacoronavirus genus and shares high homology to the severe acute respiratory syndrome coronavirus (SARS-CoV) that emerged in 2003. These are highly transmissible and pathogenic viruses which very likely originated in bats. SARS-CoV-2 uses the same receptor, angiotensin-converting enzyme 2 (ACE2) as SARS-CoV, and spreads primarily through the respiratory tract. Although several trials for vaccine development are currently underway, investigations into the virology of SARS-CoV-2 to understand the fundamental biology of the infectious cycle and the associated immunopathology underlying the clinical manifestations of COVID-19 are crucial for identification and rational design of effective therapies. This review provides an overview of how SARS-CoV-2 infects and spreads within human hosts with specific emphasis on key aspects of its lifecycle, tropism and immunopathological features.

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Use of photodynamic therapy for photodamage skin (review of literature)

Medical alphabet ◽

10.33667/2078-5631-2019-1-7(382)-19-23 ◽

2019 ◽

Vol 1 (7) ◽

pp. 19-23

Author(s):

S. I. Surkichin ◽

N. V. Gryazeva ◽

L. S. Kholupova ◽

N. V. Bochkova

Keyword(s):

Photodynamic Therapy ◽

Comparative Evaluation ◽

Clinical Manifestations ◽

Light Sources ◽

Review Of Literature ◽

Photosensitizing Agents ◽

Selection Of

The article provides an overview of the use of photodynamic therapy for photodamage of the skin. The causes, pathogenesis and clinical manifestations of skin photodamage are considered. The definition, principle of action of photodynamic therapy, including the sources of light used, the classification of photosensitizers and their main characteristics are given. Analyzed studies that show the effectiveness and comparative evaluation in the selection of various light sources and photosensitizing agents for photodynamic therapy in patients with clinical manifestations of photodamage.

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URINARY INFECTION AT DEPARTMENT OF UROLOGY OF HUE UNIVERSITY OF MEDICINE AND PHARMACY HOSPITAL

Journal of Medicine and Pharmacy ◽

10.34071/jmp.2018.3.16 ◽

2018 ◽

pp. 100-108

Author(s):

Dinh Khanh Le ◽

Dinh Dam Le ◽

Khoa Hung Nguyen ◽

Xuan My Nguyen ◽

Minh Nhat Vo ◽

...

Keyword(s):

Urinary Tract Infection ◽

Urinary Tract ◽

Tract Infection ◽

Urinary Tract Infections ◽

Urine Culture ◽

Clinical Manifestations ◽

University Hospital ◽

E Coli ◽

Positive Urine ◽

Tract Infections

Objectives: To investigate clinical characteristics, bacterial characteristics, drug resistance status in patients with urinary tract infections treated at Department of Urology, Hue University Hospital. Materials and Method: The study was conducted in 474 patients with urological disease treated at Department of Urology, Hue Universiry Hospital from July 2017 to April 2018. Urine culture was done in the patients with urine > 25 Leu/ul who have symptoms of urinary tract disease or infection symptoms. Patients with positive urine cultures were analyzed for clinical and bacterial characteristics. Results: 187/474 (39.5%) patients had symptoms associated with urinary tract infections. 85/474 (17.9%) patients were diagnosed with urinary tract infection. The positive urine culture rate was 45.5%. Symptoms of UTI were varied, and no prominent symptoms. E. coli accounts for the highest proportion (46.67%), followed by, Staphycoccus aureus (10.67%), Pseudomonas aeruginsa (8,0%), Streptococcus faecali and Proteus (2.67%). ESBL - producing E. coli was 69.23%, ESBL producing Enterobacter spp was 33.33%. Gram-negative bacteria are susceptible to meropenem, imipenem, amikacin while gram positive are vancomycin-sensitive. Conclusions: Clinical manifestations of urinary tract infections varied and its typical symptoms are unclear. E.coli is a common bacterium (46.67%). Isolated bacteria have a high rate of resistance to some common antibiotics especially the third generation cephalosporins and quinolones. Most bacteria are resistant to multiple antibiotics at the same time. Gram (+) bacteria are susceptible to vancomycin, and gram (-) bacteria are susceptible to cefoxitin, amikacin, and carbapenem. Key words: urinary tract infection

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Etiology and clinical features of epididymo-orchitis: A single-center study in Tehran, Iran

Infectious Disorders - Drug Targets ◽

10.2174/1871526520666200218115400 ◽

2020 ◽

Vol 20 ◽

Cited By ~ 1

Author(s):

Sara Abolghasemi ◽

Mohammad Alizadeh ◽

Ali Hashemi ◽

Shabnam Tehrani

Keyword(s):

Chlamydia Trachomatis ◽

Clinical Symptoms ◽

Urine Culture ◽

Clinical Manifestations ◽

Urinary Frequency ◽

Serological Tests ◽

Duration Of Symptoms ◽

Two Samples ◽

History Of ◽

Tract Infections

Introduction: Epididymo-orchitis is a common urological disease among men. Little is known about the clinical and epidemiological aspects of the disease in Iran. Thus, the present study was aimed to investigate the etiology, clinical sequelae and risk factors of patients with epididymo-orchitis in Tehran, Iran. Materials and Methods: Patients presenting with epididymo-orchitis were prospectively analyzed in order to study the etiology and pattern of the disease. Bacteriological, molecular and serological tests were undertaken to look for Chlamydia trachomatis, Neisseria gonorrhoeae, Brucella spp., Mycoplasma spp, and other bacteria. Results: Fifty patients with epididymo-orchitis were evaluated according to their clinical symptoms, duration of symptoms, physical examination, and laboratory studies. The mean age of the patients was 53 years. Fever, dysuria, pain in the flanks, urinary frequency and discharges occurred in 58.0%, 50.0%, 50.0%, 28.0% and 6.0%, respectively. Bacterial pathogen was identified in 26% (13/50) of patients by urine culture. Escherichia coli was the etiological agent in 11/13 patients (84.6%). Two out of 50 patients (4.0%) were also positive for Chlamydia trachomatis. Two samples were serologically positive for Brucella spp. High Mean age, fever, urinary frequency, history of the underlying disease and history of urinary tract infections were found to have a significant association with the positive bacteriologic urine culture (P<0.05). Conclusions: The most common clinical manifestations were fever, dysuria, and abdominal pain. E. coli and C. trachomatis were the major causative agents. Use of a set of diagnostic approaches including clinical symptoms, urine culture and more precise techniques such as PCR should be taken into consideration for the definitive diagnosis.

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Respiratory tract damage with bocavirus infection in children

CHILDREN INFECTIONS ◽

10.22627/2072-8107-2020-19-2-14-18 ◽

2020 ◽

Vol 19 (2) ◽

pp. 14-18

Author(s):

E. V. Sharipova ◽

I. V. Babachenko ◽

M. A. Shcherbatyh

Keyword(s):

Respiratory Tract ◽

Lower Respiratory Tract ◽

Clinical Manifestations ◽

Respiratory Viruses ◽

Community Acquired Pneumonia ◽

Human Bocavirus ◽

Long Time ◽

Clinically Significant ◽

Tract Infections ◽

Tract Damage

Long time the main pathogens associated with the development of community-acquired pneumonia were bacteria. However, in recent years in the Russian Federation, like all over the world, the view of the damage of lower respiratory tract changed, including a unique approach to community-acquired pneumonia as a bacterial infection, and respiratory viruses have become seen as a direct cause of lower respiratory tract damage, or as part of a viral-bacterial co-infection. These studies became possible since the widespread introduction of PCR techniques in the clinical setting, identification of respiratory viruses has increased and new microorganisms such, one as human bocavirus have been discovered. Objective: to study the features of respiratory tract damage in acute bocavirus infection in children of different ages. Materials and methods: A retrospective analysis of 97 medical hospital documentation of children with acute bocavirus infection, detected confirmed by PCR in nasopharyngeal aspirate. Results: In this work, it was shown that human bocavirus spread throughout the year with an increase in the incidence of clinically significant forms in the autumnwinter period, including during the period of an increase in the incidence of influenza. HBoV infection requiring hospitals is most significant in the first three years of life. In 74.2% of hospitalized children, bocavirus infection occurs with lower respiratory tract infections in the form of bronchitis — 77.8%, pneumonia — 28.9% and rarely bronchiolitis and is complicated by the development of respiratory failure in 28.9% of cases. Changes in the blood test are non-specific, and the level of C-reactive protein in children with various clinical manifestations of HBoV infection generally does not exceed 50 mg / l. An x-ray of the chest organs does not objectively reflect the existing volume and nature of the inflammatory process in the lungs.

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