scholarly journals The impact of super-spreaders in COVID-19: mapping genome variation worldwide

2020 ◽  
Author(s):  
Alberto Gómez-Carballa ◽  
Xabier Bello ◽  
Jacobo Pardo-Seco ◽  
Federico Martinón-Torres ◽  
Antonio Salas
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Founder Effect ◽  
Human Pathogen ◽  
High Sequence Identity ◽  
Asian Origin ◽  
Sequence Identity ◽  
Public Repositories ◽  
The Impact ◽  
Bat Coronavirus ◽  
Virus Strains

AbstractThe human pathogen severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the major pandemic of the 21st century. We analyzed >4,700 SARS-CoV-2 genomes and associated meta-data retrieved from public repositories. SARS-CoV-2 sequences have a high sequence identity (>99.9%), which drops to >96% when compared to bat coronavirus. We built a mutation-annotated reference SARS-CoV-2 phylogeny with two main macro-haplogroups, A and B, both of Asian origin, and >160 sub-branches representing virus strains of variable geographical origins worldwide, revealing a uniform mutation occurrence along branches that could complicate the design of future vaccines. The root of SARS-CoV-2 genomes locates at the Chinese haplogroup B1, with a TMRCA dating to 12 November 2019 - thus matching epidemiological records. Sub-haplogroup A2a originates in China and represents the major non-Asian outbreak. Multiple founder effect episodes, most likely associated with super-spreader hosts, explain COVID-19 pandemic to a large extent.

scholarly journals The Possible Origins of the Novel Coronavirus SARS-CoV-2

2020 ◽  
Author(s):  
Arun Shanker
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Rna Polymerase ◽  
Yunnan Province ◽  
The Novel ◽  
Rna Dependent Rna Polymerase ◽  
High Sequence Identity ◽  
Sequence Identity ◽  
Rhinolophus Affinis ◽  
Novel Coronavirus ◽  
Bat Coronavirus

Severe Acute Respiratory Syndrome (SARS) was seen as this century’s first Pandemic and was previously unknown. It was demonstrated that bats in the genus Rhinolophus are natural reservoirs of SARS-like viruses. Middle East Respiratory Syndrome-Coronavirus (MERS-CoV) was seen in 2012, it was similar to SARS CoV and is phylogenetically closely related to the bat coronaviruses (BatCoVs) HKU4 and HKU5. SARS-CoV-2 was seen in Wuhan in 2019 and SARS-CoV-2 is thought to be transmitted from animals to humans. It originated in bats and probably got into an intermediate animal and then to humans. The virus could have used the intermediate animal to adapt to transmit to humans. It was seen that a short region of RNA-dependent RNA polymerase (RdRp) from a bat coronavirus (BatCoV RaTG13) which was previously detected in Rhinolophus affinis from Yunnan province showed high sequence identity to SARS-CoV-2. We discuss the possible origins of SARS-CoV-2 here and see that there are a lot of possibilities.

scholarly journals Bat severe acute respiratory syndrome-like coronavirus ORF3b homologues display different interferon antagonist activities

2012 ◽  
Vol 93 (2) ◽  
pp. 275-281 ◽  
Author(s):  
Peng Zhou ◽  
Hongxia Li ◽  
Hanzhong Wang ◽  
Lin-Fa Wang ◽  
Zhengli Shi
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Nuclear Localization ◽  
Genome Organization ◽  
Gene Products ◽  
Regulatory Factor ◽  
High Sequence Identity ◽  
Sequence Identity ◽  
C Terminus ◽  
Potential Link ◽  
Localization Signal

The ORF3b protein of severe acute respiratory syndrome coronavirus (SARS-CoV) has a nuclear localization signal (NLS) at its C terminus and antagonizes interferon (IFN) function by modulating the activity of IFN regulatory factor 3 (IRF3). SARS-like coronaviruses (SL-CoVs) found in bats share an identical genome organization and high sequence identity for most of their gene products. In this study, ORF3b homologues were identified from three bat SL-CoV strains. These ORF3b homologues were C-terminally truncated and lacked the C-terminal NLS of SARS-CoV. IFN antagonist activities analysis demonstrated that one SL-CoV ORF3b still possessed IFN antagonist and IRF3-modulating activities. These results indicate that different ORF3b proteins display different IFN antagonist activities and this function is independent of the protein’s nuclear localization, suggesting a potential link between bat SL-CoV ORF3b function and viral pathogenesis.

scholarly journals Neurological symptoms, manifestations, and complications associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and coronavirus disease 19 (COVID-19)

2021 ◽  
Author(s):  
Biyan Nathanael Harapan ◽  
Hyeon Joo Yoo
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Case Reports ◽  
Case Series ◽  
Altered Mental Status ◽  
Neurological Complications ◽  
Neurological Symptoms ◽  
Neurological Manifestations ◽  
Fisher Syndrome ◽  
Novel Coronavirus ◽  
The Impact

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2), a novel coronavirus, is responsible for the outbreak of coronavirus disease 19 (COVID-19) and was first identified in Wuhan, China in December 2019. It is evident that the COVID-19 pandemic has become a challenging world issue. Although most COVID-19 patients primarily develop respiratory symptoms, an increasing number of neurological symptoms and manifestations associated with COVID-19 have been observed. In this narrative review, we elaborate on proposed neurotropic mechanisms and various neurological symptoms, manifestations, and complications of COVID-19 reported in the present literature. For this purpose, a review of all current published literature (studies, case reports, case series, reviews, editorials, and other articles) was conducted and neurological sequelae of COVID-19 were summarized. Essential and common neurological symptoms including gustatory and olfactory dysfunctions, myalgia, headache, altered mental status, confusion, delirium, and dizziness are presented separately in sections. Moreover, neurological manifestations and complications that are of great concern such as stroke, cerebral (sinus) venous thrombosis, seizures, meningoencephalitis, Guillain–Barré syndrome, Miller Fisher syndrome, acute myelitis, and posterior reversible encephalopathy syndrome (PRES) are also addressed systematically. Future studies that examine the impact of neurological symptoms and manifestations on the course of the disease are needed to further clarify and assess the link between neurological complications and the clinical outcome of patients with COVID-19. To limit long-term consequences, it is crucial that healthcare professionals can early detect possible neurological symptoms and are well versed in the increasingly common neurological manifestations and complications of COVID-19.

scholarly journals 375. COVID 19 infection in a Massachusetts community hospital

2020 ◽  
Vol 7 (Supplement_1) ◽  
pp. S257-S258
Author(s):  
Raul Davaro ◽  
alwyn rapose
Keyword(s):  
Intensive Care Unit ◽  
Mechanical Ventilation ◽  
Intensive Care ◽  
Essential Hypertension ◽  
Severe Acute Respiratory Syndrome ◽  
High Mortality ◽  
Case Series ◽  
World Health ◽  
Minimal Risk ◽  
The Impact

Abstract Background The ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections has led to 105690 cases and 7647 deaths in Massachusetts as of June 16. Methods The study was conducted at Saint Vincent Hospital, an academic health medical center in Worcester, Massachusetts. The institutional review board approved this case series as minimal-risk research using data collected for routine clinical practice and waived the requirement for informed consent. All consecutive patients who were sufficiently medically ill to require hospital admission with confirmed severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection by positive result on polymerase chain reaction testing of a nasopharyngeal sample were included. Results A total of 109 consecutive patients with COVID 19 were admitted between March 15 and May 31. Sixty one percent were men, the mean age of the cohort was 67. Forty one patients (37%) were transferred from nursing homes. Twenty seven patients died (24%) and the majority of the dead patients were men (62%). Fifty one patients (46%) required admission to the medical intensive care unit and 34 necessitated mechanical ventilation, twenty two patients on mechanical ventilation died (63%). The most common co-morbidities were essential hypertension (65%), obesity (60%), diabetes (33%), chronic kidney disease (22%), morbid obesity (11%), congestive heart failure (16%) and COPD (14%). Five patients required hemodialysis. Fifty five patients received hydroxychloroquine, 24 received tocilizumab, 20 received convalescent plasma and 16 received remdesivir. COVID 19 appeared in China in late 2019 and was declared a pandemic by the World Health Organization on March 11, 2020. Our study showed a high mortality in patients requiring mechanical ventilation (43%) as opposed to those who did not (5.7%). Hypertension, diabetes and obesity were highly prevalent in this aging population. Our cohort was too small to explore the impact of treatment with remdesivir, tocilizumab or convalescent plasma. Conclusion In this cohort obesity, diabetes and essential hypertension are risk factors associated with high mortality. Patients admitted to the intensive care unit who need mechanical ventilation have a mortality approaching 50 %. Disclosures All Authors: No reported disclosures

scholarly journals Cytopathology Practice in the COVID-19 Era: Focus on Sample Workload

2021 ◽  
Vol 2 (2) ◽  
pp. 109-113
Author(s):  
Antonino Iaccarino ◽  
Filippo Dello Iacovo ◽  
Pasquale Pisapia ◽  
Caterina De Luca ◽  
Umberto Malapelle ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Low Risk ◽  
Current Evidence ◽  
Drastic Reduction ◽  
Risk Of Malignancy ◽  
The Impact ◽  
Cytological Sample

Since the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreak was declared a pandemic, the magnitude of coronavirus disease 2019 (COVID-19) has continued to grow, putting an unprecedented strain on all medical fields. Its effects on cytopathology workloads have been dramatic. Indeed, despite the implementation of several laboratory biosafety recommendations, cytological screening activities and cytological sampling of patients at low risk of malignancy have been postponed to limit the risk of contagion and to lessen the strain on overwhelmed hospital facilities. In this scenario, a drastic reduction in the total number of cytological specimens has been observed worldwide. This review summarizes the current evidence of the impact of the COVID-19 pandemic on cytopathology practice by focusing on its impact on cytological sample workload.

scholarly journals Differences in the Rumen Methanogen Populations of Lactating Jersey and Holstein Dairy Cows under the Same Diet Regimen

2011 ◽  
Vol 77 (16) ◽  
pp. 5682-5687 ◽  
Author(s):  
Erin E. King ◽  
Rachel P. Smith ◽  
Benoit St-Pierre ◽  
André-Denis G. Wright
Keyword(s):  
Methanogenic Archaea ◽  
Milk Composition ◽  
Species Level ◽  
Rrna Gene ◽  
Content Type ◽  
Sequence Identity ◽  
Diet Regimen ◽  
Pcr Products ◽  
The Impact ◽  
Rumen Methanogen

ABSTRACTIn the dairy cattle industry, Holstein and Jersey are the breeds most commonly used for production. They differ in performance by various traits, such as body size, milk production, and milk composition. With increased concerns about the impact of agriculture on climate change, potential differences in other traits, such as methane emission, also need to be characterized further. Since methane is produced in the rumen by methanogenic archaea, we investigated whether the population structure of methanogen communities would differ between Holsteins and Jerseys. Breed-specific rumen methanogen 16S rRNA gene clone libraries were constructed from pooled PCR products obtained from lactating Holstein and Jersey cows, generating 180 and 185 clones, respectively. The combined 365 sequences were assigned to 55 species-level operational taxonomic units (OTUs). Twenty OTUs, representing 85% of the combined library sequences, were common to both breeds, while 23 OTUs (36 sequences) were found only in the Holstein library and 12 OTUs (18 sequences) were found only in the Jersey library, highlighting increased diversity in the Holstein library. Other differences included the observation that sequences with species-like sequence identity toMethanobrevibacter milleraewere represented more highly in the Jersey breed, whileMethanosphaera-related sequences and novel uncultured methanogen clones were more frequent in the Holstein library. In contrast, OTU sequences with species-level sequence identity toMethanobrevibacter ruminantiumwere represented similarly in both libraries. Since the sampled animals were from a single herd consisting of two breeds which were fed the same diet and maintained under the same environmental conditions, the differences we observed may be due to differences in host breed genetics.

scholarly journals P159 Factors associated between SLE and work amongst South Asian people: an explorative qualitative study

Rheumatology ◽  
2021 ◽  
Vol 60 (Supplement_1) ◽  
Author(s):  
Mandeep Ubhi ◽  
Shirish Dubey ◽  
John Reynolds ◽  
Caroline Gordon ◽  
Tochukwu Adizie ◽  
...  
Keyword(s):  
South Asian ◽  
Work Ability ◽  
Lupus Erythematosus ◽  
Full Time ◽  
Structured Interviews ◽  
Related Factors ◽  
Asian Origin ◽  
South Asian Origin ◽  
The Impact ◽  
Minority Ethnic

Abstract Background/Aims  Systemic lupus erythematosus (SLE) affect patients from minority ethnic backgrounds, with many patients experiencing symptoms that affect their daily lives despite receiving long-term controller medication. Work is a large part of most people’s lives, yet little has been explored into how people from minority ethnic backgrounds cope at work whilst living with SLE. We conducted a study to understand the impact of SLE on working lives of South Asian patients. The aim was to identify and develop support mechanisms that could assist them with remaining at work. Methods  Semi-structured interviews were conducted with ten patients of South Asian origin with SLE to explore their work experiences. Patients were recruited from three rheumatology centres in the West Midlands, UK and were interviewed between November 2019 and March 2020. Interviews were audio-recorded and typed by an independent transcribing company. Returned transcripts were analysed using thematic analysis and QSR NVivo 12 software was used to organise and manage the data. Results  The majority (n = 8) of patients were female. Eight patients were from an Indian background, and two were from a Pakistani background. Half of all patients were educated to degree level. The age range of patients was 23 - 58 years old (S.D = 10.79), and disease duration varied between 3 months-33 years (S.D = 9.52). All patients had permanent jobs; six were in full-time employment, and four were in part-time employment. Four main themes emerged from the data: 1) Disease related factors; impacting work ability; 2) Employment related factors; impacting work ability; 3) Personal and cultural related factors; impacting work ability; 4) Recommendations for improvement were made by patients. Conclusion  In this novel study we highlight patients’ experiences of being at work. This study reports low awareness of SLE and mixed support in the workplace. Patients discussed work to varying degrees with their clinicians and needed further information for employers that was not available nor provided by their clinicians. The study reports cultural barriers in understanding SLE that could lead to lack of family support to remain in employment. Moreover, recommendations made in this study require further investigation and could be used by clinicians and Lupus UK to support patients of South Asian origin at work. Disclosure  M. Ubhi: None. S. Dubey: None. J. Reynolds: None. C. Gordon: None. T. Adizie: None. T. Sheeran: None. K. Allen: None. R. Jordan: None. S. Sadhra: None. J. Adams: None. R. Daji: None. K. Kumar: None.

Covid-19 And Sudden Death with Pulmonary Manifestations- A Case Report

2021 ◽  
Vol 2 (1) ◽  
Keyword(s):  
Case Report ◽  
Severe Acute Respiratory Syndrome ◽  
Sudden Death ◽  
Common Cold ◽  
Respiratory Symptoms ◽  
Transmission Dynamics ◽  
Pulmonary Manifestations ◽  
The Family ◽  
The Common ◽  
Virus Strains

Covid 19 being a pandemic has uniformly and bizarrely affected the globe in a most unpredictable manner. So it becomes very important to unravel the transmission dynamics and the effect of the virus which has made it a deadly virus so far. Covid 19 is a member of coronavirus family, which also includes the SARS virus (Severe Acute Respiratory Syndrome) and MERS (Middle East Respiratory Symptoms) virus. The family of Coronavirus includes virus strains that the common cold and flu are caused [1].

scholarly journals Respiratory Care in Corona

2021 ◽  
Vol 58 (2) ◽  
pp. 613-620
Author(s):  
Mustafa Amdani, Dr. Swaroopa Chakole
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Human Life ◽  
The Body ◽  
Respiratory Care ◽  
The Novel ◽  
Specific Therapy ◽  
History Of ◽  
Novel Coronavirus ◽  
Almost All ◽  
The Impact

BACKGROUND The expanse of the coronavirus disease 2019 or COVID-19 is huge. The impact is multispectral and affected almost all aspects of human life. SUMMARY Respiratory impact of the COVID-19 is the most felt and widely reported impact. As the novel coronavirus maintained its history of affecting lungs as seen previously in severe acute respiratory syndrome (SARS) outbreak. Ventilators and oxygen support system are required mostly in comorbid patients particularly amongpatientsbearing illnesses like asthma, bronchial impairment and so on. CONCLUSION More study needs to be done in order to assess the impact on the respiratory functioning of the body. Respiratory care must be including proper instruments so that more efficient result can be obtained. Research is needed to promote the invention of specific therapy for targeted action for respiratory functioning improvement.

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