scholarly journals Evolutionary trajectory of SARS-CoV-2 and emerging variants

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Jalen Singh ◽  
Pranav Pandit ◽  
Andrew G. McArthur ◽  
Arinjay Banerjee ◽  
Karen Mossman
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Evolutionary History ◽  
Severe Disease ◽  
Virus Transmission ◽  
Virus Evolution ◽  
Evolutionary Trajectory ◽  
Independent Evolution ◽  
Human Coronaviruses ◽  
Novel Coronavirus ◽  
Endemic Infections

AbstractThe emergence of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), and more recently, the independent evolution of multiple SARS-CoV-2 variants has generated renewed interest in virus evolution and cross-species transmission. While all known human coronaviruses (HCoVs) are speculated to have originated in animals, very little is known about their evolutionary history and factors that enable some CoVs to co-exist with humans as low pathogenic and endemic infections (HCoV-229E, HCoV-NL63, HCoV-OC43, HCoV-HKU1), while others, such as SARS-CoV, MERS-CoV and SARS-CoV-2 have evolved to cause severe disease. In this review, we highlight the origins of all known HCoVs and map positively selected for mutations within HCoV proteins to discuss the evolutionary trajectory of SARS-CoV-2. Furthermore, we discuss emerging mutations within SARS-CoV-2 and variants of concern (VOC), along with highlighting the demonstrated or speculated impact of these mutations on virus transmission, pathogenicity, and neutralization by natural or vaccine-mediated immunity.

scholarly journals Immunological characteristics govern the transition of COVID-19 to endemicity

Science ◽  
2021 ◽  
Vol 371 (6530) ◽  
pp. 741-745 ◽  
Author(s):  
Jennie S. Lavine ◽  
Ottar N. Bjornstad ◽  
Rustom Antia
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Common Cold ◽  
Severe Disease ◽  
Epidemiological Data ◽  
Benign Nature ◽  
The Common ◽  
Human Coronaviruses ◽  
Pandemic Vaccine

We are currently faced with the question of how the severity of infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may change in the years ahead. Our analysis of immunological and epidemiological data on endemic human coronaviruses (HCoVs) shows that infection-blocking immunity wanes rapidly but that disease-reducing immunity is long-lived. Our model, incorporating these components of immunity, recapitulates both the current severity of SARS-CoV-2 infection and the benign nature of HCoVs, suggesting that once the endemic phase is reached and primary exposure is in childhood, SARS-CoV-2 may be no more virulent than the common cold. We predict a different outcome for an emergent coronavirus that causes severe disease in children. These results reinforce the importance of behavioral containment during pandemic vaccine rollout, while prompting us to evaluate scenarios for continuing vaccination in the endemic phase.

scholarly journals Jet Fans in the Underground Car Parks and Virus Transmission 

2020 ◽  
Author(s):  
Ata Nazari ◽  
Moharram Jafari ◽  
Naser Rezaei ◽  
Farzad Taghizadeh-Hesary
Keyword(s):  
Numerical Simulation ◽  
Severe Acute Respiratory Syndrome ◽  
Virus Transmission ◽  
Quantitative Understanding ◽  
Novel Coronavirus ◽  
Respiratory Droplets

Abstract Jet fans are increasingly preferred over traditional ducted systems as a means of ventilating pollutants from large spaces such as underground car parks. The spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) -which causes novel coronavirus disease (COVID-19)- through the jet fans in the underground car parks has been considered a matter of key concern. A quantitative understanding of the propagation of respiratory droplets/particles/aerosols containing the virus is important. However, to date, studies are yet to demonstrate the viral (e.g. SARS-CoV-2) transmission in the underground car parks equipped with jet fans. In this paper, the numerical simulation has been performed to assess the effects of jet fans on the spreading of viruses inside the underground car parks.

scholarly journals A comparative study on virology, epidemiology, and clinical features of SARS and COVID-19

2021 ◽  
pp. 1-23
Author(s):  
Yanmei Zhao ◽  
Qianying Lu ◽  
Xiangyan Meng ◽  
Siyu Huang ◽  
Jianfeng Zhang ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Comparative Study ◽  
Clinical Features ◽  
Human Coronavirus ◽  
Highly Pathogenic ◽  
New Type ◽  
Human Coronaviruses ◽  
Novel Coronavirus ◽  
And Control ◽  
Monitor And Control

Abstract In December 2019, an outbreak of an unknown cause of pneumonia [later named coronavirus disease 2019 (COVID-19)] occurred in Wuhan, China. This was found to be attributed to a novel coronavirus of zoonotic origin, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2; previously named 2019 novel coronavirus or 2019-nCoV). The SARS-CoV-2, a new type of highly pathogenic human coronavirus related to severe acute respiratory syndrome coronavirus (SARS-CoV), spread rapidly worldwide and caused 53,164,803 confirmed infections, including 1,300,576 deaths, by November 13, 2020 (globally, 206,196,367 cases and 4,345,424 deaths as of August 13, 2021). SARS-CoV-2 and SARS-CoV vary in their specific characteristics, regarding epidemics and pathogenesis. This article focuses on the comparison of the virology, epidemiology, and clinical features of SARS-CoV and SARS-CoV-2 to reveal their common and distinct properties, to provide an up-to-date resource for the development of advanced systems and strategies to monitor and control future epidemics of highly pathogenic human coronaviruses.

scholarly journals Risk Assessment of SARS-CoV-2 in Antarctic Wildlife

2020 ◽  
Author(s):  
Andrés Barbosa ◽  
Arvind Vansani ◽  
Virginia Morandini ◽  
Wray Grimaldi ◽  
Ralph E.T. Vanstreels ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Severe Acute Respiratory Syndrome ◽  
Virus Transmission ◽  
Host Susceptibility ◽  
Transmission Risk ◽  
The World ◽  
Human Introduction ◽  
Novel Coronavirus ◽  
Available Information ◽  
The Antarctic

The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread rapidly to most parts of the world, causing high numbers of deaths and significant social and economic impacts. SARS-CoV-2 is a novel coronavirus with a suggested zoonotic origin and with the potential for cross-species transmission among animals. Antarctica can be considered the only continent free of SARS-CoV-2 although at the end of the 2019-2020 tourist season, at least one SARS-CoV-2 positive tourist visited the Antarctic Peninsula. Therefore, concerns have been expressed regarding the potential human introduction of this virus to the continent through the activities of research or tourism with potential effects including those related to human health, but also the potential for virus transmission to Antarctic wildlife. This reverse-zoonotic transmission risk to Antarctic wildlife is assessed considering the available information on host susceptibility, dynamics of the infection in humans, and contact interactions between humans and Antarctic wildlife. Measures to reduce the risk are proposed as well as the identification of knowledge gaps related to this issue.

scholarly journals Differing susceptibility of C57BL/6J and DBA/2J mice—parents of the murine BXD family, to severe acute respiratory syndrome coronavirus infection

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Kui Li ◽  
Yang Shen ◽  
Mark A. Miller ◽  
Jennifer Stabenow ◽  
Robert W. Williams ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Severe Disease ◽  
Phenotypic Differences ◽  
Host Interactions ◽  
Sustained Weight Loss ◽  
Microbial Infections ◽  
Life Threatening ◽  
Host Genetic ◽  
Puzzling Aspect ◽  
Novel Coronavirus

AbstractThe ongoing coronavirus disease-2019 (COVID-19) pandemic, caused by a novel coronavirus termed severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) that is closely related to SARS-CoV, poses a grave threat to global health and has devastated societies worldwide. One puzzling aspect of COVID-19 is the impressive variation in disease manifestations among infected individuals, from a majority who are asymptomatic or exhibit mild symptoms to a smaller, largely age-dependent fraction who develop life-threatening conditions. Some of these differences are likely the consequence of host genetic factors. Systems genetics using diverse and replicable cohorts of isogenic mice represents a powerful way to dissect those host genetic differences that modulate microbial infections. Here we report that the two founders of the large BXD family of mice—C57BL/6J and DBA/2J, differ substantially in their susceptibility to a mouse-adapted SARS-CoV, MA15. Following intranasal viral challenge, DBA/2J develops a more severe disease than C57BL/6J as evidenced by more pronounced and sustained weight loss. Disease was accompanied by high levels of pulmonary viral replication in both strains early after infection but substantially delayed viral clearance in DBA/2J. Our data reveal that the parents of the BXD family are segregated by clear phenotypic differences during MA15 infection and support the feasibility of using this family to systemically dissect the complex virus-host interactions that modulate disease progression and outcome of infection with SARS-CoV, and provisionally also with SARS-CoV-2.

scholarly journals Surveillance of Bat Coronaviruses in Kenya Identifies Relatives of Human Coronaviruses NL63 and 229E and Their Recombination History

2017 ◽  
Vol 91 (5) ◽  
Author(s):  
Ying Tao ◽  
Mang Shi ◽  
Christina Chommanard ◽  
Krista Queen ◽  
Jing Zhang ◽  
...  
Keyword(s):  
Driving Forces ◽  
Hot Spot ◽  
Severe Disease ◽  
Virus Transmission ◽  
Content Type ◽  
Natural Recombination ◽  
Human Coronaviruses ◽  
Human Viruses ◽  
Reservoir Hosts ◽  
Interspecies Recombination

ABSTRACT Bats harbor a large diversity of coronaviruses (CoVs), several of which are related to zoonotic pathogens that cause severe disease in humans. Our screening of bat samples collected in Kenya from 2007 to 2010 not only detected RNA from several novel CoVs but, more significantly, identified sequences that were closely related to human CoVs NL63 and 229E, suggesting that these two human viruses originate from bats. We also demonstrated that human CoV NL63 is a recombinant between NL63-like viruses circulating in Triaenops bats and 229E-like viruses circulating in Hipposideros bats, with the breakpoint located near 5′ and 3′ ends of the spike (S) protein gene. In addition, two further interspecies recombination events involving the S gene were identified, suggesting that this region may represent a recombination “hot spot” in CoV genomes. Finally, using a combination of phylogenetic and distance-based approaches, we showed that the genetic diversity of bat CoVs is primarily structured by host species and subsequently by geographic distances. IMPORTANCE Understanding the driving forces of cross-species virus transmission is central to understanding the nature of disease emergence. Previous studies have demonstrated that bats are the ultimate reservoir hosts for a number of coronaviruses (CoVs), including ancestors of severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory syndrome coronavirus (MERS-CoV), and human CoV 229E (HCoV-229E). However, the evolutionary pathways of bat CoVs remain elusive. We provide evidence for natural recombination between distantly related African bat coronaviruses associated with Triaenops afer and Hipposideros sp. bats that resulted in a NL63-like virus, an ancestor of the human pathogen HCoV-NL63. These results suggest that interspecies recombination may play an important role in CoV evolution and the emergence of novel CoVs with zoonotic potential.

scholarly journals Seasonal human coronavirus antibodies are boosted upon SARS-CoV-2 infection but not associated with protection

2020 ◽  
Author(s):  
Elizabeth M. Anderson ◽  
Eileen C. Goodwin ◽  
Anurag Verma ◽  
Claudia P. Arevalo ◽  
Marcus J. Bolton ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Neutralizing Antibodies ◽  
Human Population ◽  
Serum Samples ◽  
Human Coronavirus ◽  
Nucleocapsid Proteins ◽  
Human Coronaviruses ◽  
Novel Coronavirus ◽  
Antibody Levels ◽  
Separate Cohort

SUMMARYSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has rapidly spread within the human population. Although SARS-CoV-2 is a novel coronavirus, most humans had been previously exposed to other antigenically distinct common seasonal human coronaviruses (hCoVs) before the COVID-19 pandemic. Here, we quantified levels of SARS-CoV-2-reactive antibodies and hCoV-reactive antibodies in serum samples collected from 204 humans before the COVID-19 pandemic. We then quantified pre-pandemic antibody levels in serum from a separate cohort of 252 individuals who became PCR-confirmed infected with SARS-CoV-2. Finally, we longitudinally measured hCoV and SARS-CoV-2 antibodies in the serum of hospitalized COVID-19 patients. Our studies indicate that most individuals possessed hCoV-reactive antibodies before the COVID-19 pandemic. We determined that ∼23% of these individuals possessed non-neutralizing antibodies that cross-reacted with SARS-CoV-2 spike and nucleocapsid proteins. These antibodies were not associated with protection against SARS-CoV-2 infections or hospitalizations, but paradoxically these hCoV cross-reactive antibodies were boosted upon SARS-CoV-2 infection.

Novel Coronavirus Disease (COVID-19): A Narrative Review Based on Current Status

2020 ◽  
Vol 18 ◽  
Author(s):  
Rina Das ◽  
Dinesh Kumar Mehta ◽  
Meenakshi Dhanawat
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Clinical Symptoms ◽  
Virus Disease ◽  
Relevant Literature ◽  
World Health ◽  
Current Status ◽  
Future Research ◽  
Treatment And Prevention ◽  
First Case ◽  
Novel Coronavirus

Abstract:: A novel virus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), appeared and expanded globally by the end of year in 2019 from Wuhan, China, causing severe acute respiratory syndrome. During its initial stage, the disease was called the novel coronavirus (2019-nCoV). It was named COVID-19 by the World Health Organization (WHO) on 11 February 2020. The WHO declared worldwide the SARS-CoV-2 virus a pandemic on March 2020. On 30 January 2020 the first case of Corona Virus Disease 2019 (COVID-19) was reported in India. Now in current situation the virus is floating in almost every part of the province and rest of the globe. -: On the basis of novel published evidences, we efficiently summarized the reported work with reference to COVID-19 epidemiology, pathogen, clinical symptoms, treatment and prevention. Using several worldwide electronic scientific databases such as Pubmed, Medline, Embase, Science direct, Scopus, etc were utilized for extensive investigation of relevant literature. -: This review is written in the hope of encouraging the people successfully with the key learning points from the underway efforts to perceive and manage SARS-CoV-2, suggesting sailent points for expanding future research.

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.

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