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1.
Am J Hum Genet ; 107(3): 381-402, 2020 09 03.
Article in English | MEDLINE | ID: covidwho-710246

ABSTRACT

The SARS-CoV-2 pandemic raises many scientific and clinical questions. These include how host genetic factors affect disease susceptibility and pathogenesis. New work is emerging related to SARS-CoV-2; previous work has been conducted on other coronaviruses that affect different species. We reviewed the literature on host genetic factors related to coronaviruses, systematically focusing on human studies. We identified 1,832 articles of potential relevance. Seventy-five involved human host genetic factors, 36 of which involved analysis of specific genes or loci; aside from one meta-analysis, all were candidate-driven studies, typically investigating small numbers of research subjects and loci. Three additional case reports were described. Multiple significant loci were identified, including 16 related to susceptibility (seven of which identified protective alleles) and 16 related to outcomes (three of which identified protective alleles). The types of cases and controls used varied considerably; four studies used traditional replication/validation cohorts. Among other studies, 30 involved both human and non-human host genetic factors related to coronavirus, 178 involved study of non-human (animal) host genetic factors related to coronavirus, and 984 involved study of non-genetic host factors related to coronavirus, including involving immunopathogenesis. Previous human studies have been limited by issues that may be less impactful now, including low numbers of eligible participants and limited availability of advanced genomic methods; however, these may raise additional considerations. We outline key genes and loci from animal and human host genetic studies that may bear investigation in the study of COVID-19. We also discuss how previous studies may direct current lines of inquiry.


Subject(s)
Coronavirus Infections/genetics , Genetic Predisposition to Disease , Pneumonia, Viral/genetics , Animals , Betacoronavirus , Disease Reservoirs/veterinary , Humans , Pandemics , Receptors, Virus/genetics , Species Specificity
3.
Int J Biol Sci ; 16(10): 1686-1697, 2020.
Article in English | MEDLINE | ID: covidwho-24916

ABSTRACT

Mutation and adaptation have driven the co-evolution of coronaviruses (CoVs) and their hosts, including human beings, for thousands of years. Before 2003, two human CoVs (HCoVs) were known to cause mild illness, such as common cold. The outbreaks of severe acute respiratory syndrome (SARS) and the Middle East respiratory syndrome (MERS) have flipped the coin to reveal how devastating and life-threatening an HCoV infection could be. The emergence of SARS-CoV-2 in central China at the end of 2019 has thrusted CoVs into the spotlight again and surprised us with its high transmissibility but reduced pathogenicity compared to its sister SARS-CoV. HCoV infection is a zoonosis and understanding the zoonotic origins of HCoVs would serve us well. Most HCoVs originated from bats where they are non-pathogenic. The intermediate reservoir hosts of some HCoVs are also known. Identifying the animal hosts has direct implications in the prevention of human diseases. Investigating CoV-host interactions in animals might also derive important insight on CoV pathogenesis in humans. In this review, we present an overview of the existing knowledge about the seven HCoVs, with a focus on the history of their discovery as well as their zoonotic origins and interspecies transmission. Importantly, we compare and contrast the different HCoVs from a perspective of virus evolution and genome recombination. The current CoV disease 2019 (COVID-19) epidemic is discussed in this context. In addition, the requirements for successful host switches and the implications of virus evolution on disease severity are also highlighted.


Subject(s)
Betacoronavirus/isolation & purification , Chiroptera/virology , Coronavirus/classification , Evolution, Molecular , Zoonoses/transmission , Zoonoses/virology , Animals , China , Coronavirus/isolation & purification , Coronavirus Infections , Disease Reservoirs/veterinary , Disease Reservoirs/virology , Host-Pathogen Interactions , Humans , Pandemics , Pneumonia, Viral , Rodentia/virology , SARS Virus , Severe Acute Respiratory Syndrome
5.
Infect Dis Poverty ; 9(1): 24, 2020 Feb 28.
Article in English | MEDLINE | ID: covidwho-2762

ABSTRACT

BACKGROUND: As reported by the World Health Organization, a novel coronavirus (2019-nCoV) was identified as the causative virus of Wuhan pneumonia of unknown etiology by Chinese authorities on 7 January, 2020. The virus was named as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) by International Committee on Taxonomy of Viruses on 11 February, 2020. This study aimed to develop a mathematical model for calculating the transmissibility of the virus. METHODS: In this study, we developed a Bats-Hosts-Reservoir-People transmission network model for simulating the potential transmission from the infection source (probably be bats) to the human infection. Since the Bats-Hosts-Reservoir network was hard to explore clearly and public concerns were focusing on the transmission from Huanan Seafood Wholesale Market (reservoir) to people, we simplified the model as Reservoir-People (RP) transmission network model. The next generation matrix approach was adopted to calculate the basic reproduction number (R0) from the RP model to assess the transmissibility of the SARS-CoV-2. RESULTS: The value of R0 was estimated of 2.30 from reservoir to person and 3.58 from person to person which means that the expected number of secondary infections that result from introducing a single infected individual into an otherwise susceptible population was 3.58. CONCLUSIONS: Our model showed that the transmissibility of SARS-CoV-2 was higher than the Middle East respiratory syndrome in the Middle East countries, similar to severe acute respiratory syndrome, but lower than MERS in the Republic of Korea.


Subject(s)
Betacoronavirus/growth & development , Chiroptera/virology , Coronavirus Infections/transmission , Disease Transmission, Infectious , Models, Theoretical , Pneumonia, Viral/transmission , Animals , Coronavirus Infections/epidemiology , Disease Reservoirs/veterinary , Disease Reservoirs/virology , Humans , Pneumonia, Viral/epidemiology , Time Factors
6.
J Infect Dev Ctries ; 14(1): 3-17, 2020 01 31.
Article in English | MEDLINE | ID: covidwho-1512

ABSTRACT

On 31 December 2019 the Wuhan Health Commission reported a cluster of atypical pneumonia cases that was linked to a wet market in the city of Wuhan, China. The first patients began experiencing symptoms of illness in mid-December 2019. Clinical isolates were found to contain a novel coronavirus with similarity to bat coronaviruses. As of 28 January 2020, there are in excess of 4,500 laboratory-confirmed cases, with > 100 known deaths. As with the SARS-CoV, infections in children appear to be rare. Travel-related cases have been confirmed in multiple countries and regions outside mainland China including Germany, France, Thailand, Japan, South Korea, Vietnam, Canada, and the United States, as well as Hong Kong and Taiwan. Domestically in China, the virus has also been noted in several cities and provinces with cases in all but one provinence. While zoonotic transmission appears to be the original source of infections, the most alarming development is that human-to-human transmission is now prevelant. Of particular concern is that many healthcare workers have been infected in the current epidemic. There are several critical clinical questions that need to be resolved, including how efficient is human-to-human transmission? What is the animal reservoir? Is there an intermediate animal reservoir? Do the vaccines generated to the SARS-CoV or MERS-CoV or their proteins offer protection against 2019-nCoV? We offer a research perspective on the next steps for the generation of vaccines. We also present data on the use of in silico docking in gaining insight into 2019-nCoV Spike-receptor binding to aid in therapeutic development. Diagnostic PCR protocols can be found at https://www.who.int/health-topics/coronavirus/laboratory-diagnostics-for-novel-coronavirus.


Subject(s)
Betacoronavirus , Coronavirus Infections/transmission , Disease Reservoirs/veterinary , Disease Transmission, Infectious , Pneumonia, Viral/transmission , Animals , Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Coronavirus Infections/virology , Disease Reservoirs/virology , Humans , Pandemics , Pneumonia, Viral/epidemiology , Pneumonia, Viral/virology , Sequence Analysis, Protein , Travel , Vaccination , Viral Proteins/chemistry , Viral Proteins/genetics , Viral Vaccines , Zoonoses
7.
Vet Q ; 40(1): 68-76, 2020 Dec.
Article in English | MEDLINE | ID: covidwho-561

ABSTRACT

Coronaviruses are the well-known cause of severe respiratory, enteric and systemic infections in a wide range of hosts including man, mammals, fish, and avian. The scientific interest on coronaviruses increased after the emergence of Severe Acute Respiratory Syndrome coronavirus (SARS-CoV) outbreaks in 2002-2003 followed by Middle East Respiratory Syndrome CoV (MERS-CoV). This decade's first CoV, named 2019-nCoV, emerged from Wuhan, China, and declared as 'Public Health Emergency of International Concern' on January 30th, 2020 by the World Health Organization (WHO). As on February 4, 2020, 425 deaths reported in China only and one death outside China (Philippines). In a short span of time, the virus spread has been noted in 24 countries. The zoonotic transmission (animal-to-human) is suspected as the route of disease origin. The genetic analyses predict bats as the most probable source of 2019-nCoV though further investigations needed to confirm the origin of the novel virus. The ongoing nCoV outbreak highlights the hidden wild animal reservoir of the deadly viruses and possible threat of spillover zoonoses as well. The successful virus isolation attempts have made doors open for developing better diagnostics and effective vaccines helping in combating the spread of the virus to newer areas.


Subject(s)
Betacoronavirus , Chiroptera/virology , Communicable Diseases, Emerging/virology , Coronavirus Infections/epidemiology , Disease Reservoirs/veterinary , Animals , Betacoronavirus/classification , Betacoronavirus/genetics , Communicable Diseases, Emerging/prevention & control , Communicable Diseases, Emerging/transmission , Communicable Diseases, Emerging/veterinary , Coronavirus Infections/prevention & control , Coronavirus Infections/transmission , Coronavirus Infections/virology , Disease Reservoirs/virology , Humans , Pandemics , Phylogeny , Pneumonia, Viral , Zoonoses/epidemiology , Zoonoses/prevention & control , Zoonoses/virology
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