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1.
Elife ; 92020 02 03.
Article in English | MEDLINE | ID: covidwho-774702

ABSTRACT

Bats host virulent zoonotic viruses without experiencing disease. A mechanistic understanding of the impact of bats' virus hosting capacities, including uniquely constitutive immune pathways, on cellular-scale viral dynamics is needed to elucidate zoonotic emergence. We carried out virus infectivity assays on bat cell lines expressing induced and constitutive immune phenotypes, then developed a theoretical model of our in vitro system, which we fit to empirical data. Best fit models recapitulated expected immune phenotypes for representative cell lines, supporting robust antiviral defenses in bat cells that correlated with higher estimates for within-host viral propagation rates. In general, heightened immune responses limit pathogen-induced cellular morbidity, which can facilitate the establishment of rapidly-propagating persistent infections within-host. Rapidly-transmitting viruses that have evolved with bat immune systems will likely cause enhanced virulence following emergence into secondary hosts with immune systems that diverge from those unique to bats.


Subject(s)
Chiroptera/virology , Disease Reservoirs/veterinary , Virus Diseases/veterinary , Viruses/growth & development , Zoonoses/virology , Animals , Cell Line , Chiroptera/immunology , Disease Reservoirs/virology , Host Microbial Interactions , Humans , Immunity, Cellular , Kinetics , Models, Biological , Phenotype , Risk Assessment , Virulence , Virus Diseases/immunology , Virus Diseases/transmission , Virus Diseases/virology , Viruses/immunology , Viruses/pathogenicity , Zoonoses/immunology , Zoonoses/transmission
2.
J Neuropathol Exp Neurol ; 79(8): 823-842, 2020 08 01.
Article in English | MEDLINE | ID: covidwho-639090

ABSTRACT

Biological evolution of the microbiome continually drives the emergence of human viral pathogens, a subset of which attack the nervous system. The sheer number of pathogens that have appeared, along with their abundance in the environment, demand our attention. For the most part, our innate and adaptive immune systems have successfully protected us from infection; however, in the past 5 decades, through pathogen mutation and ecosystem disruption, a dozen viruses emerged to cause significant neurologic disease. Most of these pathogens have come from sylvatic reservoirs having made the energetically difficult, and fortuitously rare, jump into humans. But the human microbiome is also replete with agents already adapted to the host that need only minor mutations to create neurotropic/toxic agents. While each host/virus symbiosis is unique, this review examines virologic and immunologic principles that govern the pathogenesis of different viral CNS infections that were described in the past 50 years (Influenza, West Nile Virus, Zika, Rift Valley Fever Virus, Hendra/Nipah, Enterovirus-A71/-D68, Human parechovirus, HIV, and SARS-CoV). Knowledge of these pathogens provides us the opportunity to respond and mitigate infection while at the same time prepare for inevitable arrival of unknown agents.


Subject(s)
Central Nervous System Viral Diseases/epidemiology , Central Nervous System Viral Diseases/transmission , Zoonoses/epidemiology , Zoonoses/transmission , Animals , Birds , Central Nervous System Viral Diseases/prevention & control , Ecosystem , Humans , Influenza in Birds/epidemiology , Influenza in Birds/prevention & control , Influenza in Birds/transmission , Influenza, Human/epidemiology , Influenza, Human/prevention & control , Influenza, Human/transmission , West Nile Fever/epidemiology , West Nile Fever/prevention & control , West Nile Fever/transmission , Zika Virus Infection/epidemiology , Zika Virus Infection/prevention & control , Zika Virus Infection/transmission , Zoonoses/prevention & control
3.
Nat Commun ; 11(1): 4235, 2020 08 25.
Article in English | MEDLINE | ID: covidwho-738373

ABSTRACT

Bats are presumed reservoirs of diverse coronaviruses (CoVs) including progenitors of Severe Acute Respiratory Syndrome (SARS)-CoV and SARS-CoV-2, the causative agent of COVID-19. However, the evolution and diversification of these coronaviruses remains poorly understood. Here we use a Bayesian statistical framework and a large sequence data set from bat-CoVs (including 630 novel CoV sequences) in China to study their macroevolution, cross-species transmission and dispersal. We find that host-switching occurs more frequently and across more distantly related host taxa in alpha- than beta-CoVs, and is more highly constrained by phylogenetic distance for beta-CoVs. We show that inter-family and -genus switching is most common in Rhinolophidae and the genus Rhinolophus. Our analyses identify the host taxa and geographic regions that define hotspots of CoV evolutionary diversity in China that could help target bat-CoV discovery for proactive zoonotic disease surveillance. Finally, we present a phylogenetic analysis suggesting a likely origin for SARS-CoV-2 in Rhinolophus spp. bats.


Subject(s)
Chiroptera/virology , Coronavirus Infections/veterinary , Coronavirus/genetics , Evolution, Molecular , Zoonoses/transmission , Animals , Bayes Theorem , Betacoronavirus/classification , Betacoronavirus/genetics , Biodiversity , China , Chiroptera/classification , Coronavirus/classification , Coronavirus Infections/transmission , Coronavirus Infections/virology , Humans , Pandemics , Phylogeny , Phylogeography , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Zoonoses/virology
4.
Vet Microbiol ; 247: 108777, 2020 Aug.
Article in English | MEDLINE | ID: covidwho-733593

ABSTRACT

Coronaviruses (CoVs) cause disease in a range of agricultural and companion animal species, and can be important causes of zoonotic infections. In humans, several coronaviruses circulate seasonally. Recently, a novel zoonotic CoV named SARS-CoV-2 emerged from a bat reservoir, resulting in the COVID-19 pandemic. With a focus on felines, we review here the evidence for SARS-CoV-2 infection in cats, ferrets and dogs, describe the relationship between SARS-CoV-2 and the natural coronaviruses known to infect these species, and provide a rationale for the relative susceptibility of these species to SARS-CoV-2 through comparative analysis of the ACE-2 receptor.


Subject(s)
Cat Diseases/virology , Coronavirus Infections/veterinary , Dog Diseases/virology , Evolution, Molecular , Pandemics/veterinary , Pneumonia, Viral/veterinary , Zoonoses/transmission , Animals , Betacoronavirus , Cats/virology , Dogs/virology , Ferrets/virology , Humans , Peptidyl-Dipeptidase A/metabolism , Receptors, Virus/genetics , Zoonoses/virology
6.
Indian J Med Microbiol ; 38(1): 1-8, 2020.
Article in English | MEDLINE | ID: covidwho-688753

ABSTRACT

A novel coronavirus infection, which began as an outbreak of unusual viral pneumonia in Wuhan, a central city in China, has evolved into a global health crisis. The outbreak is an unembellished reminder of the hazard coronaviruses pose to public health. Government and researchers around the world have been taking swift measures to control the outbreak and conduct aetiological studies to understand the various facets of the outbreak. This review is an attempt at providing an insight about the current understanding, knowledge gaps and a perspective on the future of coronavirus disease 2019 (COVID-19) infections. All the authentic data published so far on COVID-19 has been systematically analysed. PubMed, NCBI, World Health Organisation, Ministry of Health and Family Welfare (India), and Centers for Disease Control and Prevention databases and bibliographies of relevant studies up to 22nd June 2020 have been included. The Wuhan outbreak is a stark reminder of the continuing threat posed by zoonotic diseases to global health. Despite an armamentarium of Government officials, researchers and medical fraternity working towards the containment of this novel coronavirus viral pneumonia continues to spread at an alarming rate infecting multitudes and claiming hundreds of lives.


Subject(s)
Betacoronavirus/isolation & purification , Communicable Disease Control/methods , Coronavirus Infections/epidemiology , Pandemics , Pneumonia, Viral/epidemiology , Zoonoses/transmission , Adolescent , Adult , Aged , Aged, 80 and over , Animals , Biomedical Research/trends , Child , Child, Preschool , Communicable Disease Control/organization & administration , Coronavirus Infections/prevention & control , Coronavirus Infections/transmission , Female , Global Health , Humans , Infant , Infant, Newborn , Male , Middle Aged , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Pneumonia, Viral/transmission , Young Adult
7.
Am J Primatol ; 82(8): e23176, 2020 08.
Article in English | MEDLINE | ID: covidwho-656485

ABSTRACT

The emergence of SARS-CoV-2 in late 2019 and human responses to the resulting COVID-19 pandemic in early 2020 have rapidly changed many aspects of human behavior, including our interactions with wildlife. In this commentary, we identify challenges and opportunities at human-primate interfaces in light of COVID-19, focusing on examples from Asia, and make recommendations for researchers working with wild primates to reduce zoonosis risk and leverage research opportunities. First, we briefly review the evidence for zoonotic origins of SARS-CoV-2 and discuss risks of zoonosis at the human-primate interface. We then identify challenges that the pandemic has caused for primates, including reduced nutrition, increased intraspecific competition, and increased poaching risk, as well as challenges facing primatologists, including lost research opportunities. Subsequently, we highlight opportunities arising from pandemic-related lockdowns and public health messaging, including opportunities to reduce the intensity of problematic human-primate interfaces, opportunities to reduce the risk of zoonosis between humans and primates, opportunities to reduce legal and illegal trade in primates, new opportunities for research on human-primate interfaces, and opportunities for community education. Finally, we recommend specific actions that primatologists should take to reduce contact and aggression between humans and primates, to reduce demand for primates as pets, to reduce risks of zoonosis in the context of field research, and to improve understanding of human-primate interfaces. Reducing the risk of zoonosis and promoting the well-being of humans and primates at our interfaces will require substantial changes from "business as usual." We encourage primatologists to help lead the way.


Subject(s)
Coronavirus Infections/prevention & control , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Primate Diseases/prevention & control , Zoonoses/prevention & control , Animals , Conservation of Natural Resources/trends , Coronavirus Infections/transmission , Feeding Behavior/physiology , Humans , Pneumonia, Viral/transmission , Primate Diseases/transmission , Primate Diseases/virology , Primates , Risk Factors , Zoonoses/transmission
8.
Postgrad Med J ; 96(1137): 408-411, 2020 Jul.
Article in English | MEDLINE | ID: covidwho-639885

ABSTRACT

All animal life on earth is thought to have a common origin and have common genetic mechanisms. Evolution has enabled differentiation of species. Pathogens likewise have evolved within various species and mostly come to a settled dynamic equilibrium such that co-existence results (pathogens ideally should not kill their hosts). Problems arise when pathogens jump species because the new host had not developed any resistance. These infections from related species are known as zoonoses. COVID-19 is the latest example of a virus entering another species but HIV (and various strains of influenza) were previous examples.


Subject(s)
Disease Outbreaks/statistics & numerical data , HIV Infections/transmission , HIV-1/pathogenicity , Simian Acquired Immunodeficiency Syndrome/transmission , Simian Immunodeficiency Virus/pathogenicity , Zoonoses/transmission , Animals , Betacoronavirus/genetics , Betacoronavirus/pathogenicity , Coronavirus Infections/transmission , Coronavirus Infections/virology , Evolution, Molecular , HIV Infections/virology , HIV-1/genetics , Humans , Pandemics , Phylogeny , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Primates/virology , Simian Acquired Immunodeficiency Syndrome/virology , Simian Immunodeficiency Virus/genetics , Zoonoses/virology
9.
Mol Biol Evol ; 37(9): 2463-2464, 2020 09 01.
Article in English | MEDLINE | ID: covidwho-638189

ABSTRACT

Identifying the origin of SARS-CoV-2, the etiological agent of the current COVID-19 pandemic, may help us to avoid future epidemics of coronavirus and other zoonoses. Several theories about the zoonotic origin of SARS-CoV-2 have recently been proposed. Although Betacoronavirus found in Rhinolophus bats from China have been broadly implicated, their genetic dissimilarity to SARS-CoV-2 is so high that they are highly unlikely to be its direct ancestors. Thus, an intermediary host is suspected to link bat to human coronaviruses. Based on genomic CpG dinucleotide patterns in different coronaviruses from different hosts, it was suggested that SARS-CoV-2 might have evolved in a canid gastrointestinal tract prior to transmission to humans. However, similar CpG patterns are now reported in coronaviruses from other hosts, including bats themselves and pangolins. Therefore, reduced genomic CpG alone is not a highly predictive biomarker, suggesting a need for additional biomarkers to reveal intermediate hosts or tissues. The hunt for the zoonotic origin of SARS-CoV-2 continues.


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Genome, Viral , Pandemics , Pneumonia, Viral/epidemiology , Viral Proteins/genetics , Zoonoses/epidemiology , Animals , Betacoronavirus/classification , Betacoronavirus/pathogenicity , Chiroptera/virology , Coronavirus Infections/transmission , Coronavirus Infections/virology , CpG Islands , Eutheria/virology , Evolution, Molecular , Gene Expression , Mutation , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Reassortant Viruses/classification , Reassortant Viruses/genetics , Reassortant Viruses/pathogenicity , Recombination, Genetic , Viral Proteins/metabolism , Zoonoses/transmission , Zoonoses/virology
11.
Vet Microbiol ; 247: 108777, 2020 Aug.
Article in English | MEDLINE | ID: covidwho-611218

ABSTRACT

Coronaviruses (CoVs) cause disease in a range of agricultural and companion animal species, and can be important causes of zoonotic infections. In humans, several coronaviruses circulate seasonally. Recently, a novel zoonotic CoV named SARS-CoV-2 emerged from a bat reservoir, resulting in the COVID-19 pandemic. With a focus on felines, we review here the evidence for SARS-CoV-2 infection in cats, ferrets and dogs, describe the relationship between SARS-CoV-2 and the natural coronaviruses known to infect these species, and provide a rationale for the relative susceptibility of these species to SARS-CoV-2 through comparative analysis of the ACE-2 receptor.


Subject(s)
Cat Diseases/virology , Coronavirus Infections/veterinary , Dog Diseases/virology , Evolution, Molecular , Pandemics/veterinary , Pneumonia, Viral/veterinary , Zoonoses/transmission , Animals , Betacoronavirus , Cats/virology , Dogs/virology , Ferrets/virology , Humans , Peptidyl-Dipeptidase A/metabolism , Receptors, Virus/genetics , Zoonoses/virology
12.
PLoS One ; 15(6): e0235106, 2020.
Article in English | MEDLINE | ID: covidwho-611135

ABSTRACT

The COVID-19 pandemic, caused by the coronavirus SARS-CoV-2, has devastated health infrastructure around the world. Both ACE2 (an entry receptor) and TMPRSS2 (used by the virus for spike protein priming) are key proteins to SARS-CoV-2 cell entry, enabling progression to COVID-19 in humans. Comparative genomic research into critical ACE2 binding sites, associated with the spike receptor binding domain, has suggested that African and Asian primates may also be susceptible to disease from SARS-CoV-2 infection. Savanna monkeys (Chlorocebus spp.) are a widespread non-human primate with well-established potential as a bi-directional zoonotic/anthroponotic agent due to high levels of human interaction throughout their range in sub-Saharan Africa and the Caribbean. To characterize potential functional variation in savanna monkey ACE2 and TMPRSS2, we inspected recently published genomic data from 245 savanna monkeys, including 163 wild monkeys from Africa and the Caribbean and 82 captive monkeys from the Vervet Research Colony (VRC). We found several missense variants. One missense variant in ACE2 (X:14,077,550; Asp30Gly), common in Ch. sabaeus, causes a change in amino acid residue that has been inferred to reduce binding efficiency of SARS-CoV-2, suggesting potentially reduced susceptibility. The remaining populations appear as susceptible as humans, based on these criteria for receptor usage. All missense variants observed in wild Ch. sabaeus populations are also present in the VRC, along with two splice acceptor variants (at X:14,065,076) not observed in the wild sample that are potentially disruptive to ACE2 function. The presence of these variants in the VRC suggests a promising model for SARS-CoV-2 infection and vaccine and therapy development. In keeping with a One Health approach, characterizing actual susceptibility and potential for bi-directional zoonotic/anthroponotic transfer in savanna monkey populations may be an important consideration for controlling COVID-19 epidemics in communities with frequent human/non-human primate interactions that, in many cases, may have limited health infrastructure.


Subject(s)
Chlorocebus aethiops , Coronavirus Infections/veterinary , Pandemics/veterinary , Peptidyl-Dipeptidase A/genetics , Pneumonia, Viral/veterinary , Primate Diseases/genetics , Serine Endopeptidases/genetics , Animals , Betacoronavirus/metabolism , Coronavirus Infections/genetics , Coronavirus Infections/transmission , Disease Susceptibility , Pneumonia, Viral/genetics , Pneumonia, Viral/transmission , Spike Glycoprotein, Coronavirus/metabolism , Whole Genome Sequencing , Zoonoses/transmission
13.
Nat Rev Microbiol ; 18(8): 461-471, 2020 08.
Article in English | MEDLINE | ID: covidwho-596755

ABSTRACT

Most viral pathogens in humans have animal origins and arose through cross-species transmission. Over the past 50 years, several viruses, including Ebola virus, Marburg virus, Nipah virus, Hendra virus, severe acute respiratory syndrome coronavirus (SARS-CoV), Middle East respiratory coronavirus (MERS-CoV) and SARS-CoV-2, have been linked back to various bat species. Despite decades of research into bats and the pathogens they carry, the fields of bat virus ecology and molecular biology are still nascent, with many questions largely unexplored, thus hindering our ability to anticipate and prepare for the next viral outbreak. In this Review, we discuss the latest advancements and understanding of bat-borne viruses, reflecting on current knowledge gaps and outlining the potential routes for future research as well as for outbreak response and prevention efforts.


Subject(s)
Biodiversity , Chiroptera/virology , Communicable Diseases, Emerging/virology , Virus Diseases/virology , Virus Physiological Phenomena , Zoonoses/virology , Animals , Communicable Diseases, Emerging/prevention & control , Communicable Diseases, Emerging/transmission , Disease Outbreaks/prevention & control , Humans , Research/trends , Virus Diseases/prevention & control , Zoonoses/prevention & control , Zoonoses/transmission
14.
Vopr Virusol ; 65(2): 62-70, 2020.
Article in Russian | MEDLINE | ID: covidwho-593172

ABSTRACT

Since the early 2000s, three novel zooanthroponous coronaviruses (Betacoronavirus) have emerged. The first outbreak of infection (SARS) caused by SARS-CoV virus occurred in the fall of 2002 in China (Guangdong Province). A second outbreak (MERS) associated with the new MERS-CoV virus appeared in Saudi Arabia in autumn 2012. The third epidemic, which turned into a COVID-19 pandemic caused by SARS-CoV-2 virus, emerged in China (Hubei Province) in the autumn 2019. This review focuses on ecological and genetic aspects that lead to the emergence of new human zoanthroponous coronaviruses. The main mechanism of adaptation of zoonotic betacoronaviruses to humans is to changes in the receptor-binding domain of surface protein (S), as a result of which it gains the ability to bind human cellular receptors of epithelial cells in respiratory and gastrointestinal tract. This process is caused by the high genetic diversity and variability combined with frequent recombination, during virus circulation in their natural reservoir - bats (Microchiroptera, Chiroptera). Appearance of SARS-CoV, SARS-CoV-2 (subgenus Sarbecovirus), and MERS (subgenus Merbecovirus) viruses is a result of evolutionary events occurring in bat populations with further transfer of viruses to the human directly or through the intermediate vertebrate hosts, ecologically connected with bats. This review is based on the report at the meeting «Coronavirus - a global challenge to science¼ of the Scientific Council «Life Science¼ of the Russian Academy of Science: Lvov D.K., Alkhovsky S.V., Burtseva E.I. COVID-19 pandemic sources: origin, biology and genetics of coronaviruses of SARS-CoV, SARS-CoV-2, MERS-CoV (Conference hall of Presidium of RAS, 14 Leninsky Prospect, Moscow, Russia. April 16, 2020).


Subject(s)
Betacoronavirus/genetics , Coronavirus Infections/epidemiology , Pandemics , Pneumonia, Viral/epidemiology , Spike Glycoprotein, Coronavirus/genetics , Zoonoses/epidemiology , Animals , Betacoronavirus/classification , Betacoronavirus/pathogenicity , Chiroptera/virology , Coronavirus Infections/transmission , Coronavirus Infections/virology , Ecology , Evolution, Molecular , Gene Expression , Mutation , Peptidyl-Dipeptidase A/genetics , Peptidyl-Dipeptidase A/metabolism , Phylogeny , Phylogeography , Pneumonia, Viral/transmission , Pneumonia, Viral/virology , Reassortant Viruses/classification , Reassortant Viruses/genetics , Reassortant Viruses/pathogenicity , Receptors, Virus/genetics , Receptors, Virus/metabolism , Recombination, Genetic , Spike Glycoprotein, Coronavirus/metabolism , Zoonoses/transmission , Zoonoses/virology
16.
J Vet Sci ; 21(3): e51, 2020 May.
Article in English | MEDLINE | ID: covidwho-493769

ABSTRACT

A novel coronavirus emerged in human populations and spread rapidly to cause the global coronavirus disease 2019 pandemic. Although the origin of the associated virus (severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2]) remains unclear, genetic evidence suggests that bats are a reservoir host of the virus, and pangolins are a probable intermediate. SARS-CoV-2 has crossed the species barrier to infect humans and other animal species, and infected humans can facilitate reverse-zoonotic transmission to animals. Considering the rapidly changing interconnections among people, animals, and ecosystems, traditional roles of veterinarians should evolve to include transdisciplinary roles.


Subject(s)
Coronavirus Infections/prevention & control , Coronavirus Infections/transmission , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Pneumonia, Viral/transmission , Zoonoses/prevention & control , Zoonoses/transmission , Animals , Betacoronavirus/isolation & purification , Host Specificity , Humans , One Health , Veterinarians
17.
mBio ; 11(3)2020 05 29.
Article in English | MEDLINE | ID: covidwho-428675

ABSTRACT

With great apprehension, the world is now watching the birth of a novel pandemic already causing tremendous suffering, death, and disruption of normal life. Uncertainty and dread are exacerbated by the belief that what we are experiencing is new and mysterious. However, deadly pandemics and disease emergences are not new phenomena: they have been challenging human existence throughout recorded history. Some have killed sizeable percentages of humanity, but humans have always searched for, and often found, ways of mitigating their deadly effects. We here review the ancient and modern histories of such diseases, discuss factors associated with their emergences, and attempt to identify lessons that will help us meet the current challenge.


Subject(s)
Coronavirus Infections/epidemiology , Pandemics/history , Pneumonia, Viral/epidemiology , Animals , Betacoronavirus/pathogenicity , Communicable Disease Control/history , Conservation of Natural Resources , Coronavirus Infections/prevention & control , Coronavirus Infections/transmission , History, 15th Century , History, 16th Century , History, 17th Century , History, 18th Century , History, 19th Century , History, 20th Century , History, 21st Century , History, Ancient , History, Medieval , Humans , International Cooperation , Pandemics/prevention & control , Pneumonia, Viral/prevention & control , Pneumonia, Viral/transmission , Public Health/history , Zoonoses/epidemiology , Zoonoses/prevention & control , Zoonoses/transmission
18.
J Infect Dev Ctries ; 14(2): 191-198, 2020 02 29.
Article in English | MEDLINE | ID: covidwho-326127

ABSTRACT

INTRODUCTION: Camel trade in Egypt depends mainly on importation. Seemingly healthy imported camels are responsible for the ingress of serious diseases into Egypt. A striking example of this concerning public health globally is the Middle East respiratory coronavirus (MERS-CoV) which causes case fatalities of over 34%. Here, we determined the seroepidemiological situation of the MERS-CoV in imported camels and their traders in Upper Egypt. METHODOLOGY: Sera of sixty-three dromedaries and twenty-eight camel traders were recruited (January 2015-December 2016). The age, gender, and sampling locality of each sampled camel and human were obtained. Semi-quantitative anti-MERS-CoV IgG ELISAs which utilize the purified spike protein domain S1 antigen of MERS coronavirus (MERS-CoV S1) were used to detect specific IgG antibodies against the virus. RESULTS: The data showed that 58.73% of imported camels and 25% of traders had antibodies specific to MERS-CoV. Interestingly, like seroreactive camels, all seropositive humans were apparently healthy without any history of developing severe respiratory disease in the 14 days prior to sampling. Having specific antibodies among the examined camel sera was significantly different (P < 0.0001) in relation to various sampling localities, gender and age groups. In contrast, the seropositivity rate of MERS-CoV IgG in humans did not differ significantly by any of the studied factors. CONCLUSIONS: The current study provides the first serological evidence of occupational exposure of humans to MERS-CoV in Africa. Additionally, it reports that imported camels could be implicated in introducing MERS-CoV into Egypt. Accordingly, application of strict control measures to camel importation is a priority.


Subject(s)
Camelus/virology , Coronavirus Infections/epidemiology , Coronavirus Infections/veterinary , Middle East Respiratory Syndrome Coronavirus , Occupational Diseases/epidemiology , Zoonoses/epidemiology , Adult , Animals , Coronavirus Infections/diagnosis , Coronavirus Infections/transmission , Egypt/epidemiology , Female , Humans , Male , Middle Aged , Middle East Respiratory Syndrome Coronavirus/immunology , Middle East Respiratory Syndrome Coronavirus/isolation & purification , Occupational Diseases/diagnosis , Seroepidemiologic Studies , Zoonoses/diagnosis , Zoonoses/transmission
19.
Nature ; 583(7816): 437-440, 2020 07.
Article in English | MEDLINE | ID: covidwho-326050

ABSTRACT

In December 2019, coronavirus disease 2019 (COVID-19), which is caused by the new coronavirus severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was identified in Wuhan (Hubei province, China)1; it soon spread across the world. In this ongoing pandemic, public health concerns and the urgent need for effective therapeutic measures require a deep understanding of the epidemiology, transmissibility and pathogenesis of COVID-19. Here we analysed clinical, molecular and immunological data from 326 patients with confirmed SARS-CoV-2 infection in Shanghai. The genomic sequences of SARS-CoV-2, assembled from 112 high-quality samples together with sequences in the Global Initiative on Sharing All Influenza Data (GISAID) dataset, showed a stable evolution and suggested that there were two major lineages with differential exposure history during the early phase of the outbreak in Wuhan. Nevertheless, they exhibited similar virulence and clinical outcomes. Lymphocytopenia, especially reduced CD4+ and CD8+ T cell counts upon hospital admission, was predictive of disease progression. High levels of interleukin (IL)-6 and IL-8 during treatment were observed in patients with severe or critical disease and correlated with decreased lymphocyte count. The determinants of disease severity seemed to stem mostly from host factors such as age and lymphocytopenia (and its associated cytokine storm), whereas viral genetic variation did not significantly affect outcomes.


Subject(s)
Betacoronavirus/genetics , Betacoronavirus/pathogenicity , Coronavirus Infections/immunology , Coronavirus Infections/virology , Host-Pathogen Interactions/immunology , Lymphopenia/virology , Pneumonia, Viral/immunology , Pneumonia, Viral/virology , Respiratory Distress Syndrome, Adult/virology , Adolescent , Adult , Aged , Aged, 80 and over , Aging , Animals , Asymptomatic Infections/epidemiology , Betacoronavirus/classification , Betacoronavirus/isolation & purification , China/epidemiology , Cohort Studies , Coronavirus Infections/complications , Coronavirus Infections/epidemiology , Critical Illness/epidemiology , Disease Progression , Evolution, Molecular , Female , Genetic Variation , Genome, Viral/genetics , Hospitalization/statistics & numerical data , Humans , Inflammation Mediators/immunology , Interleukin-6/blood , Interleukin-6/immunology , Interleukin-8/blood , Interleukin-8/immunology , Lymphocyte Count , Lymphopenia/complications , Male , Middle Aged , Pandemics , Phylogeny , Pneumonia, Viral/complications , Pneumonia, Viral/epidemiology , Respiratory Distress Syndrome, Adult/complications , T-Lymphocytes/cytology , T-Lymphocytes/immunology , Time Factors , Treatment Outcome , Virulence/genetics , Virus Shedding , Young Adult , Zoonoses/transmission , Zoonoses/virology
20.
Mol Biol Rep ; 47(6): 4827-4833, 2020 Jun.
Article in English | MEDLINE | ID: covidwho-277073

ABSTRACT

Pangolins, or scaly anteaters, have recently been flagshiped as one of the most illegally traded mammals, and as a corollary, as potential intermediate hosts at the origin of the COVID-19 pandemic. In order to improve the traceability of their trade, we developed 20 polymorphic microsatellite loci for the white-bellied pangolin (Phataginus tricuspis), the species most frequently found on African bushmeat markets. We genotyped 24 white-bellied pangolins from the Douala market, Cameroon, originating from the Ebo forest c. 75 km north-east of Douala. The number of alleles per locus ranged from 4 to 12 (mean = 6.95), and mean observed and expected heterozygosities were 0.592 (0.208-0.875) and 0.671 (0.469-0.836), respectively. Genetic diversity was higher than that cross-estimated from microsatellite loci developed for other species of pangolins. Two loci deviated from Hardy-Weinberg equilibrium and two loci showed linkage disequilibrium. Genetic variance (PCoA) was increased with the addition of 13 pangolins of unknown origin, possibly suggesting that the Douala market is fed from differentiated source populations of white-bellied pangolins. Each of the 37 individuals had a unique multilocus genotype. The unbiased probability of identity (uPI) and the probability of identity among siblings (PIsibs) were both very low (uPI = 8.443 e-21; PIsibs = 1.011 e-07). Only five microsatellite loci were needed to reach the conservative value of PIsibs < 0.01, overall indicating a powerful discriminating power of our combined loci. These 20 newly developed microsatellite loci might prove useful in tracing the local-to-global trade of the white-bellied pangolin, and will hopefully contribute to the DNA-assisted implementation of future conservation strategies at reasonable costs.


Subject(s)
Betacoronavirus/pathogenicity , Coronavirus Infections/transmission , Eutheria/genetics , Microsatellite Repeats , Pandemics , Pneumonia, Viral/transmission , Zoonoses/transmission , Alleles , Animals , Cameroon/epidemiology , Coronavirus Infections/epidemiology , Coronavirus Infections/prevention & control , Coronavirus Infections/virology , Disease Reservoirs/virology , Eutheria/virology , Female , Genetic Loci , Genetic Markers , Genotype , Humans , Linkage Disequilibrium , Male , Pandemics/prevention & control , Pneumonia, Viral/epidemiology , Pneumonia, Viral/prevention & control , Pneumonia, Viral/virology , Zoonoses/epidemiology , Zoonoses/prevention & control , Zoonoses/virology
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