Airborne Dust / Zoonosis / Land Use

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trader32176
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Airborne Dust / Zoonosis / Land Use

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Human encroachment into forest land caused bat CoV spillover and COVID-19 emergence

8/6/20


https://www.news-medical.net/news/20200 ... gence.aspx


The COVID-19 pandemic remains something of a mystery, as scientists struggle to find out where the virus came from and how it entered the human host. This line of study is not merely academic, as it alone can tell if future pandemics caused by unknown agents are likely to arise, and where, and why. After all, this is not the first outbreak of zoonotic disease in the past few decades, and definitely not the first caused by pathogenic coronaviruses known to infect animal species in the wild.

Why Zoonoses Emerge

A new study published on the preprint server medRxiv* in August 2020 discusses the root causes underlying the emergence of such infectious diseases following their crossover of the line separating animal viruses from human. This initial event is of enormous significance.

In the present pandemic, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a 96% genomic sequence identity with a strain found in horseshoe bats. It is in these animals that we find most of the earlier ancestors of the SARSr-CoVs, making them the probable reservoir for these viruses. However, it is unclear whether this occurred directly or through an intermediate jump from bats to another species, such as the Malayan pangolin, and thence to humans.

Nonetheless, it is quite clear that a growing number of contacts between animals in the wild and humans are driving the entry of animal viruses into the human community. The researchers in the current study point out that this is the effect of several linked factors that decrease the distance and increase the rates of contact between humans and wild animals, as well as between humans themselves.

Factors that Promote Human-Wild Animal Contact

These factors include a burgeoning population restricted in various ways from spreading out into less crowded spaces, increased growth of cities; a rise in per capita income in mid-income countries; and changes in dietary patterns linked to these shifts. That is, the increasing demand for animal products that accompanies the greater availability of free cash causes more of the forest land to be claimed for farming and animal husbandry – also called forest encroachment.

This inevitably affects the ecology of the forest systems. The entry of humans into areas formerly inhabited by wild animals, the pursuit of hunting, the clearing of forests to create pastureland for livestock to graze or for animal farming, may all encourage animal viruses to enter the human community. And in addition, the loss of old forest and breaking up of a single forest into smaller, nonviable fragments causes niche animal communities to die out while favoring the survival of generalist species.

Finding the Link: Land Use and Pandemic Emergence

This research, therefore, focuses on finding a link, if such exists, between the change in the way land is used in modern times, and the COVID-19 pandemic, including as the chief drivers the fragmentation of forest and the encroachment of humans into the homeland of the wild.
The horseshoe bats of genus Rhinolophus is used as an index system to demonstrate how future outbreaks of coronavirus infections can occur, given the great variety of such bats in China, as well as of bat coronaviruses (CoVs) resembling the SARS-CoV.

The researchers found that two of the four CoV genera are found in bats, namely, alpha and beta-CoVs. All four of the betaCoV subgenera infect bats, and this includes SARS-related CoV (SARSr-CoV). SARS itself began first in southeast China and was then traced to R. sinicus and R. affinis, among other horseshoe bats. The close resemblance of the SARSr-CoV to the dangerous human SARS led them to look at disruptions of the bat habitat in association with the bats themselves. This included South and East Asia and China.

China crowded with livestock

In China, livestock is abundant within the regions with horseshoe bats. In fact, this is a diversity hotspot, relative to the rest of the country, containing higher percentages of domestic poultry, pigs and cattle. The researchers drew a circle with a 30 km radius from each bat location and found that these domestic animals were found at much higher densities than in randomly selected areas.

Loss and Fragmentation of Forests

Forest cover and fragmentation of the forest is again more obvious, statistically speaking, in the region around a random area in China compared to other regions. This shows that forest cover, and cropland density, are lower here, and the forest is broken up into bits and pieces, unlike other areas examined in the same study. This is more significant around the points where the bats are actually seen, compared to randomly picked locations outside China but in the region of distribution of the bats.

Human Encroachment

Humans have also encroached on horseshoe bat habitats, building their villages and towns there, with high population density. Thus, these two species share the same hotspots of activity. The researchers say, “These results demonstrate that China exhibits stronger signs of human encroachment, livestock density, and forest disturbance of SARSr‐CoV hosting horseshoe bat distributions than other regions. Regions close to forest fragments exhibit lower forest and cropland cover.”

In other words, China is one of the significant hotspots bringing all these factors together - fragmentation, livestock density, and human settlement, some others being in eastern Nepal, Bangladesh, North-east India, and Kerala. The researchers use this knowledge to identify spots of future potential virus spillover. This could occur if one or more of these factors cross the boundary between minor change and a hotspot state.

They conclude that the region of China to the south of the major port Shanghai is probably going to become a hotspot as forests are rapidly being fragmented there. Japan, and the northern part of the Philippines, are also ready to transition for the same cause.

Interacting Factors Increase Epidemic Risk

The geographic area between the hotspot in China and the not so hot spot in Indochina, and that around the Thai hotspot, show signs of increasing human and livestock activity, respectively. This means these regions are “suitable for SARSr‐CoV spillover from wildlife to humans [or] at risk of becoming prone to spillover” as land use patterns and human encroachments increase.

In addition to the ecological impact and the expansion of agricultural land, movement of people or animals, and trade activity, interact with the intrinsic host properties as well as the interventions adopted at this time (biosecurity, wearing personal protective equipment, strict hygiene for meat preparation and consumption) to reduce the final risk.

Future Actions

The researchers call attention to the need to counteract these dangerous tendencies seen in the threatening or potential hotspots, such as by maintaining or rebuilding forests, removing livestock pastures and farms much further away from forest borders and reducing the density of human activity in these buffer zones. Future environmental impact assessments should also consider the risk of turning the region concerned into new hotspots for spillover zoonotic diseases to emerge.
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Re: Airborne Dust / Zoonosis / Land Use

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Soil Borne Diseases of Humans

https://publications.jrc.ec.europa.eu/r ... 893enn.pdf

soils also contain microorganisms which are capable of causing diseases in humans. They act either as opportunistic pathogens which take advantage of susceptible individuals, such as those who are immuno-compromised; or as obligate pathogens which must infect humans in order to complete their life-cycles. These organisms may be capable of surviving within the soil for extended periods of time before infecting humans who come into contact with contaminated soil.


Collection, particle sizing and detection of airborne viruses


https://sfamjournals.onlinelibrary.wile ... /jam.14278

Viruses that affect humans, animals and plants are often dispersed and transmitted through airborne routes of infection. Due to current technological deficiencies, accurate determination of the presence of airborne viruses is challenging. This shortcoming limits our ability to evaluate the actual threat arising from inhalation or other relevant contact with aerosolized viruses. To improve our understanding of the mechanisms of airborne transmission of viruses, air sampling technologies that can detect the presence of aerosolized viruses, effectively collect them and maintain their viability, and determine their distribution in aerosol particles, are needed.
trader32176
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Airborne Dust / Zoonosis / Land Use

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The Dangers of Exposure to Construction Site Dust

https://www.oransi.com/page/dangers-exp ... -site-dust

Dust released into the environment is a significant concern for both the workers and people who live near the construction site. This is especially true for anyone that could be vulnerable to dust, such as people with asthma or COPD. As we discussed above, construction dust can contain harmful particles, so keeping it from being released into the air is a crucial component of public health.
trader32176
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Re: Airborne Dust / Zoonosis / Land Use

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Farmers’ occupational diseases of allergenic and zoonotic origin

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3858660/

The source of biological agents in the workplace usually is animal and vegetable products, dust, animal and human excreta, sewage and wastes. These factors are transmitted through airborne dust, airborne droplets, skin and mucous membranes, bite of vectors such as ticks, rarely by ingestion

Bioaerosols, especially from organic dusts are the most common, allergic hazard in the farmer work environment [4]. They can cause asthma, allergic alveolitis, allergic rhinitis, irritation of mucous membranes, infectious diseases and cancer. The most harmful biological agents present in the dust are bacteria and fungi, and substances produced by them with allergenic and immunotoxic properties.

Due to the special environment of farmers’ work, they are exposed to a number of biological, physical and chemical factors harmful to the health. They include noise, vibration, high physical and mechanical load associated with the work, dust, both inorganic and organic toxins. Organic dust is extremely harmful due to the huge variety of components including ingredients of plants, animal proteins, bacteria, molds and their metabolites as mycotoxins.

Another disease caused by biological activity of harmful factors is known as bronchial asthma. It is a chronic inflammatory disease of the respiratory tract, which is based on airway hyperresponsiveness and leads to recurrent attacks of dyspnea. Asthma can occur in a variety of environments as a result of exposure to organic dust, in both the agricultural and forestry sectors but also in food production. The most common allergens that can cause asthma are house dust mites, animal dander, pet bird feathers, pollen of grasses, trees, fungal spores and other components of organic dusts.

Health statistics show that most of occupational diseases of allergic origin reported in Polish farmers is caused by pathogens present in organic dusts. In Poland, lung diseases are more common in farmers than in the rest of the population, just as in other countries .
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Re:Airborne Dust / Zoonosis / Land Use

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Humans promote diseases from the animal kingdom

https://www.news-medical.net/news/20200 ... ngdom.aspx

The coronavirus pandemic, which has now infected nearly 19 million and killed more than 712,000 people, most likely originated from bats. Just like other coronavirus outbreaks in the past, a spill-over event or zoonosis caused the virus to jump from animals to humans.

Now, a team of researchers from the Centre for Biodiversity and Environment Research, Department of Genetics, Evolution and Environment, University College London, has shown that global changes in land use have disrupted the balance of wild animal communities in the environment.

The study, published in the journal Nature, highlights that animals are known to carry pathogens, or disease-causing microorganisms, were more common in areas that are intensively used by people.

Global changes in land use

The human race has altered more than half of the planet's habitable land to meet the needs of the ballooning population. Forests, deserts, and grasslands are now being turned into agricultural land, cities, and suburbs. As a result, animals begin to decline or disappear, while those who survive lose their land and resort to migrating to other areas.

When urbanization occurs, animals that are considered ecological specialists, i.e., they thrive only in a narrow range of environmental conditions or have a limited diet, tend to be the losers.

Animals called generalists, which are small and abundant, tend to win the ecological competition. These animals have fast and short lives, and are able to thrive in a wide variety of environmental conditions and can make use of a variety of different resources.

Generalist examples include rodents and bats. Omnivores are usually generalists. Herbivores are often specialists, but those that eat a variety of plants may be considered generalists. A well-known example of a specialist animal is the Koala, which subsists almost entirely on eucalyptus leaves. The raccoon is a generalist because it has a natural range that includes most of North and Central America, and it is omnivorous, eating berries, insects such as butterflies, eggs, and various small animals.

Study findings

In the study, the team revealed that the winners or generalists are much more likely to harbor disease-causing microorganisms or pathogens than their counterparts. As a result, when people convert natural habitats into cities and residential areas, they increase the chances of transmission of zoonotic infectious diseases, a phenomenon wherein viruses, bacteria, and fungi can jump from animals to humans. From there, human to human transmission can occur, leading to outbreaks and pandemics.

Many of the world's outbreaks and pandemics are caused by viruses and bacteria that come from animals, including the coronavirus disease (COVID-19), the severe acute respiratory syndrome (SARS), the Middle East respiratory syndrome (MERS), the human immunodeficiency virus (HIV) infection, H1N1 influenza, salmonellosis, plague, West Nile virus, rabies, and brucellosis, among others.

To arrive at the study findings, the researchers studied more than 6,800 ecological assemblages and 376 host species across the globe.

They found that known wildlife hosts of human-shared pathogens and parasites compose a more significant proportion of local species richness and total abundance in sites under human use, like urban, suburbs, and agricultural areas, compared to nearby undisturbed habitats.



"The magnitude of this effect varies taxonomically and is strongest for the rodent, bat and passerine bird zoonotic host species, which may be one factor that underpins the global importance of these taxa as zoonotic reservoirs," the authors wrote in the paper.

Further, the team revealed that mammal species that harbor more pathogens are more likely to happen in human-managed ecosystems.

"Our results suggest that global changes in the mode and the intensity of land use are creating expanding hazardous interfaces between people, livestock and wildlife reservoirs of zoonotic disease," the team concluded.

The Coronavirus Pandemic


The coronavirus pandemic, almost certainly caused by an animal spill-over and has so far affected 188 countries and territories worldwide. The pandemic awakened the world to the threat that zoonotic diseases pose to humans, despite persistent warnings from researchers over the years. As the pandemic grows and evolves, many people have the misconception that 'wild nature' is the most significant source of zoonotic disease.

Now, the research team wants to emphasize that the greatest zoonotic threats rise where natural areas have been converted to pastures, cities, and croplands, where people thrive and live.

The study highlights the importance of restoring degraded habitat and protecting undisturbed natural areas to prevent other outbreaks from happening in the future. Further, the study underscores the importance of surveillance for known and potentially zoonotic pathogens in human-dominated areas. This way, scientists will know the risk of future outbreaks.



"The way humans change landscapes across the world, from natural forest to farmland, for example, has consistent impacts on many wild animal species, causing some to decline while some others persist or increase," Rory Gibb, lead author from the UCL Centre for Biodiversity & Environment Research, said.

"Our findings show that the animals that remain in more human-dominated environments are those that are more likely to carry infectious diseases that can make people sick," he added.

The research ties in with another paper released this week on the preprint server medRxiv that discusses the root causes underlying the emergence of such infectious diseases following their crossover of the line separating animal viruses from human. The paper adds further weight to the evidence that a growing number of contacts between animals in the wild and humans are driving the entry of animal viruses into the human community.
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Re: Airborne Dust / Zoonosis / Land Use

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First data analysis about possible COVID-19 virus airborne diffusion due to air particulate matter (PM): The case of Lombardy (Italy)

May 7, 2020


https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7204748/

Despite that clear indications about the role of particulate matter (PM) in the virus mechanism dispersion cannot be found in literature, some researchers supposed that PM can act as virus carrier, promoting its diffusion through the air.

The results show that it is not possible to conclude that COVID-19 diffusion mechanism also occurs through the air, by using PM as a carrier.

This first study may serve as a reference to better understand and predict the factors affecting the COVID-19 diffusion and transmission routes, focusing on the role of air particulate matter in the atmosphere.

Very recent literature, and several newspapers articles published in March 2020 have suggested that the expansion of COVID-19 in Northern Italy, and in particular in Lombardy (for example in Brescia and Bergamo) was promoted by airborne particulate matter (PM) high concentration, with the idea that atmospheric particulate acts as a virus carrier (Sterpetti, 2020). This debate, concerning the virus possible airborne transmission mechanism, is based on the Italy and China situations concerning air pollution.

Some authors also reported that natural sources may have a significant contribution to airborne PM, as for example desert dust and sea salts.

A recent paper about PM characterization showed that the majority of the inhalable microorganisms found in PM (also including fungi, bacteria, and dsDNA viruses) were soil-associated and non-pathogenic to humans.

In the cases of virus infection, severe air pollution, with peaks of PM concentration, can produce negative effects. For example, infected people can be more susceptible to disease, due to a reduced body immunity, making microorganisms more invasive.

In this frame, a recent published work, based on a study realised in Lombardy, reports that PM concentration influences the immune system, with the consequence to foster the spread of some virus infection (Carugno et al., 2018). However, this is a different mechanism of PM incidence of virus on the human health, in comparison to the investigated one, i.e. the possible air transport of virus.

In the present case the concern is the survival of disease-causing microorganisms in the ambient air environment and, more precisely, their transport by means of airborne particulate matter (airborne transmission).

In this context, it is important to highlight that while the chemical composition of PM (Bilo et al., 2017) and its impacts on human health have been widely investigated (Ramli et al., 2020), the potential effect of airborne virus exposure (due to PM) remains unclear.

In particular, although the characterizations of bioaerosol have reported the presence of viruses in air, the highly diluted nature of viral bioaerosols has been a major impediment to viral aerobiological research, as for example the study of viral interactions with PM particles. A very recent paper, investigating the role of PM, highlight that the “presence” of DNA signatures, that may be associated with potential pathogens presence, should be considered as only exploratory evidence of potential risks (Qin et al., 2020). World Health Organization asserts that COVID-19 virus is primarily transmitted between people through respiratory droplets and contact routes. Airborne transmission is currently considered possible in specific circumstances, such as procedures that generate aerosols (WHO, Scientific brief 2020).

Then, the question is if PM can act in two ways: it is already recognized as a chronic stress factor that makes the population more vulnerable to an epidemic. However, concerning the recent proposed possibility that PM acts as a vehicle, then revealing that it allows the COVID-19 virus carried through the air, this is the actual debate.

This first study may serve as a reference to better understand and predict the factors affecting the COVID-19 diffusion and transmission routes, focusing on the role of air particulate matter in the atmosphere.
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Study shows SARS-CoV-2 jumps back and forth between animals and humans on mink farms

9/2/20

https://www.news-medical.net/news/20200 ... farms.aspx


An in-depth investigation of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) outbreaks on 16 mink farms by researchers from the Netherlands revealed that minks might serve as a reservoir for persistent infection in humans. The study is currently available on bioRxiv* preprint server.

The zoonotic origin of the coronavirus disease pandemic (COVID-19), caused by the SARS-CoV-2, is thus far unknown. Animal experiments have demonstrated that non-human primates, ferrets, cats, rabbits, hamsters and bats can be infected by this virus.

A recent introduction to this menagerie is the farmed mink. More specifically, infections in minks were observed in several farms in the Netherlands, while inhalable dust particles in the air of the mink houses were found to harbor SARS-CoV-2 genetic material.

The virus was initially diagnosed on two mink farms in the Netherlands on Apr 23 and Apr 25, 2020. After the initial detection of the virus on these farms, an in-depth investigation was initiated to look for potential transmission routes and to conduct an occupational and environmental risk assessment.

In this new study, Dutch researchers from a range of institutions conducted an in-depth investigation into the SARS-CoV-2 outbreak in mink farms and mink farm employees in the Netherlands, combining surveillance data, epidemiological information, and whole-genome sequencing on the human-animal interface.

From initial detection to whole-genome sequencing

Farm owners at the 16 mink farms positive for SARS-CoV-2 were contacted by the municipal health services in order to conduct the investigation, and their samples were taken for reverse transcription-polymerase chain reaction (RT-PCR) and serological diagnostics.

The researchers selected all available near full-length Dutch SARS-CoV-2 genomes in the national database that was available on Jul 1, 2020 (1,775 in total) and aligned with the sequences obtained in this study by using MUSCLE (multiple sequence comparison by log-expectation).

Additionally, to discriminate between mink farm-related SARS-CoV-2 infection and locally acquired ones, as well as to ascertain the potential risk for people residing in the proximity of mink farms, whole-genome sequencing was also performed on 34 SARS-CoV-2 positive samples from people who live in the same postal code area concerning the first four mink farms.

High sequence diversity of SARS-CoV-2 genomes

This study clearly shows an ongoing SARS-CoV-2 transmission in mink farms, but also pinpoints specific spill-over events to humans. A total of 68% of the tested farmworkers, their relatives, or contacts were shown to be infected with the virus – implying that the contact with SARS-CoV-2-infected mink represents a risk factor for contracting COVID-19.

Moreover, phylogenetic analysis of the mink SARS-CoV-2 genomes revealed that mink sequences of 16 farms could be grouped into five different clusters. There were no obvious distinctions in the presentation of disease in animals or humans between clusters based on the currently available data.

However, high diversity in the sequences from some mink farms has been observed, likely due to many generations of infected animals before a mortality surge, but possibly also as a result of already circulating virus in specific mink farms.

Animal surveillance as a prerogative

"To the best of our knowledge, these are the first animal to human SARS-CoV-2 transmission events documented", say study authors. "More research in minks and other mustelid species, to demonstrate if these species can be a true reservoir of SARS-CoV-2 although from our observations we consider this likely", they add.

Following the observations from this study, SARS-CoV-2 infections have also been unveiled in mink farms in Spain, Denmark, and the United States. Furthermore, it is important to emphasize that mink farming is also pervasive in other regions of the world, especially in China, where approximately 26 million mink pelts are produced every year.



"At the moment, despite enhanced biosecurity, early warning surveillance and immediate culling of infected farms, there is an ongoing transmission between mink farms with three big transmission clusters with unknown modes of transmission," highlight study authors in this bioRxiv study.

In conclusion, the structure and population size of mink farms open the door for sustained circulation of SARS-CoV-2 after its initial introduction. Hence, careful monitoring and collaboration between human and animal health services/experts remain pivotal for preventing the animals from serving as a reservoir for continued human infection.
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Health expert warns of the increasing threat of animal-to-human coronaviruses

9/1/20

https://www.news-medical.net/news/20200 ... ruses.aspx

The coronavirus outbreaks, including the severe acute respiratory syndrome (SARS), the Middle East respiratory syndrome (MERS), and the currently spreading coronavirus disease (COVID-19), all came via animal-to-human transmission or zoonosis.

Zoonosis is any disease or infection that is naturally transmissible from animals to humans, which may be bacterial, viral, or parasitic.

Now, a University of Oxford scientist, who is working on a candidate vaccine against the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), warns of an increased risk of outbreaks spreading from animals to people.

Increased threat of future outbreaks

Professor Sarah Gilbert said that human activity, such as urbanization and globalization, is driving the increasing threat. Animals start to live near communities and residential areas, while some animals are forced out of their habitats due to the continuous use of land for industrial and agricultural needs.

"Greater population density, greater travel, deforestation – all of these things make it more likely that these outbreaks will happen, and then something will spread," Gilbert said in a statement.

The warning comes after a mutated strain of coronavirus, which is ten times more infectious, was detected in Indonesia, as well as nearby countries like Malaysia and Singapore. The spread of SARS-CoV-2, the virus that causes COVID-19, has impacted economies and livelihood and overwhelmed health systems around the world.

Source of SARS-CoV-2

Until now, it is still unclear where the SARS-CoV-2 came from, but data shows that it came from an animal origin. Coronaviruses are known to thrive in bats found in jungles across the globe. From bats, the virus may transfer to intermediate hosts, such as camels, pangolins, palm civets, and raccoon dogs.

In the coronavirus pandemic spreading across the globe, scientists point to pangolins as potential intermediate hosts. Further, the SARS-CoV-2 outbreak first emerged in a seafood market in Wuhan City, where wild animals are sold.

The presence of the virus in the intermediate host could have been a short-term event. If the virus jumped from a bat to another animal and from the animal to humans, there is no guarantee the virus is still circulating in the animal population. However, if the cycle repeats itself in the future, there is a considerable possibility of another coronavirus outbreak, which may be akin to what is happening to the world today, or worse.

Causes of zoonosis

In July, the International Livestock Research Institute (ILRI) in the United Kingdom has reported seven trends driving the increasing emergence of zoonotic diseases, including the increasing demand for animal protein, climate change crisis, and the unsustainable farming practices, among others.

The report also reveals ten practical steps that countries can do to reduce the risk of future coronavirus outbreaks, which include improved regulation of food systems, expanded research on zoonotic diseases, and incentivizing sustainable land management practices.

"The science is clear that if we keep exploiting wildlife and destroying our ecosystems, then we can expect to see a steady stream of these diseases jumping from animals to humans in the years ahead," Inger Andersen, UNEP Executive Director, said.

"Pandemics are devastating to our lives and our economies, and as we have seen over the past months, it is the poorest and the most vulnerable who suffer the most. To prevent future outbreaks, we must become much more deliberate about protecting our natural environment," he added.

Global toll

The coronavirus pandemic has now infected more than 25.59 million people and has killed at least 852,000. The hardest-hit countries include the United States, with more than 6 million confirmed cases and more than 184,000 deaths, and Brazil, with more than 3.90 million cases and a death toll reaching 122,000.

The other countries with high case tolls include India, with more than 3.69 million cases, Russia, with more than 997,000 cases, Peru, with more than 652,000, and South Africa, with more than 628,000.
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Susceptibility to SARS-CoV-2 infection varies across bat species

9/9/20

https://www.news-medical.net/news/20200 ... ecies.aspx

A recent study by researchers at Wuhan University, China, reveals that many bat species are not potential carriers of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) because of genetic mutations in angiotensin-converting enzyme 2 (ACE2) that prevent the entry of viruses inside bat cells. The study is currently available on the bioRxiv* preprint server.

SARS-CoV-2, a deadly virus responsible for the coronavirus disease 2019 (COVID-19) pandemic, primarily transmit from human to human through respiratory droplets. However, other members of the coronavirus family, such as SARS-CoV, are known to have an animal origin. Given the similarity in genetic sequences between bat and human viruses, it has been postulated that horseshoe bats can be potential natural reservoirs of SARS-CoV-2.

The interaction between SARS-CoV-2 spike protein and host cell receptor, ACE2, is the primary determinant of viral entry to the host cells and induction of infection. In the current study, scientists thoroughly investigated this interaction to find out the possibility of bats being the natural hosts of SARS-CoV-2.
Study design

The scientists investigated ACE2 orthologs obtained from 46 different bat species residing in rural or urban areas. Bat species from urban areas are expected to be in close proximity to humans, whereas rural bat species are expected to have minimal human contact. Overall, the experimental bat species covered about 96% of all bat species.

Important observations

After sequence alignment of bat ACE2 orthologs, they analyzed critical amino acid residues that are responsible for interacting with viral spike protein. Genetic variations were observed in all 25 critical residues that they analyzed in the study. Moreover, about 22 amino acid sites were found to be under positive natural selection; of these sites, 4 were located in the ACE2-spike protein binding region.

To study the interaction between bat ACE2 and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, they created stable cell lines exogenously expressing each ACE2 ortholog and recombinant fusion proteins comprising of viral RBD and human IgG Fc region. Using immunofluorescence or flow cytometry-based RBD-human Fc fusion protein-binding assay, they observed that bat ACE2 orthologs have different levels of affinity and selectivity for SARS-CoV-2. Considering this observation, the scientists suggest that not all bat species are susceptible to SARS-CoV-2 infection via ACE2-RBD binding.

To further validate their findings, the scientists developed SARS-CoV-2 spike pseudotyped viruses. They observed that the ability of bat ACE2 orthologs to support the viral entry varies between species, with some bat species showing susceptibility and some showing complete resistance to the viral entry. Experiments conducted on horseshoe bats showed that none of them support the entry of SARS-CoV-2. These observations potentially indicate that the function of ACE2 is species-dependent, and many bat species lack the ability to become natural hosts of SARS-CoV-2.

Interestingly, the scientists observed that some bat species that efficiently bind SARS-CoV-2 RBD do not get the infection, indicating that high-affinity receptor binding is not always sufficient for viral entry. Similarly, bat species that show less efficient binding to SARS-CoV-2 RBD get the infection. This indicates that some bat ACE2 orthologs may support the viral entry despite having minimal binding efficiency.

To evaluate the genetic mutations in the RBD-binding sites of bat ACE2 orthologs, the scientists selected two pairs of bat species that are phylogenetically close but have contrasting receptor binding and viral entry efficiencies. Of these four bat species, two were resistant to viral RBD binding and infection; one showed efficient RBD binding and infection, and the last one showed effective viral infection but less efficient RBD binding.

By introducing mutations in specific amino acid residues of bat ACE2 orthologs that are vital for RBD binding, the scientists observed that the substitution mutations are sufficient to reverse the function of ACE2 orthologs completely. Through structural analysis of bat ACE2 orthologs, they observed that these critical residues are located in the interface between the viral spike protein and ACE2 receptor, and any genetic alteration in these residues can significantly alter the receptor activity.

Study significance

The current study findings provide clear evidence that the susceptibility of getting SARS-CoV-2 infection varies between different bat species. Furthermore, it is not scientifically correct to assume that all bat species can serve as potential SARS-CoV-2 reservoirs. The scientists believe that because some bat species are susceptible to human coronaviruses, humans infected with SARS-CoV-2 should restrict their activities on natural bat habitats to prevent possible zoonotic spillover.
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Scientists claim serious data discrepancies in RaTG13 sequence

9/9/20


https://www.news-medical.net/news/20200 ... uence.aspx

Even as the COVID-19 pandemic enters its ninth month, scientists continue to debate the origin of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) intensely. A new preprint* published in September 2020 by molecular biologists at the All India Institute of Medical Sciences, New Delhi, and the Indraprastha Institute of Information Technology Delhi discusses the current issues with the bat coronavirus (CoV) strain that is often considered to have very close homology with the above-mentioned virus, concluding that there are inadequate grounds to consider it to be the ancestral pool of SARS-CoV-2.

Many scientists mention the genome sequence of this bat CoVs, RaTG13, as being part of the ancestral descent of the current virus. A recent paper in the journal Nature also mentions its 96.2% homology with SARS-CoV-2, considering it to be a fossil record of a strain whose current existence is doubtful, but which may have been the original pool from which the current virus developed.

The scientists assembled the viral genome from scratch, performed a metagenomic analysis, and looked at data quality. They concluded that the RaTG13 genome had serious issues and all data related to it required a full review.

The researchers say, “This work is a call to action for the scientific community to better collate scientific evidence about the origins of SARS-CoV-2 so that future incidence of such pandemics may be effectively mitigated.”


Poor Reproducibility

COVID-19 is a complex disease, and so is its ancestry.
However, several groups have discussed the similarities and dissimilarities between these two viruses. The focus of the current paper is on the accuracy of the data on these sequences.

The same group of researchers initially published both sequences, but there is a qualitative difference between the papers. Full experimental details backed up the published genomic sequence of SARS-CoV-2, but not so that of the RaTG13. This is documented by several papers that have shown up the holes in the dataset underlying the published genome of the bat virus.

The researchers comment, “Since this has been the single most important piece of evidence about the origins of the SARS-CoV-2, our work highlights the need to examine this data closely prior to basing further scientific studies on it.”

The dataset that has been published in support of the RaTG13 genome, almost 30 kb long, has been found inadequate to reproduce the sequence or the experimental observations based on this dataset. While the dataset is unique and contains much information beyond the fragmented coronavirus sequence, not much is known about how it was generated. This information is vital to the quest for the origin of the SARS-CoV-2.

De novo RaTG13 Assembly Not Possible

The researchers found that using the available data, they were unable to detect any contiguous sequences larger than 17 kb, using several different settings. Several matching sequences were found, but none over a fifth of the length of the reported sequence. A gap spanning 111 positions was found, and it is unclear on what basis this was filled in the published sequence.
Contamination Likely

The researchers also uncovered proof that DNA contamination is likely to have occurred. For instance, the largest contig contains genetic material with 98% similarity to the full-length mitochondrial sequence of the Chinese rufous horseshoe bat (Rhinolophus sinicus), an unlikely event since a complete assembly of such a sequence is typically interrupted by stop codons.

Secondly, non-adapter-related repetitive sequences were found in most reads, often at the same end of the read, comprising one G-quadruplex sequence and its reverse complement. This is unlikely to happen on the same end of an RNA sample since only one strand is dominant. The researchers say more information about how the experiments were carried out is crucial to rule out the possibility of gross RNA sample contamination by DNA.

Poor Data Quality

The researchers also calculated that the average coverage is 9.73, indicating a low value. This may be why only partial segments of the RaTG13 sequence are assembled. The coverage is only 2 or less for about 3,000 bases, which could markedly impair the accuracy. They draw attention to multiple ambiguous bases in the first end that could prevent de novo assembly, and to many unreliable second end reads as well.

Again, the researchers point out that sequence length distribution in the first end is quite different in one segment concerning the rest, lacking sequences of read length 151, 149, or between 18 to 39. While this might be attributed to post-generation processing or to sequence trimming, the unusual distribution is unlikely to be explicable this way. Ambiguous base calls are also found to be distributed in a non-random tile-wise manner.

Another example is the presence of a 150 bp 18S rRNA segment, which is present in almost 15,800 times in the sequence, of which ~4,300 are 151 bp long. In all of the latter, a base-calling error was found at position 151, indicating a non-random error. The same is reflected on end 2, with another read number.

Experimental Procedural Concerns

The significantly large differences in the bacterial content of the two referenced datasets are surprising, say the researchers, since both purport to be from similar sites, fecal and oral samples. One has only 0.65% bacteria, and ~68% Eukaryota, with the rest being unidentified. The other is ~91% bacteria and ~4% Eukaryota. This concern has been raised before.

Again, 0.1% of the first dataset is similar to plant genomes like rice and maize, which is unexpected from bat samples from creatures like the intermediate horseshoe bat Rhinolophus affinis. The researchers attribute this to contamination by possible index hopping because of evidence that the same platform has been used to sequence maize earlier. Multiplex sequencing of maize and the CoV genome of interest could lead to such contamination.

Again, the dataset also contains material identical to that of the Malayan pangolin Manis javanica, a totally different order. This again could be due to index hopping of some fragments for the same reason. This could have misdirected the discussion on the origin of the novel CoV, as some have reported that pangolin CoV genomic sequences also have close homology with that of the former.

Thus, the inference could also be that contamination accounts for the presence of various portions of the RaTG13 in the dataset, accounting for 0.0008% of the total.

The second run also has sequences resembling another virus accession number, apart from its own accession number. This dataset is supposed to have a separate lane, and index hopping may be supposed not to have occurred here, but cross-contamination still seems to have occurred. The researchers note that this “raises a distinct possibility that sample from previous runs might not have been guarded against either index hopping or cross-contamination.”

This could explain the discrepancies in the earlier dataset. Furthermore, some sequences seem to have been derived from retroviruses such as the greater horseshoe bat Rhinolophus ferrumequinum, but a whole virus could not be assembled.

Implications

While most work on the origins of SARS-CoV-2 has focused on the human CoV sequence, the current study shows that equal importance must be given to the other half of the equation, namely, RaTG13, in order to justify giving it a role in the narrative. Secondly, discussions may instead be withheld, while the precise details of the methods used to generate the RaTG13 are awaited. And thirdly, this genome should not be used in further studies until its scientific reliability is established in entirety, by independent researchers with access to the full dataset and methods used for its generation.

The researchers conclude: “In this paper, we report that the currently specified level of details are grossly insufficient to draw inferences about the origin of SARS-CoV-2. This work is a call to action for the scientific community to better collate scientific evidence about the origins of SARS-CoV-2.”
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