Airborne Dust / Zoonosis / Land Use

This forum is to discuss general things concerning TSOI.
trader32176
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Re: Airborne Dust / Zoonosis / Land Use

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White-tailed deer susceptible to SARS-CoV-2, finds study

3/15/21


https://www.news-medical.net/news/20210 ... study.aspx


White-tailed deer have been observed to be susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). They can also transmit the virus both through direct and indirect contact to one another, researchers find. The research paper is available to be read online in the Journal of Virology.

The origins of SARS-CoV-2, the underlying causative agent for coronavirus disease 2019 (COVID-19), are still unknown. Genome sequencing of the virus has so far provided evidence of an origination event in horseshoe bats. However, as no evidence can be found for direct bat-human transmission, it seems likely that COVID-19 was passed to humans through an intermediate animal host, as has been observed in previous coronavirus outbreaks.

COVID-19 has been observed to be transmissible from humans to various animal species, such as ferrets, minks, dogs, cats, hamsters, and, unsurprisingly, non-human primates. This cross-species transmissibility has raised concerns about local wildlife outbreaks of the pandemic.

SARS-CoV-2 binds to the angiotensin-converting enzyme 2 (ACE2) receptor of human cells. Researchers in the United States suspected that some species of deer, such as the white-tailed deer (Odocoileus virginiaus), would also be susceptible to the virus, as their ACE2 receptors are highly homologous to human-ACE2.

Diego Diel and colleagues experimentally inoculated a small group of 4 white-tailed deer fawns with SARS-CoV-2 and housed them in a pen neighboring 2 healthy fawns divided by a plexiglass screen. No clinical signs of illness were observed in the animals; however, the virus was able to rapidly replicate itself and shed to the healthy animals through fecal droplets and nasal secretions.

This research paper’s findings are important, assuming the zoonotic origin of SARS-CoV-2, as it has identified more animal species susceptible to the disease.

The authors note that all individual animals used were just six weeks old at the start of the study, and none had any discernible underlying health conditions. In humans, 80% of cases are either asymptomatic or mild. The majority of severe and fatal cases being found in elderly or predisposed individuals – the researchers suspect the same would likely be true in wild white-tailed deer populations.

Two other species of deer, Elephurus davidianus and Rangifer tarandus, have similar ACE2 homology. So the virus would likely be able to establish itself in these species too, though the effects of which are as yet unknown.

The researchers also noted that other cervid species must be considered in future investigations to identify species that may act as COVID-19 reservoirs.

COVID-19 has repeatedly shown been shown to be highly transmissible across human and animal hosts and appears to show little discrimination for cross-species transmission. This further highlights the need for tighter restrictions to prevent virus transmission to susceptible wildlife animal populations, and to prevent continued outbreaks in local communities.

Journal reference:


Palmer M, et al. Susceptibility of white-tailed deer (Odocoileus virginianus) to SARS-CoV-2. Journal of Virology, 2021. doi: https://doi.org/10.1128/JVI.00083-21, https://jvi.asm.org/content/early/2021/ ... I.00083-21
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Re: Airborne Dust / Zoonosis / Land Use

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Study shows how ACE2 mutations influence SARS-CoV-2 spike binding in humans and animals

3/18/21


https://www.news-medical.net/news/20210 ... imals.aspx


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has spread worldwide, infecting more than 121 million individuals and causing more than 2.68 million deaths since its emergence in December 2019.

Coronaviruses come from animal reservoirs that find their way to infect human populations
. Outbreaks, such as the severe acute respiratory syndrome (SARS), the Middle East respiratory syndrome (MERS), and COVID-19, were caused by coronaviruses.

The SARS-CoV-2 pathogen can also jump from humans to animals
, warranting the need for preventive measures to prevent outbreaks in livestock farms.

Researchers at the University of Wisconsin–Madison aimed to better understand how SARS-CoV-2 interacts with various mammalian angiotensin-converting enzyme 2 (ACE2) receptors. This way, they can identify the factors that influence intra- and cross-species virus transmission.

The study, which appeared on the pre-print server bioRxiv*, showed how mutations in human and other mammalian ACE2s affect spike protein binding using a yeast surface display-based screening method. It can help in the development of effective new vaccines for both humans and livestock animals.

SARS-CoV-2 in humans and animals

SARS-CoV-2 can transfer from animals to humans and vice versa. Over the past year that the pandemic ravaged across the globe, many reports of COVID-19 infections in animals were reported.

Aside from that, SARS-CoV-2 has exhibited a substantial ability to mutate to increase its infectivity and transmissibility in humans. These mutations can potentially reduce the efficacy of existing SARS-CoV-2 vaccines.

It is, therefore crucial to understand how sequence variation in both the ACE2 receptor and the viral spike protein influences transmission within the human population and across species barriers.

The study

The researchers studied how mutations in humans and other mammal ACE2 can impact spike protein binding to arrive at the study findings. They found that ACE2 substitutions at ACE2 amino acid positions 34, 42, and 79 elevated spike binding in various ACE2 orthologs.

In fact, the strengthened binding of Gln42Leu and Leu79Ile mutations should be focused on since Gln is at position 42 in 83 percent of annotated mammalian ACE2s, and Leu appeared at position 79 in 56 percent of these proteins.

The study findings that showed ACE2 mutations have similar impacts upon spike binding across many ACE2 orthologs show that spike protein mutations can also control the ACE2-spike binding interaction in a species-independent way.

Further, the team explained that mutant SARS-CoV-2 or other emergent coronaviruses could feature spike proteins that show cross-species transmission tendencies higher than those for SARS-CoV-2 strains currently studied. The findings are significant in vaccine development, animal farming practices to prevent COVID-19 outbreaks, and novel coronavirus strain prospecting.

The results, combined with the structural analysis of ACE2-spike binding interactions, existing evidence on SARS-CoV-2 mutations, and ACE2 sequences among mammalian species, can help shed light on the potential of viral emergence and transmission.

This could also help with the implementation of measures to mitigate the economic and social effects of the current and future coronavirus outbreaks.

“The findings presented in this work, as well as other related computational and experimental pursuits, will contribute to our understanding of how ACE2 and spike RBD amino acid sequences influence SARS-CoV-2 transmission among humans and other mammals. This heightened understanding could play an important role in developing novel vaccines for both humans and animals and contribute to global food security by facilitating the establishment of effective practices for ensuring the health of farmed animal populations,” the authors concluded.

*Important Notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Source:

COVID-19 Dashboard by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU) - https://gisanddata.maps.arcgis.com/apps ... 7b48e9ecf6

Journal reference:

Heinzelman, P., and Romero, P. (2021). Identification of ACE2 mutations that modulate SARS-CoV-2 spike binding across multiple mammalian species. bioRxiv. https://www.biorxiv.org/content/10.1101 ... 6.435705v1
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Re: Airborne Dust / Zoonosis / Land Use

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Wildlife protection, surveillance of zoonosis are the key to preventing future pandemics

3/20/21


https://www.news-medical.net/news/20210 ... emics.aspx


Understanding animal disease is essential if we want to prevent future pandemics, writes Keith Hamilton.

As the first WHO-organised joint mission to Wuhan, China comes to a close, critical questions remain on the origins of the SARS-CoV-2 virus. While there is evidence that it has origins in bat populations, how did the virus evolve and enter the human population?

As a participant expert in the WHO Wuhan mission, I can say there is a long road ahead of us. Official investigations to establish the origins of COVID-19 credibly will be highly complex and require years of research.

Zoonotic diseases on the rise


After a month in Wuhan, conducting field site-visits and interviews, the current evidence points towards a natural origin from an animal source. Zoonotic diseases are those infections that can pass between species from animals to humans, as well as from humans to animals.

Most (60.3 per cent) emerging infectious diseases affecting humans had an animal origin and the majority of these (71.8 per cent) came from wildlife, according to a 2008 study. While big disease outbreaks in humans generate news headlines, there are actually countless zoonotic events occurring globally, which mostly go unnoticed by scientists.

While COVID-19’s original jump to humans occurred quietly, the long-term consequences of this transmission are undeniable. As of March 2021, there have been more than 2.5 million confirmed deaths worldwide, 100 million reported human infections, and reports of transmission from humans into a variety of new animal species.

The World Bank’s recent analysis warned that COVID-19 has pushed an additional 88 million people into extreme poverty in 2020. Compounding the seriousness of this figure, between January 2020 and January 2021, global food prices rose by almost 20 per cent.

Human-animal-environment interface


Intensified contact between animals and humans increases the likelihood of zoonotic transmission events. For example, deforestation and climate change result in natural habitat loss and push animals, in their search for food or a new home, into human settlements.

Illegal and poorly regulated wildlife trade can also pose similar zoonotic risks because it brings together a large number of animals from diverse species, generally unseen in nature. In poor sanitary conditions, an unprecedented transmission of pathogens both within and among species can occur.

Furthermore, wildlife trade has resulted in severe detrimental effects on biodiversity, species conservation and depletion of national resources of many countries. While it is an important source of protein, income and livelihoods for many local or rural communities, this must be balanced with the reality of zoonotic disease spillover.

There are many gaps in the evidence to explain the association between human activity, wildlife trade, and disease emergence, and therefore gaps in how to reduce risk. With more research available, it will be easier to establish legal, sustainable and responsible wildlife use, based on a foundation of scientific guidance, standards, regulation, and risk management tools.

The costs of investing in appropriate surveillance systems and networks, and in wildlife health management, are not negligible, but the costs and risks of not doing so are much greater.

Protecting wildlife


One Health is not solely a buzzword thrown around by international institutions, it is a reframing of how humans interact and value the animals and environment around them. The World Organisation for Animal Health (OIE), the standard-setting organisation for animal health and welfare, champions this approach and is developing guidelines and standards for wildlife trade which support animal welfare and biodiversity conservation.

We have released a Wildlife Health Framework, calling on our 182 member countries to commit to increased involvement in wildlife protection, yet with innovation in mind. The OIE will work to develop new regulatory models to manage zoonotic risk in wildlife in a way that better respects and incorporates local customs of communities who regularly interact with wildlife. Given the higher inclusion of voices, implementing new regulations will mean not only working with national authorities, but also working closely with local communities.

We will also support our members to improve surveillance systems of zoonosis through the early detection, notification, and management of wildlife diseases. To ensure the prevention of a future pandemic, invigorated commitment to animal disease reporting by all countries is needed.

The global community currently does not conduct regular disease surveillance on wildlife. Yet if we do not conduct research on diseases while they are in the wild, it is impossible to evaluate the risks and develop suitable risk mitigation strategies.

To achieve these goals, it is essential that countries increase their investment in national veterinary services, which are responsible for ensuring animal health and welfare and are often at the forefront of zoonotic disease management. In turn, national veterinary services need to increase their collaboration with wildlife authorities and expand their own involvement in ensuring wildlife health.

These two services are the key actors in the early detection of spillover events at the human-animal-environment interface. The OIE will work to promote these types of One Health collaborations, without which we will not be prepared for disease X that is surely waiting for us.

Source:


SciDev.Net
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Re: Airborne Dust / Zoonosis / Land Use

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Next Pandemic: Scientists Fear Another Coronavirus Could Jump From Animals To Humans

3/19/21





When the pandemic began last year, scientists went looking for the origins of the coronavirus. Right away, they made a huge discovery. It looked like the virus jumped from a bat into humans.

Now, scientists are worried that another coronavirus will strike again, from either a bat or some other animal. So they've gone hunting for potential sources — and the news is a bit concerning.

"Coronaviruses are under our feet in rodents. They are above our heads in bats. We live in a kind of coronavirus world," says virologist Edward Holmes at the University of Sydney.

This past year, Holmes and his colleagues trapped several hundred bats in a tiny section of the Yunnan province in southern China — an area about the size of Los Angeles International Airport. They took samples of the bats' saliva, urine and feces. Then they looked for coronavirus genes inside the samples. What they found surprised him.

"So in this very small area that we sampled, about 1,100 hectare, there's an amazing number of bat viruses," says Holmes, who reported the findings online last week.

Holmes and his team found that the bats harbored 24 new coronaviruses, including four closely related to the virus that causes COVID-19, or SARS-CoV-2, and three viruses closely related to SARS-CoV, which caused a smaller outbreak back in 2003.

On top of that, Holmes says, the bat species carrying these viruses are common across most of Southeast Asia. "So imagine if you ran our experiment across the whole of Southeast Asia. You'd find an amazing diversity of coronaviruses," Holmes says. "And there's just an enormous number of them."

And depending on how you define a virus species, Holmes says, there are likely thousands of different coronaviruses all around the world. "We're only just starting to scratch the surface," he says. "The virusphere of coronaviruses is just immense."

And these pathogens aren't just hanging out in bats. Many types of animals carry these viruses, including dogs, cats, birds, chickens, pigs and rodents.

Now the two big questions are: How often do these viruses jump from animals into people and how often do they make people sick?

Back in 2018, scientists at the nonprofit EcoHealth Alliance tried to answer that question in communities from southern China, including villages in the same province where Holmes trapped the bats. The team drew blood from about 400 people and looked for signs of coronavirus antibodies in their blood.

In one area, they found that nearly 3% of people had been infected with an unknown coronavirus in the past few years. "That's pretty high," says Peter Daszak, who helped to lead the study.

If you expand those findings to all parts of Southeast Asia where people are exposed to these bats, Daszak estimates that more than a million people are infected with unknown coronaviruses each year.

In other words, new coronaviruses are constantly jumping from bats and other animals into people — a process scientists call "spillover."

"It's happening every day," Daszak says. "I look at the spillover event a bit like rain or snow. These viruses are getting into and trickling across our populations."

The vast majority of these spillover events do very little, he says. But each one gives the virus the opportunity to adapt and spread more easily from person to person. Every once in a while, a contagious virus infects a person who finds their way to a dense city, such as Wuhan.

Both Daszak and Edward Holmes agree: The next coronavirus outbreak could be right around the corner.

"I think we need to face reality here," Holmes says. "Coronavirus pandemics are not a once in a hundred year event. "The next one could come at any time. It could come in 50 years or in 10 years. Or it could be next year."
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Re: Airborne Dust / Zoonosis / Land Use

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Using ACE2 structure to predict SARS-CoV-2 susceptibility in animals

3/31/21


https://www.news-medical.net/news/20210 ... imals.aspx


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused the coronavirus disease 2019 (COVID-19) pandemic, gains entry to the host cell by binding to the angiotensin-converting enzyme 2 (ACE2). COVID-19 has repeatedly demonstrated its ability to infect an increasing number of mammalian species, such as tigers, mink, white-tailed deer, and many more.

Researchers based at the Rice University, Texas, USA, have now demonstrated a novel method of predicting a species' susceptibility to contracting COVID-19, based on the animal's structure of ACE2.

A pre-print version of the research paper is available to read in full on the bioRxiv*server.

What was the study

SARS-CoV-2 has always been presumed to have a zoonotic origin, either arising from bat or pangolin coronaviruses. While it is still unknown exactly which of these it first spread from, its ability for cross-species transmission is what has allowed the global COVID-19 pandemic to ensue, after being passed to humans at some point in late 2019.

Since the identification of the virus, multiple reported cases of COVID-19 have been confirmed in a number of domestic and wild mammal species. This has raised concerns that cross-species transmissibility may result in both local ecological outbreaks, but also that infected animals may re-transmit the virus back onto humans.

Previous research has suggested that pangolin coronaviruses were more likely to have been the ancestral virus for SARS-CoV-2, as pangolin ACE2 receptors in host cells to which the virus binds to are similar in both humans and pangolins. Additionally, experimental infection of white-tailed deer, which also share a similar ACE2 structure, have shown susceptibility to the disease.

Dr. Ryan Cheng and colleagues of the Rice University set out to therefore experimentally predict species that may be at risk of contracting COVID-19, based on the protein sequence of ACE2, to establish a theoretical list of species potentially at-risk to the virus.

The study

ACE2 topology is widely variable amongst mammal species, and frequently many species distantly related may share ACE2 receptors with very similar appearances.

Cheng and colleagues examined a selection of ACE2 topologies from 63 animals and assessed the potential of each of these to allow the SARS-CoV-2 virus to bind. To do this, they used the "energetic frustration" concept, a part of protein folding theory, as a proxy for binding affinity.

Essentially, the more dissimilar a protein receptor is to a subject trying to enter it, the more energy will be expelled as that subject attempts to bind. Therefore, a foreign protein or virus subject may be prevented from cell entry through a "kinetic trap," as it would take more energy to enter the cell than it can expend. More significant energetic frustration, therefore, represents lower ACE2 binding affinity, whilst minimal frustration represents higher affinity, allowing COVID-19 to enter a host cell.

Using human ACE2 as a template, an energy-landscape analysis was conducted on the models of the animal ACE2, measuring how favorable each receptor was to COVID-19 spike binding.

What the study found

The researchers' findings suggest high susceptibility to SARS-CoV-2 infection for 16 of the 63 animals, with moderate susceptibility for a further 14. The remaining animals were predicted to have resistance to virus binding.

These findings corroborate well with experimental observations of SARS-CoV-2 infection in some of the animal species, however, with two exceptions: ferrets and dogs. The authors provide a plausible explanation for this:

"SARS-CoV-2 has only been observed to replicate in the upper respiratory tract of ferrets, and viral replication has been observed to be low in dogs."

Concluding remarks

The study's authors have demonstrated a potentially powerful tool for indicating species that may be at risk from SARS-CoV-2. Whilst right now the researchers only analyzed potential susceptibility through ACE2 – there are many more potential determinants at play most likely – it represents how an energy landscape-based analysis can be used to assess the interactions of ACE2 and SARS-CoV-2.

Important notice

bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:


Cheng R., et al. Evolutionary differences in the ACE2 reveals the molecular origins of COVID-19 susceptibility. bioRxiv, 2021, doi: https://doi.org/10.1101/2021.03.25.437113, https://www.biorxiv.org/content/10.1101 ... 5.437113v1
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Re: Airborne Dust / Zoonosis / Land Use

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Low Risk of Researchers Passing Coronavirus to North American Bats

Risk Assessment Examined Likelihood of Transmission During Winter Research Season

3/30/21


https://www.usgs.gov/news/low-risk-rese ... rican-bats


The risk is low that scientists could pass coronavirus to North American bats during winter research, according to a new study led by the U.S. Geological Survey.

Scientists find the overall risk to be 1 in 1,000 if no protective measures are taken, and the risk falls lower, to 1 in 3,333 or less, with proper use of personal protective equipment or if scientists test negative for COVID-19 before beginning research.

The research specifically looked at the potential transmission of SARS-CoV-2, which is the type of coronavirus that causes COVID-19, from people to bats. Scientists did not examine potential transmission from bats to people.

“This is a small number, but the consequences of human-to-bat transmission of coronavirus are potentially large,” said USGS scientist Evan Grant, an author of the new rapid risk assessment. “The virus has not been identified in North American bats, but if it is introduced, it could lead to illness and mortality, which may imperil long-term bat conservation. It could also represent a source for new exposure and infection in humans.”

“These are hard risks for wildlife managers and other decision makers to weigh as they consider whether and how to allow researchers to study bats in their winter colonies,” continued Grant.

Bats provide natural services that people value; for example, previous USGS studies found that bats save the U.S. agriculture industry more than $3 billion per year by eating pests that damage crops, reducing the need for pesticides. Yet they are often erroneously portrayed as menacing creatures at Halloween and in horror movies. They are also under duress from white-nose syndrome, a disease that has killed millions of bats in North America.

The origin of SARS-CoV-2 is not confirmed, but studies indicate the virus likely originated from similar viruses found in bats in the Eastern Hemisphere.

The rapid risk assessment conducted by the USGS and U.S. Fish and Wildlife Service focused on the winter season, when some wildlife scientists conduct field work that may require close contact with or direct handling of the animals. This includes research on white-nose syndrome and population studies that support Endangered Species Act decisions.

“If scientists wear protective equipment, particularly properly fitted masks with high filtration efficiency, or test negative for COVID-19 before conducting the research, they greatly reduce the risk of transmission to North American bats,” said USGS scientist Michael Runge, another author on the new assessment.

“The current assessment represents the best available information and is useful for informing time-sensitive management decisions, but there are still many unknowns about how susceptible North American bats are to SARS-CoV-2 and how future virus variants may affect transmission,” said Grant.

“The potential for SARS-CoV-2 to infect wildlife is a real concern for state and federal wildlife management agencies and reflects the important connections between human health and healthy environments,” said Jeremy Coleman, National White-nose Syndrome Coordinator for the USFWS and an author of the paper. “Natural resource managers need information from these kinds of analyses to make science-based decisions that advance conservation efforts while also protecting the health of people, bats, and other wildlife.”

Three bat species – free-tailed bats, little brown bats and big brown bats – were included in the analysis. They were chosen because they have physical and behavioral differences and are typical of the kinds of bats studied in winter. Scientists considered different ways the virus could be transmitted between humans and bats, with airborne transmission as the main pathway.

This study estimates transmission risk to at least one bat during a typical winter survey, which includes a team of five scientists spending one hour in a cave colonized by 1,000 bats.

This research builds on a USGS-led study published last year that examined the likelihood of researchers transmitting SARS-CoV-2 to bats during summer research. Since that study, a substantial amount of new data and knowledge on the virus has been acquired and applied. Winter and summer research can involve different settings and activities.

The USGS research was conducted through the Eastern Ecological Science Center at the Patuxent Research Refuge and National Wildlife Health Center.

Read the study, “Risks Posed by SARS-CoV-2 to North American Bats During Winter Field Work” published in Conservation Science and Practice at https://conbio.onlinelibrary.wiley.com/ ... 1/csp2.410.
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Re: Airborne Dust / Zoonosis / Land Use

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Study reports on two cats that caught COVID-19

3/31/21


(file this one under reverse zoonosis)

https://www.news-medical.net/news/20210 ... ID-19.aspx


Our feline friends are also vulnerable to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, according to new research posted to the preprint server bioRxiv*. The researchers diagnosed two cats living in France with mild symptomatic COVID-19 illness. The virus was most likely transmitted from their owners.

Previous studies have shown increasing evidence of feline-to-feline transmission and human-to-feline SARS-CoV-2 transmission — but not the other way around. Feline infection by one of the variants of concern remains unknown but is a rising concern for pet and non-pet owners.

The researchers write:

"This question will become rapidly crucial in the very near future as the British variant, known to be much more infectious, is currently removing the ancestral variant of SARS-CoV-2 in France as well in other countries of Europe. Therefore, it is becoming more and more important to implement a One Health approach to face SARS-CoV-2 epidemic that takes into account infection and viral circulation in pets."

First cat

The two cats came from two separate households during France's second coronavirus wave from October 2020 to November 2020. The team collected RNA samples using nasopharyngeal and rectal samples. They use PCR to confirm a coronavirus diagnosis. One cat underwent serological analysis for antibodies specific to either the nucleocapsid protein (N protein) or the spike protein.

The first participant was a 5-year-old female European cat who was raised in a single-pet indoor-only household. Her only contact with the outside world during the pandemic was her owner. She had vaccinations 3 years ago and had no previous history of medical conditions.

Her owner was positive with symptomatic SARS-CoV-2 infection, and 10 days later, on October 24, 2020, the cat started showing symptoms as well. She showed continuous sneezing with non-purulent nasal secretions; there was an absence of digestive and other symptoms indicative of SARS-CoV-2.

Five days after symptom presentation, the cat displayed pink mucous membranes, an increased heartbeat of 175 bpm, increased rectal temperature ranging from 38°C-39°C, dehydration, urea seric concentration of 0.49g/l, and a creatinine seric concentration of 12.7mg/l.

The cat was treated with one doxybactin tablet for 10 days and a daily dose of Meloxoral for 3 days, with a noticeable improvement 3 days into treatment.

The team assessed serum from blood samples to look for SARS-CoV-2 antibodies following recovery. They found antibodies specific to the N protein, the spike protein's receptor binding domain, and tri-spike SARS-CoV-2 proteins. Because of the poor conservation of swab samples, the researchers could not perform genomic surveillance for SARS-CoV-2 variants.

Second cat

The second participant was a 13-year-old male European with a history of chronic rhinitis and living in a multi-pet household. He tested positive for SARS-CoV-2 infection after the pet owner — who was also positive — reported mild symptoms. Further testing found retro-mandibular adenopathy but no other symptoms.

Similar to the first cat, poor storage of samples made it difficult to evaluate the SARS-CoV-2 genome. The researchers only managed to sequence 5 partial fragments from oropharyngeal swabs. They did not find a 11288-11296 deletion, suggesting coronavirus infection was not from the B.1.1.7, B.1.351, and P.1 variant. While the researchers did not find any evidence of variants because it was potentially before their emergence, they note understanding the variants' effects on cats is limited. It remains unknown how the variants affect the transmissibility and severity of the disease.

One sequenced fragment had a genetic mutation to the amino acid Q57H. The researchers note the H57 mutation has been found worldwide and was present in about 70% of sequences analyzed in France from October and December 2020.

The results suggest their owners most likely infected both cats. "Although we cannot definitively rule out infection of the cats by an individual outside the household, the information provided by owners, including the exclusive and unique contact with its owner for cat 1 and the general deterioration in the condition of all cats of the cat 2 owner, strongly suggests a transmission from owners to cats," writes the research team.

Important Notice

*bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:

Fritz M, et al. New detection of SARS-CoV-2 in two cats height months after COVID-19 outbreak appearance in France. bioRxiv, 2021. doi: https://doi.org/10.1101/2021.03.24.436830, https://www.biorxiv.org/content/10.1101 ... 4.436830v1
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Re: Airborne Dust / Zoonosis / Land Use

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Scientists Collected Human DNA From the Air In a Breakthrough

The first reported collection of human and animal DNA from ambient air is a boon for researchers in forensic archeology, ecology, and population studies.

3/31/21


https://www.vice.com/en/article/88awgb/ ... eakthrough


In a first, scientists have revealed that animal and human DNA can be plucked straight out of thin air. The development heralds a promising new scientific technique with possible applications for ecology, forensics, and medicine, according to a new study.

Because animals shed cells into their environments, researchers can use water or soil samples to hunt for environmental DNA (eDNA), which provides a novel source of information about the lifeforms that inhabit any given area even if they are not present for DNA collection. The collection of eDNA has been pioneered in aquatic and underground environments, offering a data-rich and non-invasive way to examine species and their habitats.

Now, a team led by Elizabeth Clare, senior lecturer at Queen Mary University of London (QMUL), has provided the “first proof of concept demonstration that air samples are a viable source of DNA for the identification of species in the environment,” according to a study published on Wednesday in the journal PeerJ.

Plant and fungal eDNA has been snatched from the air before, but Clare was surprised to find that there were no analogous studies for animals in the scientific literature. She noted, though, that a pair of high school students from Japan presented a bird-focused eDNA concept at a science fair.

“There were a number of papers that speculated about it—that it will be the next thing that should be tried—but no one had done it,” Clare said in a call. “So, we gave it a try, and we just happened to have a really good experimental setup that allowed us to find a way that would give us the best possible chance of success early on.”

The setup for the DNA-grabbing experiment was a room containing “Colony Omega,” a group of naked mole-rats that have been studied and cared for by QMUL researchers for years. Naked mole-rats are fascinating animals for numerous reasons, but this colony also served as an ideal test subject for eDNA since they had lived in the same place for so long, allowing shed cells to build up in the environment. As the species’ name implies, naked mole-rats also don’t have fur or hair, which upped the odds that they would shed skin cells that are a better source of eDNA.

“They were just a really wonderful experimental system to start with,” Clare said.

Clare and her colleagues didn’t know what to expect from the experiment, so they used the same type of commercially available Sterivex-HV pressure filters that are common in aquatic eDNA studies. The filter component is located inside a plastic chamber that keeps samples sterile, and a pump attached to the equipment sucks air into the filter system to make collection more efficient.

To the team’s delight, the pressure filters successfully picked up naked mole-rat eDNA from the air inside the rodents’ burrows, and within the room itself, without needing to be adapted at all for a different medium.

What’s more, the experiment also picked up human eDNA that had been shed by researchers and caretakers of the rodents over time. At first, Clare’s team was disappointed by the presence of the human DNA, viewing it as a contaminant of the animal study. Soon, however, the researchers realized that there could be enormous implications for both sets of samples.

“That was the first thing we all discussed and said: ‘Well, isn't that terrible? It's so contaminated with human DNA,’” Clare recalled. “And then we thought: ‘No, that's a different form of DNA. We're just mammals in the environment as well.’”

The discovery of this exciting new eDNA source is bound to impact multiple scientific disciplines. Unlike DNA collected directly from one individual animal, eDNA samples can be gathered passively from an environment with no animals immediately present. These samples often contain a mixture of genetic fragments from multiple organisms that just happen to end up in filters at a certain place and time.

For this reason, eDNA is better suited for large-scale ecological studies of populations and biodiversity, such as tests for the presence of invasive species or making inventories of species that live in a selected habitat, as opposed to detecting and monitoring individuals.

Clare, who has extensively studied bats, sees special potential for ecologists hoping to non-invasively capture information about animals that live in inaccessible or potentially hazardous habitats such as caves, tree hollows, or subterranean burrows.

“We see it as another tool in the toolbox of being able to monitor different forms of life,” Clare said. “We have camera traps in forests, and we have different types of nets and aquatic filtering for waterways. We're hoping this is a way we could sample different forms of terrestrial life.”

The human eDNA also offers tantalizing possibilities for fields such as forensic anthropology or forensic archaeology, which involve data collection from human remains. For instance, specialists who study ancient remains, such as mummies, might be able to collect eDNA from within a tomb without invasively opening it, though this has not been tried yet.

Airborne eDNA could also complement existing techniques for studying the spread of pathogens, such as coronavirus
. Pathogens have evolved to be robust and long-lived as they travel through the air—as opposed to shedded DNA, which quickly deteriorates—so scientists have already developed many ways to study infectious disease transmission. Still, eDNA from the air could help to contextualize the kinds of information gathered by more established techniques.

Clare and her colleagues are already busy with follow-up studies that will shed more light on the future applications and best practices for eDNA collection from the air.

“It's fun to speculate,” she said, “but we're also quite a long way from being able to know what this material will do. Step number two is to figure out under what conditions can we even collect it.”

“What we’ve done is show it’s possible,” Clare concluded. “Now we have to figure out under what context is it possible before we actually can apply it anywhere, in particular.”
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Natural selection and adaptation of SARS-CoV-2 in mammals

4/6/21


https://www.news-medical.net/news/20210 ... mmals.aspx


Researchers of the Hubei University of Medicine, China, have analyzed several mutations in different variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from mammal species that suggest natural selection and host adaptation are occurring in the virus.

A pre-print version of the research paper is available to read in full on the bioRxiv*server.

Context

SARS-CoV-2 is the causative agent for the coronavirus 2019 (COVID-19) pandemic, which continues to be a global crisis.

While the virus can transmit from human-to-human hosts easily, multiple cases of human-to-animal and animal-to-human transmission have also been observed.

A wide range of animals has been observed or suspected to be susceptible to the virus. Cats, dogs, lions, tigers, gorillas, snow leopards, white-tailed deer, ferrets and mink have all tested positive for having acquired SARS-CoV-2.

Most notably, mink in farms in The Netherlands were reported to be contracting the virus from humans, but then also transmitting the virus both to mink and back to humans.

Thus, keeping the spread of the virus under control is essential to prevent local outbreaks in both wild and captive animal populations. Acknowledging the mutations SARS-CoV-2 variant strains acquire in different animal species is also crucial in achieving this goal.

The study


Professor Long Liu, of the Hubei University of Medicine, and colleagues analyzed multiple variants of SARS-CoV-2 found in different mammal species and compared these to the initial “Wuhan” circulating strain of the virus during the first wave of the pandemic.

The team used SARS-CoV-2 genome sequences from humans, cats, dogs, tigers, lions, ferrets and mink.

These sequences were used to construct a phylogenetic tree to infer the evolutionary history of the viral genomes. The researchers then used an adaptive evolution server (Datamonkey) to identify branches where the virus had been under selective pressure.

Following this, Liu and colleagues used the codon adaptive index (CAI) to assess the variety of mutations between the different variants.

SARS-CoV-2 binds to angiotensin-converting enzyme 2 (ACE2), an enzyme located on the outside of (primarily) respiratory cells, to access the cell. The researchers recreated the structures of human ACE2 and the crystal complex of SARS-CoV-2 to model binding efficiency between variants. Structures of mink ACE2 and the mink viral spike were also constructed and used in the analysis.

Results

The researchers found that SARS-CoV-2 of the mink cluster group had more substitution mutations compared to the reference strain.

Substitutions of cytidine in mink-CoV account for nearly 50% of the substitutions, while in other animals, cytidine accounts for only 30% of the substitutions,” say the authors, “The substitution of adenine in SARS-CoV-2 in other animals is threefold higher than that in mink-CoV.”

Cytidine-to-uracil mutations occurred over 40% of the time and 8x more so than mutations of the reverse. Substitution of adenine and guanine was also 3x higher in nonsynonymous mutations than in synonymous mutations.

Notable and convergent mutations were also observed in the spike protein of the mink SARS-CoV-2 variants. Variations in the spike protein were observed in all variants for animal species from the reference strain, D614G and A222V, most commonly found. The researchers found that these sites, as well as sites 262 and 439, were exposed to strong positive selective pressure, while other sites (294, 413, 1018 and 1100) were negatively selected for.

To determine the optimization of SARS-CoV-2 to hosts, the researchers calculated the average CAI of the spike region and the full genome of the virus. Higher CAI scores correspond to increased host optimization; these scores were lower (compared to humans) in pangolins, cats, dogs, tigers, and lions, but higher in bat hosts.

Mink SARS-CoV-2 additionally showed greater preference for mink ACE2 over human ACE2, following mutation at site 453 from Y453 (found in humans) to F453.

Concluding remarks

SARS-CoV-2 is suspected to have had a zoonotic origin, from either bat or pangolin coronaviruses. Its willingness to jump intraspecies hosts should be of great concern.

Professor Liu and her team have identified evidence for natural selection and host adaptation in SARS-CoV-2 in mink, with a great number of variations also found between other mammal hosts. Thus, understanding these mutations and the selective pressures that drive them is critical in preventing ecological outbreaks or new variants of the virus from arising.

*Important notice


bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Journal reference:


Lei Z., et al. Substitutions and codon usage in SARS-CoV-2 in mammals indicate natural selection and host adaptation. bioRxiv, 2021. doi: https://doi.org/10.1101/2021.03.15.435309, https://www.biorxiv.org/content/10.1101 ... 4.438417v1
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