Airborne Dust / Zoonosis / Land Use

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

Post by trader32176 »

Researchers discover close SARS-CoV-2-relative in animal hosts outside China

11/25/20 ... China.aspx

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the pathogen responsible for the coronavirus disease 2019 (COVID-19) pandemic, is believed to have originated in Wuhan, China, from a zoonotic origin.

Zoonosis occurs when a virus originating in animals is able to jump to, and transmit between, human hosts. SARS-CoV-2 is a betacoronavirus, in the same family as SARS-CoV and MERS-CoV, which are animal-derived pathogens characterized by their lipid envelope and positive-strand RNA structure as well as their crown-like spike proteins, from which they derive their name.

These spike proteins (or S proteins) allow the virus to attach itself to the angiotensin-converting enzyme 2 (ACE2) receptor of host cells. After binding to the ACE2 receptor, the virus instigates membrane fusion, hijacks the cell’s metabolic processes and commences viral replication.

The ACE2 receptor is abundantly present in the human epithelial cell tissue that lines the respiratory and intestinal tracts; it is by this means that the virus is primarily respiratory and has been able to infect humans, typically finding its way to the lungs through the mouth, nose or eyes.

Researchers have so far traced the virus’s origin back to a horseshoe bat species at a ‘wet market’ in Wuhan, China. Pangolins, widely sold and consumed in China, were initially thought to be an intermediary host in SARS-CoV-2’s jump to humans, but many now believe this is not the case. An intermediary host is yet to be verified.

In a major new discovery that might deepen our understanding of SARS-CoV-2’s animal origins and its genetic evolution, coronaviruses very closely related to SARS-CoV-2 have been discovered in two horseshoe bats outside of China.

What? Where? When? And how?

A very similar coronavirus pathogen to SARS-CoV-2 has been detected in two Shamel’s horseshoe bats (Rhinolophus shameli) in Cambodia. The bats were captured in northern Cambodia in 2010 and frozen as samples for scientific research.

Dr. Veasna Duong, a virologist at the Pasteur Institute in Cambodia, led a team of international researchers to search through old samples in Cambodia to hunt for close genetic relatives to SARS-CoV-2. They had announced this discovery earlier this month (November 2020).

What does this mean for our understanding of SARS-CoV-2?

Scientists are still sequencing the viral genome to gain a better sense of its exact phylogeny as well as its relation to SARS-CoV-2. To provide such insights, the virus would have to share more than 97% of its genome with SARS-CoV-2. This would be more than its closest currently known relative, say the researchers.

What this means for our understanding of the pandemic, then, is yet to be borne out. But even if the pathogen proves to be less closely related than anticipated, it may still be useful in helping scientists learn more about the diversity of this betacoronavirus family.

What we do know so far is that this groundbreaking finding, together with an earlier discovery in a Japanese bat of a more distant relative of SARS-CoV-2 in 2013, confirms that Rhinolophus bats are the reservoirs of these viruses.

The real significance of Dr. Duong and their team’s discovery will shortly be unraveled as more of the details of these coronaviruses are determined.

The ongoing crisis

To date, over 60 million people have been infected with SARS-CoV-2 across 191 countries and territories, and over 1.41 million have died.

As the Northern Hemisphere enters colder months – a climate that favors SARS-CoV-2 transmission – a series of ‘second waves’ have been reported. Many parts of Europe – including Italy, Belgium and the United Kingdom – have reinstated nationwide lockdowns in an attempt to curb the virus’s spread.

While major advances have occurred over the last few months in terms of promising vaccine candidates, no targeted, safe and effective antiviral or prophylactic treatment has been developed and rolled out to combat SARS-CoV-2. Non-pharmaceutical interventions (NPIs) like social distancing, regular handwashing and mask-wearing in public remain the most effective measures to limit the spread of the virus.


COVID-19 Dashboard by the Center for Systems Science and Engineering (CSSE) at Johns Hopkins University (JHU): ... 7b48e9ecf6

Journal reference:

Mallapaty, Smriti. (2020) Coronaviruses closely related to the pandemic virus discovered in Japan and Cambodia. Nature. doi:,
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Re: Airborne Dust / Zoonosis / Land Use

Post by trader32176 »

Genomic analysis provides clues about SARS-CoV-2 ancestry and transmission

11/25/20 ... ssion.aspx

Researchers in the UK conducting a genomic analysis of severe acute respiratory virus syndrome coronavirus 2 (SARS-CoV-2) and SARS-like coronaviruses in the bat and pangolin have identified strong host-associated divergences that could provide clues about the ancestry and interspecies transmission of SARS-CoV-2.

SARS-CoV-2 is the agent responsible for the current coronavirus disease 2019 (COVID-19) pandemic that continues to pose a significant ongoing threat to human life and the worldwide economy.

The study also identified a number of high-impact variants in several bat and pangolin coronaviruses that could be of functional relevance in the design of therapies and vaccines for SARS-CoV-2.

The team – from the University of Edinburgh and Aberystwyth University in Wales – says the evolutionary origins of the virus remain elusive and understanding its complex mutational signatures could guide vaccine design and development.

“Through employing a number of genomic analysis methodologies, this study has aimed to bring understanding of the diversity across SARS-CoV-2 and SARS-CoV-2-like coronaviruses by comparing a wide selection of available genomes from the starting point of the pandemic,” write Barbara Shih (University of Edinburgh) and colleagues.

Researchers have been trying to understand the ancestry and transmission of SARS-CoV-2

Since SARS-CoV-2 first emerged in Wuhan, China, late last year (2019), significant efforts have been made to understand its transmission and how it might be contained and treated.

Coronaviruses (CoVs) are a family of large single-stranded, enveloped RNA viruses that can be divided into four subfamilies: the alphaCoVs, betaCoVs, gammaCoVs, and deltaCoVs. Like SARS-CoV-1 and Middle East respiratory syndrome (MERS) CoV, SARS-CoV-2 belongs to the betaCoV subfamily.

The CoVs exhibit at least six open reading frames (ORFs) and four structural proteins: membrane (M), nucleocapsid (N), envelope (E), and spike (S) – the latter being the main surface structure the viruses use to enter host cells.

Interestingly, at the whole-genome level, SARS-CoV-1 and MERS-CoV only share 79.5% and 50.0% sequence similarity with SARS-CoV-2. On the other hand, SARS-CoV-2-like coronaviruses found in pangolins (pangolin-CoVs) and the bat-CoV RaTG13 share 91.0% and 96.0% similarity, respectively.

The potential role of bats and pangolins as reservoir species in the emergence of SARS-CoV-2, as well as the role other intermediary hosts potentially played, has spurred a number of research approaches and collaborations between experts of different fields.

As such, the current study was carried out as part of a “CoronaHack” hackathon event that took place in April 2020. There, the authors gained access to all the genomes and related metadata that was available at the time (between December 2019 and April 2020).

What did the researchers do?

The team employed a number of contemporary methodologies to analyze a wide range of genomic sequences isolated from human SARS-CoV-2 (n=163), bats (n=215), and pangolins (n=7).

The sequences were systematically compared at the whole-genome, gene, codon usage and variant levels to investigate the similarities and differences that exist across 89 different host species.
What did they find?

At the whole-genome levels, bat-CoV RaTG13 still shared the most similarity with SARS-CoV-2. However, all 7 pangolin-CoV genomes were more closely related to SARS-CoV-2 than the remaining 214 bat-CoV genomes.

“This relationship has previously been reported, and a recombination event between pangolin-CoVs and RaTG13 has been theorized,” say Shih and colleagues.

Gene-gene network analysis showed strong host-associated divergences in ORF3a, ORF6, ORF7a, ORF8 and the spike (S) protein. Strong host-species separations were also observed in codon usage bias profiles.

For example, three bat-CoV ORF8 genes were more similar to SARS-CoV-2 than most of the pangolin-CoV ORF8 genes.

By contrast, the S genes of pangolin-CoV and SARS-CoV-2 were more similar to each other (97.5%), than the S genes of RaTG13 and SARS-CoV-2 (95.4%).

“This is significant as the S protein plays an important role in the initial penetration and infection of host cell,” say the researchers.

However, the S gene in RaTG13 was still more similar to that of SARS-CoV-2 than to those of all other bat-CoVs analyzed in this study, they add

“This supports the theory that neither a currently sequenced pangolin-CoV or bat-CoV is the most recent ancestor of SARS-CoV-2,” writes the team.

The researchers identified strong host-species separation in the overall codon usage when multiple genes were combined in the analysis.

They found very little variation in codon usage bias within the SARS-CoV-2 isolates, but all pangolin-CoVs and three bat-CoVs had more similar codon usage to SARS-CoV-2.

Identifying high-impact variants

The team also identified several high-impact variants in bat-CoV samples, including a stop-gain for ORF10 and inframe insertions and deletions for the nucleocapsid (N) protein.

Importantly, the stop-gain was identified at amino acid position 26 in ORF10 among 57 of the 59 bat-CoV genomes, where ORF10 shared more than 80% similarity with SARS-CoV-2.

In a previous study of SAR-CoV-2 and pangolin CoV genomes, position 26 was also identified as a region of population-level variation, say Shih and colleagues.

In the N gene, the team observed multiple inframe variants for the same amino acid position in two groups of bat-CoVs. The analysis revealed two inframe insertions at amino acid position 7 and two inframe deletions at positions 238 and 385.

What are the study implications?

“These naturally occurring variants we observed across bat-CoV and pangolin-CoV may be associated with selection advantages, such as virulence or the efficiency infect a specific host species,” suggest Shih and colleagues.

The researchers say the study has revealed a high degree of host-species separation in ORF3a, ORF6, ORF7a, ORF8 and S, as well as in codon usage.

It has also identified a number of amino acid positions that demonstrate high impact variants in several bat-CoVs and pangolin-CoVs.

“These are potentially functionally important positions of the protein and warrant further research,” concludes the 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:

Shih B, et al. Hacking the diversity of SARS-CoV-2 and SARS-like coronaviruses in human, bat and pangolin populations. bioRxiv, 2020. doi:, ... 4.391763v1
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Re: Airborne Dust / Zoonosis / Land Use

Post by trader32176 »

A mutant SARS-CoV-2 subspecies from minks may evade antibody detection

11/30/20 ... ction.aspx

In a recent research letter published on the bioRxiv* preprint server, scientists from Japan discovered that the mutation of spike glycoprotein in the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) derived from farmed minks can also be found in the group of individuals with coronavirus disease (COVID-19) and subsequently evade detection by our immune system.

We are now well aware that minks and ferrets can be easily infected with SARS-CoV-2 and that keeping farmed minks in a high-density environment may prompt SARS-CoV-2 proliferation. This may consequently select viral mutants with the propensity to jeopardize the efficacy of potential drugs and vaccine candidates against COVID-19.

Such natural selection "adaptation" in SARS-CoV-2 may arise during coronavirus amplification in farmed minks by introducing mutations not specific for the viral cycle in humans. Furthermore, the infection with a specific mutant strain of SARS-CoV-2 from farmed minks – known as Y453F – can be widely spread among humans.

More specifically, this strain harbors amino acid mutation Y453F in the sequence that encodes spike glycoprotein and has been found in approximately 300 viral sequences isolated from humans in the Netherlands and around Europe, but also in minks.

This is why a research group led by Dr. Takuma Hayashi from the National Hospital Organization Kyoto Medical Center and Japan Science and Technology Agency in Tokyo, decided to investigate the virologic characteristics of the aforementioned SARS-CoV-2 mutant with the use of three-dimensional protein structural analysis.

The use of complex modeling programs

A vast amount of data regarding the three-dimensional structure of the receptor-binding domain (RBD) of the SARS-CoV-2 spike glycoprotein was used in their research approach. This was coupled with the data on the three-dimensional structure of six neutralizing antibodies known to bind to the spike glycoprotein of the virus.

The structure of the mutant was predicted with the use of the Spanner program. In short, Spanner utilizes structural fragments in order to generate a hybrid template by querying a database of structural fragments (primarily relying on the geometry of the endpoints of the gap).

Finally, the researchers have evaluated binding characteristics of the spike glycoprotein Y453F viral mutant to human angiotensin-converting enzyme 2 (ACE2) and appraised its affinity to six neutralizing monoclonal antibodies employing the MOE modeling program and Cn3D macromolecular structure viewer.

Escaping antibody detection

In short, the Y453F mutation did not have an impact on the three-dimensional structure of conventional SARS-CoV-2 spike glycoproteins. Moreover, the study has shown that the spike glycoprotein Y453F mutant binding to human ACE2 was somewhat weaker in comparison to the conventional SARS-CoV-2 spike glycoprotein.

Also, this study demonstrated that the affinity between the spike glycoprotein Y453F mutant and four of the six tested monoclonal antibodies was plainly weak when compared to the conventional SARS-CoV-2 spike glycoprotein, suggesting that this mutation may be used to escape detection from neutralizing antibodies.

Therefore, it is thought that the affinity between corresponding amino acid residues in the variable region of the antibody and the spike glycoprotein of the Y453F SARS-CoV-2 mutant decreased due to inadequate recognition of the monoclonal antibody to spike glycoproteins.

Minks as a potential cause of new infectious wave

Taking these results into account, we have to bear in mind that data on all SARS-CoV-2 mutants have thus far not been published. Hence, it is still a puzzle whether SARS-CoV-2 mutants in people working on mink farms actually stem from the farmed minks.

Nevertheless, in this study, the subspecies of SARS-CoV2 that has been derived from farmed minks were actually detected in the group of infected individuals, strengthening the hypothesis implicating this transmission pathway.

"Mutations in SARS-CoV-2 that lead to generation of SARS-CoV-2 subspecies have made humans and animals susceptible to infection through easy propagation in the host, thereby making it difficult to identify the effects of therapeutic agents or vaccines for COVID-19", accentuate study authors in this bioRxiv paper.

In any case, SARS-CoV-2 variants in millions of infected farmed mink are basically uncontrolled, which is a valid reason for concern that infection with SARS-CoV-2 mutants may cause serious symptoms in humans and elicit another wave of the COVID-19 pandemic if we are not careful and vigilant.

*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:

Hayashi, T., Yaegashi, N. & Konishi, I. (2020). Effect of RBD mutation (Y453F) in spike glycoprotein of SARS-CoV-2 on neutralizing antibody affinity. bioRxiv., ... 7.401893v1
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Re: Airborne Dust / Zoonosis / Land Use

Post by trader32176 »

Mink infected with mutated coronavirus strain escaped from Oregon farm afflicted by COVID-19 outbreak

12/29/20 ... 075579001/

Oregon state officials confirmed that a mink infected with coronavirus escaped from a farm that was quarantined in November following an outbreak that affected both mink and humans.

The runaway mink was caught Dec. 13 by a team of state biologists, according to the Oregon Department of Agriculture, and tested positive for low levels of the virus just over a week later.

Five opossums and two cats were also captured around the same time as the mink. None of the other animals tested positive for COVID-19.

“There is no evidence that SARS-CoV-2 is circulating or has been established in the wild,” said Dr. Ryan Scholz, a veterinarian for the Oregon Department of Agriculture, in a statement.

“Still, we are taking this situation very seriously and continuing to survey and trap near the farm.”

State officials declined to disclose the farm's location, citing medical privacy.

Animal welfare experts warn that farm-raised mink pose “serious concerns about disease transmission and safety protocols.”

The outbreak may affect wildlife populations, said Jonathan Evans, a legal director and attorney at the Center for Biological Diversity, and may also “pose new risks” for more COVID-19 mutations.

“With a nationwide surge in COVID-19, Oregon officials must do more to reduce and control disease outbreaks from factory farms by requiring increased safety protocols for fur farms and better reporting about where these disease outbreaks are occurring,” he said in a statement to USA TODAY.

In Denmark, where a mink outbreak was first reported, the mass culling and rushed burial of the nation's entire population of mink resulted in mink "popping up" from shallow graves. A government official later resigned following his handling of the situation.

Officials confirmed the mink at the Oregon farm have recovered from the November outbreak. Guidance from the U.S. Centers for Disease Control and Prevention and the Food and Drug Administration mandates one more round of testing before the farm is no longer under lockdown.
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Re: Airborne Dust / Zoonosis / Land Use

Post by trader32176 »

Researchers map genetic changes that may have facilitated SARS-CoV-2’s jump from bats to humans

1/13/21 ... umans.aspx

The coronavirus disease 2019 (COVID-19) pandemic continues to ravage the globe. To date, over 91.62 million cases and more than 1.96 million deaths have been reported worldwide.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, is commonly thought to be a zoonotic disease that originated in bats and then subsequently jumped to humans. This is thought to have occurred via an as yet unidentified intermediate host that may have brought the virus to Wuhan City, China, where the pathogen was first detected in December 2019.

Now, a new study by based researchers at the University of Cambridge and the Pirbright Institute in the UK has identified key genetic changes in SARS-CoV-2 that may be responsible for the virus’s jump from bats to humans. The team also determined which animals contain cellular receptors that allow the virus to enter cells more effectively, zoning in on potential animals that acted as an intermediary host in facilitating SARS-CoV-2’s zoonosis.

The coronavirus pandemic

SARS-CoV-2 first emerged in late 2019 in China, and has since spread to 191 countries and territories. To date, it has caused more than 91.71 million cases and 1.96 million deaths.

Coronaviruses commonly circulate among bat species, and SARS-CoV-2 – a positive-strand RNA pathogen of the betacoronavirus family – is also thought to have originated in the Chiroptera species in China. Yet, whether the virus directly jumped to humans or through an intermediate host is still unclear. However, it has been established that the virus can infect companion animals, pets, wildlife, and livestock.

New variants of the virus are circulating across the globe, leading to successive waves of infections. Many governments in especially hard-hit countries – such as the UK, where a highly infectious new strain has been identified – have reimposed travel bans, restrictions, and lockdown orders to try and contain the virus's spread.

Bats to humans

The study, published in the journal PLOS Biology, used a combination of surrogate entry assays and live virus to demonstrate that aside from the human angiotensin-converting enzyme 2 (ACE2), the spike glycoprotein of SARS-CoV-2 (also known as the spike protein or S protein) has a wide range of host tropisms for mammalian ACE2 receptors. This is despite divergence in the amino acids at the spike protein’s receptor binding site.

Further, they found that the genetic adaptations identified were similar to those made by the severe acute respiratory syndrome coronavirus (SARS-CoV), which caused the 2002-2003 severe acute respiratory syndrome (SARS) outbreak. The study findings suggest that there may be a common mechanism by which coronaviruses mutate for them to jump from animal hosts to humans.

With relatives of SARS-CoV-2 – SARS-CoV and the Middle East Respiratory Syndrome coronavirus (MERS-CoV), which emerged in Saudi Arabia in 2012 – the animal reservoir is thought to be bats. Viral spillover into humans has been suspected and scientists believe this occurred via an intermediate host in both cases. The SARS-CoV is thought to come from chivets and MERS-CoV from camels.

Coronaviruses typically use their spike proteins to enter cells by binding with human cell surface receptors like the ACE2. These binding sites act like a lock and key, wherein the spike protein needs to be the right shape to fit into the receptors and facilitate viral entry. However, different species express receptors with varying shapes, which means that the virus’s spike proteins may bind with the receptors more tightly in certain animals than others.

Identifying the animal reservoir of SARS-CoV-2 and any intermediate hosts may help provide insights into how, where, and when the virus emerged and was eventually passed on to humans. It may also inform the development of preventative measures to ensure this form of zoonosis does not recur.

RaTG13 virus

In the SARS outbreak, scientists identified closely related isolates in both bats and civets, where the virus is thought to have emerged. In the current outbreak, however, further studies are still needed to determine the exact source of the virus and the intermediate host.

The SARS-CoV-2 virus has the sequence of a related bat coronavirus known as RaTG13, which shares 96 percent similarity to the genome of SARS-CoV-2.

To assess if the differences between SARS-CoV-2 and RaTG13 were involved in the adaptation of the virus to humans, the researchers interchanged the regions and observed how well the spike proteins bound with the human ACE2 receptors.

The study findings showed that the spike proteins of SARS-CoV-2 that contains RaTG13 regions could not bind to human ACE2 receptors effectively. On the other hand, RaTG13 spikes containing SARS-CoV-2 regions could bind more effectively to human receptors. The findings showed that similar changes in the spike protein happened historically, which may have played an essential role in the viral spillover.

Animal infection

Apart from the study findings, the researchers also found that dog, cattle, and cat ACE2 receptors have the strongest interactors with the SARS-CoV-2 spike protein. This means that these animals are at a higher risk of being infected with SARS-CoV-2.

" As we saw with the outbreaks in Danish mink farms last year, it’s essential to understand which animals can be infected by SARS-CoV-2 and how mutations in the viral spike protein change its ability to infect different species,”

- Dr. Stephen Graham in the University of Cambridge’s Department of Pathology

However, further research is needed to establish if these animals can acquire infection and if they could act as animal reservoirs.

Journal reference:

Conceicao, C., Thakur, N., Humana, S., Kelly, J., Logan, L., et al. (2021). The SARS-CoV-2 Spike protein has a broad tropism for mammalian ACE2 proteins. PLOS BIOLOGY., ... io.3001016
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Re: Airborne Dust / Zoonosis / Land Use

Post by trader32176 »

What are the SARS-CoV-2 exposure risks for workers on mink farms?

1/15/21 ... farms.aspx

Within just a year, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – the causative pathogen of the coronavirus disease 2019 (COVID-19) pandemic – has caused more than 91.23 million recorded infections and over 1.99 million deaths.

Key to this is the rapid transmissibility of SARS-CoV-2, which is thought to have jumped the species barrier – from a Chinese horseshoe bat species, through an unknown intermediate, and then on humans hosts. Many smaller mammals were then reported to be susceptible to infection. Subsequently, large-scale infection was then detected in farmed mink, first in the Netherlands, but then also in the US, Denmark and in other countries across Europe.

A new preprint on the medRxiv* server reports on the risk of COVID-19 among workers on these farms, and in the communities living around such farms. The study was aimed at measuring the levels of the virus in the air on mink farms by portable samplers. The researchers also looked at the outdoor air, in order to understand the dispersion of the virus in the environment. Finally, they examined surfaces and materials in the mink cages, for SARS-CoV-2 contamination.

The researchers found that viral RNA was detected in every farm in at least a third of samples collected over six hours each. These samples represented dust in the air, that could be inhaled. In the second farm, one of two eight-hour samples was positive. The mean concentration in these four samples was 4 x 103 RNA copies/m3 (Ct values 35 to 36).

Settled dust showed the presence of viral RNA in over 80% of samples.
All the Electrostatic Dustfall Collectors (EDCs) used showed positive results at all farms, at the first visit, and for the second and third visits, all EDCs at one farm were positive, whereas 73% to 80% were positive at the second, and 64% and 27% at the third, visit, for the other two farms, respectively.

Thus, viral RNA reduced significantly over time at all farms, by a four to fivefold reduction each week. EDCs close to the mink cages recorded viral RNA titers that were on average threefold higher than those placed at a greater distance.

None of the residential air samples were positive over seven days.

At the fourth farm, which was tested earlier in the outbreak, three of six samples collected over six hours each, and both the samples collected over eight hours, were positive, with higher concentrations in personal air samples relative to the stationary air samples. Both personal particulate matter ( PM10) samples, and two of six stationary PM10 samples, were positive, but the concentrations were lower than with inhalable dust samples.

Outdoor samples were contaminated at locations within 1.5 meters from the farm entrance, as well as much farther away. Inhalable dust samples were also contaminated.

Mink cages were almost universally contaminated, as was the bedding, and about half the fecal samples. Drinker cups and some residual food samples were contaminated, at about a third and a tenth, respectively. The fourth farm, NB4, mentioned above, had sevenfold higher viral loads in cage swipe samples, and 50 times higher levels in beddng, relative to the farms tested later. Similarly, mink cages where the animals had recently died were heavily contaminated, as were drinker cup swabs in such cages, vs those housing live animals.

Post-culling samples had much lower viral RNA titers compared to those sampled pre-culling at the fourth farm, but almost 15% and over 20% of cage swipe samples and fecal samples were positive. Bedding was positive in over 55% (top bedding layer) and 85% (bottom bedding layer), but the viral load was 100-fold less in the top layer. The bottom bedding layer showed only a tenfold reduction, however.

The study confirms the presence of heavy contamination with viral RNA, whether in the air, as inhalable dust, or on surfaces, or settling dust. Concentrations of viral RNAs in outdoor air were very low. This finding suggests that workers on these farms are at high risk of infection, while neighboring communities are at negligible risk.

In this scenario, environmental contamination was so heavy and so prevalent as to suggest a prominent role for this factor in the transmission of this virus between minks, as well as between minks and workers. Animal handling, which peaks in the period April to June, is one probable route of exposure for farmworkers, but in other months, when animals are not typically handled, zoonotic transmission is also likely.

Air also contains smaller particles less than 10 micrometers in size as well as larger particles, both of which may be inhaled and may transport the virus to the respiratory tract. Inhalable dust contained high concentrations of viral RNA.

The question is whether airborne SARS-CoV-2 RNA is due to sneezing or coughing, by the infected animal, or through shedding into the environment, which then becomes contaminated. Both probably operate together. The highest occupational exposure was when the outbreak among minks was at its peak, in the acute phase of the outbreak, so that settling dust from this period was found to be contaminated by viral RNA in empty rows even several meters away from the animals.

The last cleaning of the mink cages occurred several months before the outbreak began, making its results independent. Sporadic cleaning was inadequate to contain or prevent the transmission of infection. RNA breakdown is influenced by the local temperature, humidity level, chemicals in the environment, including alkylating agents, and radiation such as ultraviolet radiation. Even two weeks after culling, viral RNA contaminates the environment. Thus, proper cleaning is required, along with precautions against touching or inhaling contaminated objects, surfaces or air.

Our occupational and environmental risk assessment supports earlier reported whole genome sequencing research showing mink-to-human transmission in farm workers but no direct zoonotic transmission events to nearby communities.”

*Important Notice

medRxiv 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:

De Rooji, M. M. T. et al. (2021). Occupational and environmental exposure to SARS-CoV-2 in and around infected mink farms. medRxiv preprint. doi:, ... 20248760v1
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Re: Airborne Dust / Zoonosis / Land Use

Post by trader32176 »

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

1/15/21 ... finds.aspx

A team of scientists from the United States has recently demonstrated that white-tailed deer are highly susceptible to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Moreover, the infected animals are capable of transmitting the virus to their non-infected counterparts via indirect contact. The study is currently available on the bioRxiv* preprint server.


Although there is uncertainty about the exact origin of SARS-CoV-2, a pathogen spillover from animals to humans is likely responsible for the emergence of coronavirus disease 2019 (COVID-19) pandemic. Genomic analysis studies have revealed that SARS-CoV-2 shares high genetic similarities with coronaviruses found in bats, especially horseshoe bats. However, current evidence indicates that the virus might have transmitted from an animal source to humans via an intermediate host. Although initially it was hypothesized that pangolins are the intermediate hosts for SARS-CoV-2, phylogenetic and molecular genetic sequencing analyses have failed to support the hypothesis. Thus, to accurately understand the viral origin as well as the mechanism of cross-species transmission, it is important to identify the animal species that are susceptible to SARS-CoV-2 infection and can serve as a potential zoonotic reservoir for the virus.

Current study design

In the study, the scientists investigated whether white-tailed deer are susceptible to SARS-CoV-2 infection, because the angiotensin-converting enzyme 2 (ACE2) found in white-tailed deer shares a high degree of similarity to human ACE2.

Specifically, they have intranasally infected white-deer fawns with SARS-CoV-2 to check the viral infectivity and pathogenicity. Moreover, they have investigated whether infected fawns are capable of transmitting the infection to non-infected fawns via indirect contact exposure.

Important observations

Using immunofluorescence staining approaches, the scientists have observed that SARS-CoV-2 is capable of infecting the lung cells obtained from infected fawns. Moreover, an efficient replication of SARS-CoV-2 has been observed in infected lung cells, indicating the susceptibility of white-tailed deer to SARS-CoV-2 infection and replication.

Throughout the study period (21 days), the infected fawns had not shown any COVID-19-related clinical symptoms or respiratory distress, except for a slight and temporary increase in body temperature. Moreover, no obvious lesions have been observed in post-mortem examinations.

To investigate the pattern of SARS-CoV-2 infection in the respiratory and gastrointestinal tracts, the scientists have analyzed the nasal and rectal swab samples collected from infected and indirect contact fawns. Although no evidence of viral entry into the bloodstream has been found, nasal secretions from infected fawns did show the presence of viral RNA. Interestingly, high viral load has also been detected in nasal secretions from indirect contact animals. However, a transient shedding of SARS-CoV-2 has been observed in fecal samples collected from both infected and indirect contact fawns.

Regarding tissue distribution of SARS-CoV-2, consistently higher viral loads have been observed in nasal turbinates, palatine tonsils, and retropharyngeal lymph nodes obtained from both infected and indirect contact fawns. No tissue distribution of viral RNA has been observed in the lung, kidney, intestine, brain, or mesenteric lymph nodes.

To investigate immune responses against SARS-CoV-2, the scientists measured the levels of nucleocapsid- and spike receptor-binding domain (RBD)-specific antibodies as well as neutralizing antibodies in serum samples obtained from infected and indirect contact animals. The presence of neutralizing and spike-RBD-specific antibodies in serum has been observed already after seven days of infection, and the levels of these antibodies have been shown to increase over time.

Overall, the study findings reveal that white-tailed deer are susceptible to subclinical SARS-CoV-2 infection and that intra-species transmission of the infection is possible via indirect contact. The study provides significant information about animal hosts that are susceptible to SARS-CoV-2 infection and that the findings can be potentially used to develop interventions to prevent possible reverse zoonosis.

*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:

BioRxiv preprint server. 2021. Palmer MV. Susceptibility of white-tailed deer (Odocoileus virginianus) to SARS-CoV-2. doi:, ... 3.426628v1
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Re: Airborne Dust / Zoonosis / Land Use

Post by trader32176 »

Predicting future mamalian hosts of SARS-CoV-2

2/4/21 ... CoV-2.aspx

Coronaviruses can infect both animals and humans. Coronavirus infections are common, and some strains are zoonotic, which means they can be transmitted between animals and humans.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes the coronavirus disease (COVID-19), emerged in Wuhan City, China, in late December 2019. Though the exact animal reservoir of the virus is yet to be identified, scientists believe the virus came from a horseshoe bat and jumped to an intermediate host before making its way to the human population.

Researchers at the Beijing Computational Science Research Center and Peking University analyzed sequences of the angiotensin-converting enzyme 2 (ACE2) proteins from 16 mammals and predicted the structures of ACE2- receptor-binding domain (RBD) complexes.

The team has found that the ACE2 proteins of bovine, cat, and panda form a robust binding with the RBD. Meanwhile, the ACE2 proteins of rats, horseshoe bat, pig, horse, mouse, and civet interact weakly with RBD.

The study suggests that those animals with strong binding ACE2 to RBD are more likely to be infected or become hosts of the virus.

Zoonotic infections

Over the past years, several zoonotic events have occurred across the globe. These include zoonotic influenza, such as the H1N1 flu or swine flu, salmonellosis, West Nile virus, plague, rabies, Lyme disease, and emerging coronaviruses, such as the severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), and SARS-CoV-2, among others.

Some coronaviruses cause cold-like illnesses in people, while others cause illness in some animals, such as cattle, bats, and camels. Meanwhile, some coronaviruses, such as feline and canine coronaviruses, infect only animals. However, zoonotic spillovers can happen, just like in the current coronavirus pandemic, which has now spread to 192 countries and territories. To date, there are more than 104 million COVID-19 cases globally. Over 2.25 people have died from the infection.

The study

The current study, published on the pre-print server bioRxiv*, wanted to determine which animals could be potential hosts for SARS-CoV-2 so as to help prevent future outbreaks.

ACE2 is a protein on the surface of many cell types. It is an enzyme that generates small proteins by cutting up the larger protein angiotensinogen, which then regulates functions in the cell.

Using the spike-like protein on its surface, the SARS-CoV-2 virus binds to ACE2. Once the spike protein, particularly the RBD, binds with the ACE2, the virus can enter the human cell and cause infection.

Since ACE2 is widely seen in mammals, it is crucial to investigate RBD interactions and the ACE2 of other mammals.

To arrive at the study findings, the researchers analyzed the sequences of ACE2 proteins from 16 mammals and predicted the structures of ACE2-RBD complexes. The team studied the sequence, structure, and dynamics of these complexes, providing valuable insights into the interactions between ACE2 and RBD.

The ACE2 sources selected in the study included humans, bovine or cow, cat, Chinese Horseshoe bat, dog, giant panda, horse, Least Horseshoe bat, Malayan pangolin, mouse, Palm civet, pig, rabbit, rat, sheep, and the Siberian tiger.

The team obtained the ACE2 sequences from the NCBI and uniport databases. They modeled structures for 15 mammalian ACE2 proteins. Then, the SARS-CoV-2 RBD and ACE2 complexes were assembled.

The team computed and visualized the electrostatic potential maps at the ACE2-RBD complex interfaces. Meanwhile, they also carried out molecular dynamics simulations of ACE2-RBD complexes.

The study findings showed that cats, pandas, bovine or cows, and humans form strong interactions with the RBD, while the ACE2-RBD are weaker in dogs, Siberian tigers, Malayan pangolins, sheep, and rabbits. In mice, civets, horses, rats, pigs, and least Horseshoe bats, the interactions were much weaker. Further, the ACE2 of bovine and sheep manifest high sequence identities to human ACE2.

"This study provides a molecular basis for differential interactions between ACE2 and RBD in 16 mammals and will be useful in predicting the host range of the SARS-CoV-2," the study authors concluded. Knowing the host range of the novel coronavirus can help predict and prevent future outbreaks.

*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:

Lupala, C., Kumar, V., Su, X., and Liu, H. (2021). Computational insights into differential interaction of mamalian ACE2 with the SARS-CoV-2 spike receptor binding domain. bioRxiv.,
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Re: Airborne Dust / Zoonosis / Land Use

Post by trader32176 »

A pangolin coronavirus spike glycoprotein sheds light on SARS-CoV-2’s evolution

2/16/21 ... ution.aspx

As the coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), continues to wreak havoc globally, the virus's exact source remains unclear.

Back in December 2019, a novel pneumonia-like illness was reported in Wuhan City, Hubei Province, China. By March 2020, the World Health Organization (WHO) had declared the global COVID-19 outbreak a pandemic.

Now, more than a year since it first emerged, the virus has reached 192 countries and territories. To date, more than 109.14 million cases have been confirmed, and over 2.40 million have lost their lives.

As the exact zoonotic origin and evolution of SARS-CoV-2 remain unresolved, scientists at the Francis Crick Institute in London, UK, explored the structure and binding properties of a Pangolin coronavirus spike glycoprotein to see if it could shed light on the evolution of SARS-CoV-2.

SARS-CoV-2 source

Since the virus was first reported, many scientists have been exploring its zoonotic and phylogenic origins. Like previous outbreaks of betacoronaviruses (in the same subgenus as SARS-CoV-2) – such as the severe acute respiratory syndrome (SARS) in 2002 in China and the Middle East Respiratory Syndrome (MERS) in 2012 in Saudi Arabia – horseshoe bats were considered the likely source. From there, the virus is believed to have jumped from an as yet unidentified intermediate host.

Coronaviruses of bats and pangolins have been implicated in the origin and evolution of the COVID-19 pandemic. As aforementioned, SARS-CoV-2 belongs to the subgenus of sarbecoviruses, which thrive in both horseshoe bats and pangolins.

Through a previous study, the current research team demonstrated that the bat coronavirus RaTG13, the closest known relative of SARS-CoV-2, is unlikely to infect human cells since its spike protein has a low affinity for the human angiotensin-converting enzyme 2 (ACE2) receptor.

As a result, it has been theorized that SARS-CoV-2 could have jumped to humans through an intermediate host. Several studies reported the existence of sarbecoviruses highly similar to SARS-CoV-2 in diseased Malayan pangolins. As such, pangolins were considered to have played a role in the emergence of the pandemic.

ACE2-binding properties

In the study, published in the journal Nature Communications, the team analyzed ACE2-binding properties and S protein structure from a Pangolin coronavirus (CoV) closely related to SARS-CoV-2.

To arrive at the study findings, the researchers expressed and purified two various Pangolin-CoV spike ectodomains, which can characterize the pangolin virus spike and compare it with that of SARS-CoV-2. The team based these on sequences of viruses isolated from pangolins seized in China's Guangdong province in 2019.

Further, the team generated ectodomains of ACE2 proteins from humans, bats, and pangolins to perform comparative assays.

The team has found that pangolin proteins demonstrated strong binding to the human ACE2, about ten-fold weaker binding to pangolin ACE2, and fragile binding to bat ACE2. A similar pattern of binding was noted for SARS-CoV-2, which had a strong binding to human ACE2.

The team added that the Pangolin-CoV S structure is similar to the closed-form of the SARS-CoV-2 S and the RatG13 S.

All of the observations suggest many sequence-based differences that make the Pangolin coronavirus spike adopt an all-closed conformation. The Pangolin-CoV S's closed conformation is remarkably similar, outside of the receptor-binding domain (RBD), to the RaTG13 S, suggesting that the latter's structure was potentially not materially impacted by the crosslinking.

The scientists believe that the closed conformation role was for shielding the fusion apparatus, while the open confirmation status is required to facilitate receptor binding.

The study also showed that the presence of ACE2 receptors enhances the opening of the RBDs of the SARS-CoV-2 spike and its priming for succeeding membrane fusion. An open conformation of the SARS-CoV-2's spike may help create an early kinetic event in the binding process.

Further, the SARS-CoV-2 S protein non-RBD component is comparable to that of the bat virus RaTG13 protein, with a 96 percent identity with S1. Meanwhile, their sequence identity is just 76 percent in the RBD.

Contrarily, the sequence and SARS-CoV-2's RBD is similar to that of Pangolin-CoV, mainly at the ACE2-binding site. The close similarity of the RBD between Pangolin-CoV and SARS-CoV-2 links to the near-identical binding properties of their two S proteins.

The researchers suggest that the effective zoonotic range for this class of coronaviruses beyond bats may include other species like pangolins. These animals have ACE2 receptors akin to the human ACE2. There might be unidentified pathogens like viruses that harbor RBDs of similar sequence and binding properties to SARS-CoV-2 and Pangolin-CoVs.

Understanding these similarities and differences can also help scientists explore other potential host animals, which can, in turn, guide preventative measures for similar zoonotic spill-overs in the future.

Journal reference:

Wrobel, A., Benton, D., Xu, P., et al. (2021). Structure and binding properties of Pangolin-CoV spike glycoprotein inform the evolution of SARS-CoV-2. Nature Communications.,
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Re: Airborne Dust / Zoonosis / Land Use

Post by trader32176 »

Bats and pangolins in Southeast Asia harbor SARS-CoV-2-related coronaviruses, study finds

2/17/21 ... finds.aspx

The sudden and devastating emergence of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) – the etiological agent of the ongoing coronavirus disease 2019 (COVID-19) pandemic – has raised many questions as to where it came from. The possibility of potential animal viral reservoirs, as evidenced by the ready transmission of the virus to mink and back again to mink farmworkers, is also very real. Thus, it is important to understand how this virus arose, and how it is transmitted from its initial animal reservoir to humans.

A new paper published in the journal Nature Communications recently reported evidence that SARS-CoV-2 related coronaviruses (SC2r-CoVs) are circulating in bats in Southeast Asia. This has extended the geographical area where SC2r-CoVs are found, underscoring the urgency of identifying the immediate ancestor of SARS-CoV-2.

This virus is one of the SARSr-CoVs among the betacoronaviruses, with 96% whole-genome identity with the bat SC2r-CoV, RaTG13. The latter has therefore been suspected of having given rise to the pandemic virus. Other closely related genomes have been found in pangolins from China and other bats in Eastern China and Japan.

The immediate progenitor has escaped identification, which hampers measures to prevent future outbreaks of the same sort. For this reason, the investigators looked at bats and pangolins to identify SC2r-CoVs, using serological surveys. These, while lacking the definitive nature of polymerase chain reaction (PCR) testing and genome sequencing, are better at identifying infection long after it has resolved.

Identifying new bat- SC2r-CoV in Thailand

The investigators located a colony of 300 bats in an artificial cave in a wildlife sanctuary in eastern Thailand. A third of them were sampled in June 2020. All belonged to the species Rhinolophus acuminatus.

Of the 100 animals, 13 had positive rectal swabs by PCR testing. This showed the presence of a bat CoV that was 96% identical to RaTG13. The most dominant strain of this was named RacCS203, and found to be 94% identical to the bat CoV, RmYN02. RacCS203 is thus a new member of the SC2r-CoV lineage.

It has differences in the ORFs 1ab, 7 and 8, and in part of the nucleocapsid (N) gene, relative to the RmYN02. Orthologous proteins also show different sequences. Moreover, the ORF8 of this strain is closer to that of ZC45 than of RmYN02. The RacCS203 ORF10 is identical to that of the strain ZXC21, but different from that of both the other strains mentioned above.

RacCS203 receptor binding domain

ACE2, or the angiotensin-converting enzyme 2 (ACE2), acts as the entry receptor for SARS-CoV-2 in humans. The virus attaches to the receptor via its receptor-binding domain (RBD).

The RacCS203 RBD showed nucleotide sequences that corresponded to non-ACE2-dependent SARSr-CoVs, including RmYN02 and ZC45. This was confirmed experimentally by the lack of ACE2 binding. A pseudovirus expressing the full-length viral spike failed to infect cells in culture when expressing RacCS203 spike, but the successful infection was established with SARS-CoV-2 spike expression.

Serological survey in bats

The researchers used a SARS-CoV-2 surrogate virus neutralization test (sVNT) to explore how far SC2r-CoVs circulated in the region. This test avoided using live SARS-CoV-2 while providing high specificity for antibody-mediated inhibition of RBD-ACE2 binding by this virus.

They found that 4/98 samples had neutralizing antibodies for SARS-CoV-2 RBD-ACE2 binding, with two of them showing 88% and 97% inhibition. This occurred despite the fact that they do not bind ACE2. This inhibition level is surprising, since bat antibodies typically show a lower neutralizing titer than human or rabbit antibodies. In fact, even COVID-19 patients do not show such high titers, for the most part.

The high sequence homology between the RBDs of RacCS203 RBD and SARS-CoV-2 may have elicited cross-neutralizing antibodies without involving ACE2.

Another explanation could be that these reflect cross-neutralization by antibodies induced by other circulating SC2r-CoV that are even more similar to SARS-CoV-2 than RacCS203. In support of this, the PCR positivity was higher among the bats than sVNT, especially for the two samples, which showed high sVNT values.

Pangolin serology

Ten pangolin sera from central and southern Thailand, obtained from confiscated pangolins of unknown country of origin, were also available. The animals all belonged to the species Manis javanica. One of them showed 91% inhibition by the sVNT assay, linking it to a similar result reported from China in another pangolin, 17 years ago.

This shows that these animals can be infected by SC2r-CoVs. They could not be confirmed to be the spillover hosts, however. PCR testing using pan-CoV primers was negative in all samples.

When tested against patient antibody-containing sera from COVID-19 patients, the researchers found that the strongest reactivity was seen with SARS-CoV-2, RaTG13, and GX-P5L, with ZC45 and RmYN02 showing weak reactivity to these antibodies. SARS-CoV showed the least reactivity.

With patient sera from SARS-CoV, low reactivity was observed against all these viruses.

Rabbit sera containing antibodies to RaTG13 RBD were found to be more reactive to the SARS-CoV-2 RBD than when raised against RmYN02 RBD. Both types of sera neutralized SARS-CoV-2, however, by sVNT and by plaque reduction neutralization tests (PRNT).

Geographical range

Rhinolophus bats known to carry SC2r-CoVs are found to occupy a lower latitude than those carrying SARS-CoV-related viruses (SC1r-CoVs). This shows that bats carrying CoVs closely related to SARS-CoV-2 are found to occupy a vast range, extending across multiple regions and countries in Asia, from Japan’s Iwata Prefecture in the north to Chachoengsao, Thailand, in the south; and from Yunnan in the southwest to Zheijang in the east.

So far, five Rhinolophus bat species show the presence of these viruses. Further expansion of these studies, involving different countries, is likely to demonstrate the presence of more SC2r-CoVs in other Rhinolophus species.

What are the implications?

The order of binding affinity to human ACE2 is as follows: GX-P5L>SARS-CoV-2>SARS-CoV>RaTG13. Thus, despite the fact that RaTG13 is the only bat CoV with an RBD that binds hACE2, it has the lowest ranking in order of affinity, while the highest is from the Malayan pangolin. In other words, ACE2 binding does not match with genome sequence identity to SC2r-CoVs or SC1r-CoVs.

These findings suggest that “either these viruses have undergone recombination at the RBD region or ACE2 is not the only or main entry receptor used by these viruses in bats.”

Southeast Asia is likely to harbor many such viruses. The SC2r-CoV lineage is also capable of great diversity, showing multiple mutations unique to each of the viral lineages in this group. This indicates “that there is a high probability to find the immediate progenitor virus of SARS-CoV-2 with intensified and internationally coordinated surveillance.”

Journal reference:

Warachapluesadee, S. et al. (2021). Evidence for SARS-CoV-2 related coronaviruses circulating in bats and pangolins in Southeast Asia. Nature communications.
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