Wuhan Virus Update

Officially, China says 28k are infected and 563 dead.  Personal projection for tomorrow is 33k and 660 dead.  By Monday, it will be 50k and 1k, imo.

A recent post on Tencent that went back down really fast claimed the infections and deaths are way, way higher than the official numbers.  The Wuhan coronavirus would have a 1:6 kill rate (over 16%) if accurate.

Another report says the infection rate is undercounted and makes it seem the deaths are at a higher percentage than they are.

Singapore has at least 28 infected and business people are getting infected when visiting.

The 12th US case has been detected in Wisconsin.

Two cruise ships are quarantined.  More than 10 tested positive on the cruise ship off Japan.

Wuhan Virus Update

By the time this gets published, China will probably have over 3,000 confirmed cases and over 80 deaths.  15 cities are in quarantine.  China has started suspending at least some of intercity travel services.  Hong Kong has started selectively blocking mainlanders from entering the territory.

China has started testing an HIV drug to see if it will work to combat the disease.

5 million people left Wuhan before the lockdown.

The US has 5 cases.  One of them is in Maricopa County, AZ.  Arizona is a noted location for the elderly to move to and the virus preferentially kills the elderly.  This could get exciting.

Several countries the world over now infections.  France and Africa (Gabon) appear to have their first cases.  It does not, yet, seem to be spreading within those countries.

The US and France are evacuating their citizens from Wuhan.  The Americans are being shipped to San Francisco.

The disease is infectious during the incubation period.  The incubation period is averaging 10 days, some as long as 14 days, some as short as 1.  The interesting case is the woman from Chicago: she was in Wuhan a month ago and came down with the symptoms only this last few days.  She may be an outlier or was in contact with someone with the virus more recently than her trip and has not been identified.  There are reports some people never seem to develop symptoms, but are carriers.

NY Times has fairly good updates.

One Quarter of all Pigs in the World Died of Swine Flu...in China

Swine fever devastated China’s stock because with unsound governance, even sound regulations have perverse effects.

On a recent visit to my hometown by the Yangtze River in eastern China, relatives welcomed me, as ever, with a feast: steamed perch and hairy crab, deep-fried river shrimp — and braised pork. My 84-year-old father made sure to serve pork, even though it was now twice as expensive as the year before. This time, he didn’t get the meat from my brother, who until this fall had been the village’s largest pork producer: All 150 pigs on my brother’s farm had either died or been culled because of African swine fever.

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Gangs are spreading swine flu by drone to attempt to extort farmers into selling their stock for well below market prices.  So there is that, too.

New Chinese Respiratory Virus Outbreak Update

China will step up efforts to contain the coronavirus outbreak in Wuhan ahead of the Lunar New Year holidays as a rise in confirmed cases fanned fears the virus could spread to other countries.

...

Wuhan’s health authority confirmed earlier on Sunday 17 more cases of the virus in the city, bringing the total number of known patients there to 62.

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Japan has confirmed its first case of infection from a newly-identified coronavirus that has killed one person and infected at least 40 more in China, as well as prompting a travel alert from the U.S. State Department.

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An outbreak of a new coronavirus in China has spread to more cities, Chinese authorities said on Monday, as the number of patients tripled and a third person died, stoking concerns about the containment of the virus.

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Nature states the new virus needs China to cooperate internationally.

Science notes folks are alarmed.

China has a new Respiratory Virus Outbreak...and it's not SARS

Chinese health authorities have not been able to identify a mysterious strain of pneumonia that has infected dozens of people and put the rest of Asia on alert -- although they have ruled out a return of the deadly severe acute respiratory syndrome (SARS) virus.

A total of 59 cases of unknown viral pneumonia have been reported in the city of Wuhan, central China, with seven patients in critical condition, the Wuhan Municipal Health Commission said in a statement on Sunday. All patients are being treated in quarantine and no deaths have been reported.

According to the World Health Organization (WHO), symptoms of the pneumonia are mainly fever, with a number of patients having difficulty breathing, and chest radiographs showing invasive lesions of both lungs.

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Paleolithic Papers #5

General:

Discover Magazine has placed online an article about the hominin sites of South Africa.

Why humans are the higher energy ape. 

Genus Homo:

Modern Humans (Homo sapiens):

Here's a paper on the technology behind early cave painting.

How durable were the jewelry made by stone age humans from marine resources?

What influenced the collagen isotopic content in the Neolithic?

The oldest known hafted axe was found in Australia from 45,000 years ago during the Pleistocene.

Evidence was found of pre Clovis Native Americans in Florida from 14,5000 years ago.

Neandertals (Homo neanderthalensis):

Could diseases brought by modern humans helped bring about the demise of the Neandertals similar, but not as extreme, as what happened to the Native Americans when Europeans came?

Was the Châtelperronian stone tool assemblage evidence of interaction between Neandertals and modern humans?

Modern humans and Neandertals had different food gathering strategies.

Climate changes seem to have impacted diet for Neandertals.

Here are investigations of the Neandertal clavical.

Homo erectus:

Some Chinese hominin teeth might have been attributed to H. erectus, but really belong to another species.

John Hawks writes about the Dmanisi hominins  and the dispersal of genus Homo out of africa.

Homo naledi: 

A symposium on H. naledi was held in Atlanta.

Genus Australopitchecus:

Australopithecus sediba:

The fossils for A. sediba are now on Morphospace.

How old are the caves A. sediba were found in?

The Native American Depopulation From European Disease had Significant Ecological Impacts

There is little dispute that in the wake of European colonists' arrival in the New World, Native American populations were decimated by disease and conflict. But when it comes to the timing, magnitude, and effects of this depopulation -- it depends on who you ask.

Many scholars claim that disease struck the native population shortly after their first contact with Europeans, and spread with such ferocity that it left tell-tale fingerprints on the global climate. Others, however, argue that -- though still devastating -- the process was far more gradual, and took place over many years.

A new Harvard study, however, suggests both theories are wrong.

Led by Matt Liebmann, the John and Ruth Hazel Associate Professor of the Social Sciences in the Department of Anthropology, a team of researchers was able to show that, in what is now northern New Mexico, disease didn't break out until nearly a century after the first European contact with Native Americans, coinciding with the establishment of mission churches.

But when it did finally strike, the study shows, the effects of disease were devastating. In just 60 years, native populations dropped from approximately 6,500 to fewer than 900 among the 18 villages they investigated. The study is described in a Jan. 25, 2016 paper published in the Proceedings of the National Academy of Sciences.

In addition to Liebmann, the study was co-authored by Joshua Farella and Thomas Swetnam from the University of Arizona and Christopher Roos from Southern Methodist University.

"In the Southwest, first contact between native people and Europeans occurred in 1539," Liebmann said. "We found that disease didn't really start to take effect until after 1620, but we then see a very rapid depopulation from 1620 to 1680. (The death rate) was staggeringly high -- about 87 percent of the Native population died in that short period.

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CRISPR Used for First Time to Treat Genetic Disorder in Adult Mice

Researchers have used CRISPR to treat an adult mouse model of Duchenne muscular dystrophy. This marks the first time that CRISPR has successfully treated a genetic disease inside a fully developed living mammal with a strategy that has the potential to be translated to human therapy.

Researchers from Duke University had previously used CRISPR to correct genetic mutations in cultured cells from Duchenne patients, and other labs had corrected genes in single-cell embryos in a laboratory environment. But the latter approach is currently unethical to attempt in humans, and the former faces many obstacles in delivering treated cells back to muscle tissues.

Another approach, which involves taking CRISPR directly to the affected tissues through gene therapy techniques, also faces challenges, particularly with delivery. In the new study, Duke University researchers overcame several of these obstacles by using a non-pathogenic carrier called adeno-associated virus, or AAV, to deliver the gene-editing system.

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Mosquito Born Zika Virus Outbreak Causing Microcephaly in Newborns in Brazil

Authorities in Brazil have recently issued an unusual and unprecedented announcement to women: don’t get pregnant, at least not just yet. Amidst an intractable outbreak of the mosquito-borne Zika virus, public health authorities in Brazil are highly suspicious of an unusual surge of cases of microcephaly among newborn children.

Much like the emerging Chikungunya virus, Zika virus was first identified in east Africa in the mid-twentieth century and has rapidly swept through Central and South America in the past year. For children and adults, the infection is relatively benign, causing a mild fever with rash, conjunctivitis or pink eye, and muscle and joint pain.

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Irish Potato Blight Pathogen Originated in South America

Using some ancient DNA detective work, a new study led by University of California Berkeley postdoctoral researcher Mike D. Martin and University of Copenhagen professor Tom Gilbert has linked the culprit behind the 19th-century Irish potato famine, which was transported to Europe in the 1840s, to a fungus-like organism that originated in South America.

Just how the pathogen, called Phytophthora infestans, made the transatlantic leap to destroy potato crops on a global scale is a "Guns, Germs, and Steel"-like tale of New World exploration and devastation published in the advanced online edition of Molecular Biology and Evolution.

The authors used genome sequences from 71 modern and historical samples of the microbial pathogen, a unique collection culled from worldwide private archives, to construct the ancestral tree of the pathogen. The origin of the species dates back to 1558 AD, the age when the first Europeans explored South America.

The research team further observed that the species was first introduced to 19th-century Europe shortly after it evolved and diversified. They found a close connection between a present-day sister species, P. andina (found only in the highlands of Ecuador and Peru) and the ancient P. infestans that triggered the first global outbreak in 1845 and the catastrophic Irish potato famine.

The authors speculate that after being found in South America, the pathogen either spread from South America directly to the U.S., or was simultaneously introduced from Mexico into South America and the U.S. prior to its infestation of Europe. "We think early European activities in the New World led to the origin of this devastating pathogen. Countless improbable events led to the introduction of this species to Europe in 1845, but our work narrows down the evolutionary possibilities to exactly two," said Martin.

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Plague Samples Discovered from 2800 BC

Plague infections were common in humans 3,300 years earlier than the historical record suggests, reports a study published October 22 in Cell. By sequencing the DNA of tooth samples from Bronze Age individuals from Europe and Asia, the researchers discovered evidence of plague infections roughly 4,800 years ago. But it was at least another thousand years until the bacterium that causes the disease, Yersinia pestis, acquired key changes in virulence genes, allowing it to spread via fleas and evade the host immune system.

"We found that the Y. pestis lineage originated and was widespread much earlier than previously thought, and we narrowed the time window as to when it developed," says senior study author Eske Willerslev of the Center for GeoGenetics, University of Copenhagen. "This study changes our view of when and how plague influenced human populations and opens new avenues for studying the evolution of diseases."

Y. pestis was the notorious culprit behind the sixth century's Plague of Justinian, the Black Death, which killed 30%-50% of the European population in the mid-1300s, and the Third Pandemic, which emerged in China in the 1850s. Earlier putative plagues, such as the Plague of Athens nearly 2,500 years ago and the second century's Antonine Plague, have been linked to the decline of Classical Greece and the undermining of the Roman army. However, it has been unclear whether Y. pestis could have been responsible for these early epidemics because direct molecular evidence for this bacterium has not been obtained from skeletal material older than 1,500 years.

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The New Technique That Finds All Known Human Viruses in Your Blood

Ian Lipkin, a virus hunter from Columbia University, recently received a blood sample from colleagues at the National Institutes of Health. They came from a man who had received a bone-marrow transplant and had fallen mysteriously ill, with evidence of severely inflamed blood vessels. In analyzing a similar case a few years back, Lipkin had discovered a new polyomavirus, part of a family that can cause disease in people with compromised immune systems. Perhaps this new case would yield another new virus.

It didn't. Instead, when Lipkin's team ran the sample through a system that they had devised to detect human viruses, they found that the man was infected with dengue virus. In hindsight, that made sense—he had recently returned from Vietnam, where dengue is prevalent. But the thing is: The team wasn't looking for dengue virus.

“It wasn't what we anticipated, but we didn't have to make a priori decisions about what we planned to find,” Lipkin says. “When people analyze samples from people who are ill, they have some idea in mind. This is probably an enterovirus, or maybe it's a herpesvirues. They then do a specific assay for that particular agent. They don't usually have the capacity to look broadly.”

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MERS is *FAR* From Gone: 19 Dead in Saudi Arabia This Week

Deaths from the MERS coronavirus have surged in Saudi Arabia ahead of the hajj pilgrimage, with 19 fatalities recorded in a week, according to health ministry statistics.

A total of 502 people have died in the kingdom since the virus first appeared in 2012, according to updated figures posted on the ministry's website, including 19, all Saudis, since last Thursday.

The number of MERS infections has also surged to 1,171 cases, the website said.

A surge in infections forced health authorities to shut the emergency ward at a main hospital in Riyadh last week, after at least 46 people, including medical staff, contracted the Middle East Respiratory Syndrome.

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South Korea Reports Sixth Middle East Respiratory Syndrome Virus Death, 87 Infections, 2300 Quarantined

South Korea recorded its sixth death and biggest single day jump in Middle East Respiratory Syndrome (MERS) infections on Monday, with 23 new cases in the largest outbreak of the potentially deadly virus outside Saudi Arabia.

From just four cases two weeks ago, the total number of infections now stands at 87, including six people who have died.

The latest fatality was a man in his 80s who had been diagnosed in Daejeon, 140 kilometres south of Seoul, and died in hospital on Monday morning, local officials said.

The outbreak has triggered widespread public concern in South Korea, with 2,300 people placed under quarantine orders and nearly 1,900 schools -- mostly in Seoul and surrounding Gyeonggi province -- closed down.

Among the 23 new cases, 17 were infected at the Samsung Medical Centre in southern Seoul, the health ministry said.

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MERS Outbreak in Korea Climbs to 35 Infected, 2 Deaths

Hundreds more schools closed on Thursday in South Korea as officials struggled to ease growing panic over an outbreak of the MERS virus that has infected 35 people, killed two and caused thousands to cancel travel plans.

More than 700 schools -- from kindergartens to colleges -- have now shut their gates in response to public fears over what has become the largest outbreak of Middle East Respiratory Syndrome (MERS) outside Saudi Arabia.

Five more cases were confirmed on Thursday, bringing the total number of known infections to 35, the health ministry said.

The first case -- reported on May 20 -- was of a 68-year-old man diagnosed after a trip to Saudi Arabia.

Since then, more than 1,300 people who may have been exposed directly or indirectly to the virus have been placed under varying levels of quarantine.

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Pin Pointing new Potential Rodent Reservoirs for Disease Caused by Global Warming

Machine learning can pinpoint rodent species that harbor diseases and geographic hotspots vulnerable to new parasites and pathogens. So reports a new study in the Proceedings of the National Academy of Sciences led by Barbara A. Han, a disease ecologist at the Cary Institute of Ecosystem Studies.

Most emerging infectious diseases are transmitted from animals to humans, with more than a billion people suffering annually. Safeguarding public health requires effective surveillance tools.

Han comments: "Historically, emerging infectious diseases have been dealt with reactively, with efforts focused on containing outbreaks after they've spread. We were interested in how machine learning could inform early warning surveillance by revealing the distribution of rodent species that are effective disease reservoirs."

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Bill Gates Worries About the Next Epidemic

Have They Found a Cure for HPV?

New research presented at the Society for Integrative Oncology (SIO) 11th International Conference in Houston, TX showed for the first time that it is possible to eliminate HPV infection in women using a readily available nutritional supplement, AHCC.

The study, presented by Dr. Judith A. Smith, Pharm.D., associate professor in the Department of Obstetrics, Gynecology and Reproductive Sciences at The University of Texas Health Science Center at Houston (UTHealth) Medical School, was selected for special research platform presentation as "Best of SIO."

"HPV is associated with 99% of cervical cancers as well as many other life threatening cancers," said Dr. Smith. "Patients who learn that they have HPV, and their doctors, are understandably frustrated because all we can do is monitor them for the abnormal changes associated with cancer. What we need is a safe, effective treatment for HPV before the cancer occurs."

In the study ten women who tested HPV-positive with the Cervista HPV HR Test were treated orally with the Japanese mushroom extract AHCC (active hexose correlated compound) once daily for up to six months. Five achieved a negative HPV test result – three with confirmed eradication after stopping AHCC – and the remaining two responders continue on the study.

Further investigation in a formal phase II randomized placebo controlled study is now being enrolled at The University of Texas Health Science Center at Houston (UTHealth) Medical School.

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Chagas in the PreColumbian Pecos Canyonlands

Prehistoric Earth Oven Facilities and the Pathoecology of Chagas Disease in the Lower Pecos Canyonlands

Authors:

Reinhard et al

Abstract:

Understanding the endemic region of a disease is part of developing a concept of the disease’s natural history and its threat to human health in both ancient and modern times. Chagas disease is caused by the parasite Trypanosoma cruzi and has recently been identified as an emergent disease in North America. Ancient endemicity and reemergence has been demonstrated by an examination of a mummy found on the border between Coahuila, Mexico and Texas, USA. This mummified man, who died over 1,000 years ago, exhibits the gross pathology of megacolon, which is consistent with Chagas disease. We are now exploring the human behavior that resulted in this parasitic infection. Trypanosoma cruzi infection exists in a sylvatic cycle involving woodrats (Neotoma spp.) and triatomine insects (Triatoma spp.) in the lower Lower Pecos Canyonlands. The Archaic subsistence strategy may have impacted this life cycle directly through predation on wood rats and through the construction of baking pits. This would have expanded the habitat suitable for both woodrats and triatomine insects. We are proposing that archaeologists develop field methods to test this hypothesis.

Ebola's Miocene Neogene Roots

A new study is helping to rewrite Ebola's family history.

The research shows that filoviruses — a family to which Ebola and its similarly lethal relative, Marburg, belong — are at least 16-23 million years old.

Filoviruses likely existed in the Miocene Epoch, and at that time, the evolutionary lines leading to Ebola and Marburg had already diverged, the study concludes.

The research was published in the journal PeerJ in September. It adds to scientists' developing knowledge about known filoviruses, which experts once believed came into being some 10,000 years ago, coinciding with the rise of agriculture. The new study pushes back the family's age to the time when great apes arose.

"Filoviruses are far more ancient than previously thought," says lead researcher Derek Taylor, PhD, a University at Buffalo professor of biological sciences. "These things have been interacting with mammals for a long time, several million years."

According to the PeerJ article, knowing more about Ebola and Marburg's comparative evolution could "affect design of vaccines and programs that identify emerging pathogens."

The research does not address the age of the modern-day Ebolavirus. Instead, it shows that Ebola and Marburg are each members of ancient evolutionary lines, and that these two viruses last shared a common ancestor sometime prior to 16-23 million years ago.

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