Pathogens and their impacts

[Tor Bejnar]

When in university, my brother gave me a 'protest button' with:
             New Mexico
       Land of the flea
     Home of the plague

From the New Mexico Dept. of Health:

Plague is an infectious disease of animals and humans caused by a bacterium named Yersinia pestis. People usually get plague from the bite of a rodent flea that is carrying plague bacteria or by handling an infected animal.

Although plague is a rare disease, about half of US cases each year occur in New Mexico. Antibiotics are effective against plague, but if an infected person is not treated promptly the disease can be life-threatening.

...

There has been one Human Plague Case in New Mexico in 2019 ...
There have been no human plague cases in 2018.
There were four Human Plague Case in New Mexico in 2017 ...
There were four Human Plague Cases in New Mexico in 2016 ... All survived the illness.

[vox_mundi]

DR Congo Measles: Nearly 5,000 Dead In Major Outbreak
https://www.bbc.co.uk/news/world-africa-50506743

Measles has killed nearly 5,000 people in the Democratic Republic of Congo in 2019, authorities said, after the disease spread to all the provinces in the country. Close to a quarter of a million people have been infected this year alone.

The World Health Organization (WHO) says this is the world's largest and fastest-moving epidemic.

Four million children have been vaccinated, but experts warn that this amounts to less than half of the total in the country - and not enough vaccines are available. The majority of those infected with measles in the country are infants.

Measles in DR Congo has now killed more than twice the number who have died of Ebola there in the last 15 months.

It is estimated that a global total of 110,000 people die from measles each year.

[vox_mundi]

Border Patrol Denies Undocumented Immigrants Free Influenza Vaccine
https://abcnews.go.com/amp/Health/border-patrol-denies-undocumented-immigrants-free-influenza-vaccine/story?id=67237256

Peak flu season is fast approaching North America and the U.S. government is actively encouraging anyone over 6 months old to vaccinate – that is, unless you are one of the thousands of people being detained in Customs and Border Protection facilities for undocumented entry

“To us in the medical community the situation is alarming. When the CBP stated in August that they weren’t planning on vaccinating we saw this as egregious to deny basic health care access to people forced to stay in their care," said Dr. Bonnie Arzuaga, a Boston-based pediatrician and one of the founders of Doctors for Camp Closure.

The organization is a volunteer group of 2,000 U.S. based physicians who support the closing of the Customs and Border camps because of public health concerns. The organization volunteered to provide free influenza vaccines to those detained but the government never responded.

“We got no response, not even an acknowledgement of the letter," said Arzuaga.

[kassy]

Polio eradication program faces hard choices as endgame strategy fails

The “endgame” in the decadeslong campaign to eradicate polio suffered major setbacks in 2019. While the effort lost ground in Afghanistan and Pakistan, which recorded 116 cases of wild polio—four times the number in 2018—an especially alarming situation developed in Africa. In 12 countries, 196 children were paralyzed not by the wild virus, but by a strain derived from a live vaccine that has regained its virulence and ability to spread. Fighting these flare-ups will mean difficult decisions in the coming year.

The culprit in Africa is vaccine-derived polio virus type 2, and the fear is that it will jump continents and reseed outbreaks across the globe. A brand new vaccine is now being rushed through development to quash type 2 outbreaks. Mass production has already begun, even though the vaccine is still in clinical trials; it could be rolled out for emergency use as early as mid-2020. At the same time, the Global Polio Eradication Initiative (GPEI) is debating whether to combat the resurgent virus by re-enlisting a triple-whammy vaccine pulled from global use in 2016. That would be a controversial move, setting back the initiative several years, as well as a potential public relations disaster—an admission that the carefully crafted endgame strategy has failed.

...

The heart of the problem is the live oral polio vaccine (OPV), the workhorse of the eradication program—the only polio vaccine powerful enough to stop viral circulation. Given as two drops into a child’s mouth, OPV for decades contained a mix of three weakened polio viruses, one for each of the three wild serotypes that have long plagued humanity. All three serotypes in the vaccine have the potential to revert to more dangerous versions; that’s why the endgame strategy calls for deploying OPV in massive campaigns to eradicate the wild virus, then ending its use entirely.

Wild serotype 2 was last sighted in 1999, so in 2016, as a first step in the endgame, all 155 countries using OPV replaced the trivalent version with a bivalent one, lacking the type 2 component. Announced with great fanfare, “the switch” was billed as the biggest vaccine rollout ever. Some type 2 outbreaks would inevitably occur for several years, GPEI realized, but those would be fought, somewhat paradoxically, by rushing in essentially the same vaccine that gave rise to them in the first place: a live, monovalent vaccine targeted against type 2 (mOPV2). If used in well-run campaigns, and only in outbreak regions, mOPV2 could stop outbreaks without seeding new ones, models suggested.

It often has not turned out that way. Instead of fading away, the number of type 2 outbreaks in Africa almost tripled from 2018 to 2019. Most of today’s outbreaks stem from mOPV2 responses to previous ones, and GPEI is burning through its emergency stockpile of mOPV2 faster than it can be replenished. (Based on a small study in Mozambique, a WHO advisory panel recently recommended halving the dose to one drop if supplies run critically low, despite what it calls “a relatively weak level of evidence” that the smaller dose is as effective.) Meanwhile, the risk of explosive outbreaks around the globe is ratcheting up, because millions of children born since the switch have little or no immunity to type 2 virus.

https://www.sciencemag.org/news/2019/12/polio-eradication-program-faces-hard-choices-endgame-strategy-fails

[sidd]

Polio and the CIA: Pakistanis distrust vaccine campaigns

https://www.abc.net.au/news/2014-05-27/polio-resurges-as-health-emergency-in-pakistan/5478144

sidd

[vox_mundi]

China Investigates SARS-like Virus as Dozens Struck by Pneumonia
https://dw.com/en/china-investigates-sars-like-virus-as-dozens-struck-by-pneumonia/a-51843861

Chinese health authorities on Tuesday said they are investigating 27 cases of viral pneumonia in central Hubei province, amid online speculation that it could be linked to the SARS flu-like virus that killed hundreds of people a decade ago.

Wuhan health officials issued an emergency notification on Monday after local hospitals treated a "successive series of patients with unexplained pneumonia."

Of the 27 reported cases, seven are in a critical condition and 18 are stable, the Wuhan Municipal Health Commission said on Tuesday on its Weibo social media account. ...

A 2003 outbreak of the highly-contagious SARS virus was covered up and killed hundreds of people.

--------------------------

[vox_mundi]

China Confirms More Cases of Mystery Viral Pneumonia
https://medicalxpress.com/news/2020-01-china-cases-mystery-viral-pneumonia.html

China on Friday confirmed more cases of a mystery viral pneumonia that has sparked fears about a resurgence of SARS, the flu-like virus that killed hundreds of people more than a decade ago.

The 44 cases, up from the initial 27 announced Tuesday, include 11 "severe cases," health authorities in the central Chinese city of Wuhan said in a statement.

The authorities are still in the process of identifying the cause of the infection, but "influenza, avian influenza, adenovirus infection and other common respiratory diseases have been excluded," the Wuhan health commission said on Friday, without mentioning SARS, which is caused by a coronavirus.

[vox_mundi]

Coronavirus Infections in China Feared To Be More Widespread Than Officially Reported
https://www.abc.net.au/news/2020-01-23/wuhan-coronavirus-overwhelms-hospitals-fears-it-will-spread/11888588

Hospitals in the Chinese city of Wuhan are reportedly dealing with huge numbers of ill patients, raising fears the new coronavirus is spreading faster than official reports suggest.

This comes as the state-owned Global Times newspaper in an editorial appeared to lash authorities in Wuhan for being slow to report the virus had spread to medical workers — a key sign of human-to-human transmission and potential "super-spreaders".

The novel coronavirus has so far infected about 440 people across China, the country's National Health Commission said on Wednesday, with nine confirmed deaths.

That was a jump from about 300 infections and six confirmed deaths yesterday.

Authorities say they have also confirmed 2,197 cases where people have had close contact with patients.

The number of confirmed coronavirus cases includes dozens of people in Beijing, Shanghai, Guangdong province and Zhejiang province, with the majority in central Hubei province, where the city of Wuhan is located.

However, according to messages in a private WeChat group for Chinese medical professionals viewed by the ABC, one hospital in Wuhan has been overwhelmed with patients, with nearly 300 people in that facility alone exhibiting symptoms of the coronavirus.

Video footage appeared to back up the reports, showing large lines of patients wearing face masks at a hospital in Wuhan, crowding the wards as doctors moved through checking on them.

... Cases of the virus have already been reported in the United States, Japan, South Korea and Thailand and Hong Kong, while one man in Brisbane was briefly placed in isolation after returning from Wuhan with flu-like symptoms, but subsequently released.

Hong Kong also reported 118 suspected cases, according to the South China Morning Post, however 88 of those people have since been discharged.

Macau, another special administrative region of China, also announced its first confirmed case of the virus on Wednesday.

--------------------------------

Pandemic Fears Grow as New Coronavirus Spreads
https://www.dw.com/en/pandemic-fears-grow-as-new-coronavirus-spreads/a-52103638

The World Health Organization (WHO) will hold an emergency meeting on Wednesday to determine whether to declare a global public health emergency over a new viral illness which has spread through east Asia and reached the United States.

Authorities in China, where the virus originated, said the number of cases of a new virus had jumped to 444 and the death toll had risen to 17.



President Donald Trump told reporters Wednesday his administration has a plan to block any outbreak of the coronavirus, saying the CDC "has been terrific."



See Also: https://forum.arctic-sea-ice.net/index.php/topic,681.msg183635.html#msg183635

https://www.cdc.gov/coronavirus/2019-nCoV/summary.html

-----------------------------

Trump: Chinese Coronavirus 'Totally Under Control'
https://www.politico.com/news/2020/01/22/trump-chinese-coronavirus-totally-under-control-102054

President Donald Trump said today the U.S. has a deadly Chinese coronavirus “totally under control” and there are no worries of a pandemic. ... “It’s going to be just fine.”

... The World Health Organization is convening an expert panel today to discuss whether the Wuhan virus should be designated "public health emergency of international concern," a rare step aimed at getting more money and resources from global donors to fight an outbreak.

The emergency designation has been used just five times: against polio, the swine flu, the Zika virus and two recent Ebola virus outbreaks in Africa.t.

[vox_mundi]

Coronavirus: China To Bar 11 Million Residents From Leaving City at Centre of Outbreak
https://www.theguardian.com/world/2020/jan/22/coronavirus-china-measures-rein-spread-mutate-disease-death-toll

Chinese authorities will suspend all outbound transport from Wuhan, the city at the epicenter of an outbreak of the mysterious Sars-like coronavirus, which has so far killed 17 people.

Bus, subway, ferry and long-distance passenger transportation networks from the city will be suspended from 10am local time on Thursday, state media reported. The city’s airport and train stations will also be closed to outgoing passengers.

https://mobile.twitter.com/PDChina/status/1220060879112282117



... The local government has cancelled public activities during the holiday, including the annual prayer-giving at the city’s Guiyan Temple, which attracted 700,000 tourists last year.

The commission noted the virus is being treated as a class A disease, which means authorities can quarantine patients and put affected areas on lockdown.

[nanning]

^^
Many are trying to get out which results in overcrowded trainstations and airports, the best recipe for fast transfer of the pathogen.

[blumenkraft]

https://en.wikipedia.org/wiki/List_of_epidemics

[vox_mundi]

Coronavirus: Chinese Hospitals in Chaos as Lockdown Spreads to Affect 33 Million People
https://www.theguardian.com/science/2020/jan/24/coronavirus-chinese-hospitals-in-chaos-as-lockdown-spreads-to-affect-25m-people
https://www.businessinsider.com/china-virus-wuhan-building-new-hospital-coronavirus-2020-1?amp

Public transport suspended in at least 10 cities as death toll rises and heath care centres struggle to cope with influx of patients

Hospitals in the Chinese city of Wuhan have been thrown into chaos and the movement of about 33 million people has been restricted by an unprecedented and indefinite lockdown imposed to halt the spread of the deadly new coronavirus.

At least 10 cities in central Hubei province have been shut down in an effort to stop the virus, which by Friday had killed 26 people across China and affected more than 800.

In the city of Wuhan, where most cases have occurred, the race to build a new 1,000-bed hospital in just six days began on Thursday night. Diggers and bulldozers beginning work on the site of a holiday complex once intended for local workers, according to Chinese media. ... the new Wuhan hospital “is to solve the shortage of existing medical resources”.



Doctors in Wuhan say that people have to queue for hours for medical attention, that screening the disease is difficult, that there is not enough protective gear, and that some doctors were told not to go to work over fears they could catch the virus.

... People who sought treatment in Wuhan this week told the Guardian they had been turned away from hospitals, which have been inundated with patients. Facilities are reportedly running out of beds and diagnostic kits for patients who present with fever-like symptoms.



Videos taken elsewhere in Wuhan showed shop shelves emptied by shoppers who rushed to stock up on foods, and barricades going up across Wuhan.

The cities of Wuhan, Ezhou, Huanggang, Chibi, Qianjiang, Zhijiang, Jingmen and Xiantao have all been placed under lockdown.

In Zhijiang city, all public venues have been shut down except hospitals, supermarkets, farmers’ markets, gas stations and drug stores. Indoor entertainment venues in Enshi city have also been shut down.

Officials worry the weeklong lunar new year holiday, which begins on Saturday and usually sees hundreds of millions of Chinese crisscross the country, will exacerbate an outbreak that has reached almost all of China’s provinces.

[Tom_Mazanec]

I suspect they are closing the barn door after the horse runs out.
EDIT
Also tomorrow is CNY and I suspect a sizable number will violate the quarantine as that is just human nature.

[vox_mundi]

Chinese officials on Friday expanded a mass quarantine effort and transport restrictions in the outbreak's epicenter, Wuhan, to at least 13 cities.

A total of around 41 million people are currently affected by the lockdown.

Authorities in Hubei, the province where Wuhan is located, said on Friday that they have sought greater financial support from the central government.

... In spite of a rising death toll in China, the WHO said it was "too early" to declare an official international health emergency. The Chinese government on Friday said there had been at least 26 fatalities and more than 800 cases of the virus in total so far. Authorities were also examining 1,072 suspected cases.

There are more than 830 confirmed cases of infection, and at least 26 people have died. A total of 8,420 people are reported to be under observation.

https://dw.com/en/china-extends-lockdown-on-millions-in-coronavirus-outbreak/a-52131828

... Quarantine is "purely an illusion", said Bruno Halioua, a historian of medicine at the University of Paris IV.

"Quarantine has never worked. Each time, there have been problems."

"Especially people with money and connections, they're going to make a run for it... and they'll probably be successful," Zi Yang, a senior analyst at the S. Rajaratnam School of International Studies in Singapore, told AFP.

And after seeing the situation in Wuhan first-hand, Guan Yi of Hong Kong University shared an equally pessimistic outlook.

"I've never felt scared," Guan said. "This time I'm scared."

----------------------------------

Coronavirus Traps Wuhan Residents in a Real Life Horror Movie as Chinese city Locks Down
https://mobile.abc.net.au/news/2020-01-24/wuhan-coronavirus-traps-locals-in-a-real-life-horror-movie/11892202



... Speaking to the ABC, Ms Cong said her [vacation] timing could not have been worse — she was en route to Wuhan when health authorities announced a significant development: the virus was contagious and could spread from person-to-person.

... "I was on the train back to Wuhan when [the announcement] was live on TV. Before that, we knew it was serious — but we didn't know it was that serious" ...

Ms Cong said not everyone on the train was wearing masks; luckily, friends had warned her that many stores in Wuhan had already sold out, so she bought multiple packs before leaving Beijing.

Her parents also stocked up on food last week ahead of the Lunar New Year holiday — a smart move, given their local neighbourhood grocery store is now "closed for sterilisation".

... Other Wuhan residents have expressed extreme fear about the situation — writing on social media they feel trapped inside the outbreak's ground zero.

"I am worried because the transmission was human-to-human, which was already confirmed, and that's the scary part because Wuhan is a really populated place.

"We don't even have public transportation now. We are more scared than anyone."

"I found the transportation in Wuhan was completely blocked down, I am getting more and more scared," one local wrote on Weibo, China's version of Twitter.

... The sprawling metropolis of Wuhan is home to more than 11 million people: a population significantly larger than that of other more well-known cities like New York City and London.

... "Many Beijing companies have notified their staff [that] they will have to be quarantined for 14 days before going back to work.

-------------------------------

According to the Xinhua News Agency, the Chinese rail authority is expecting to send 440 million people on trips over the next six weeks, making it one of the biggest annual mass migrations on the planet.

... “Clearly there’s a risk of cases being dispersed more widely geographically within China, and we’re certainly seeing that”

... With there being no vaccine or cure, curtailing coronavirus is going to be a logistical nightmare for the authorities to deal with. “We've seen before with the previous coronavirus outbreaks like Sars in Hong Kong and Mers across the Middle East, and also things like Ebola that the logistics and efforts required to quell these things are really quite extensive and expensive, and involving lots and lots of public health interventions,” says Michael Head, senior research fellow in global health at the University of Southampton. “So, this Chinese New Year mass migration is very likely to spread it further.”

-------------------------------------------

https://www.imperial.ac.uk/mrc-global-infectious-disease-analysis/news--wuhan-coronavirus/

Open Access: Natsuko Imai, et.al.Report 2: Estimating the potential total number of novel Coronavirus cases in Wuhan City, China, WHO Collaborating Centre for Infectious Disease Modelling, MRC Centre for Global Infectious Disease Analysis, J-IDEA, Imperial College London, UK (2020)

Our estimates of the size of the outbreak in Wuhan have more than doubled since our first report.

... We estimate that a total of 4,000 cases of 2019-nCoV in Wuhan City (uncertainty range: 1,000 – 9,700) had onset of symptoms by 18th January 2020 (the last reported onset date of any case) [15].

Our estimates should not be interpreted as implying the outbreak has doubled in size in the period 12th January to 18th January – delays in confirming and reporting exported cases and incomplete information about dates of symptom onset together with the still very small numbers of exported cases mean we are unable to estimate the epidemic growth rate at the current time.

This estimate is based on the following assumptions:

• Wuhan International Airport has a catchment population of 19 million individuals [1].
• There is a mean 10-day delay between infection and detection, comprising a 5-6 day incubation period [16,17]  and a 4-5 day delay from symptom onset to detection/hospitalisation of a case (the cases detected in Thailand and Japan were hospitalised 3 and 7 days after onset, respectively) [4,18].
• Total volume of international travel from Wuhan over the last two months has been 3,301 passengers per day. This estimate is derived from the 3,418 foreign passengers per day in the top 20 country destinations based on 2018 IATA data [19], and uses 2016 IATA data held by Imperial College London to correct for the travel surge at Chinese New Year present in the latter data (which has not happened yet this year) and for travel to countries outside the top 20 destination list.
• Exit screening (which reportedly came into force on the 15th January [13]) had no impact on exported cases reported up to 16th January. Exit screening may have reduced exports in recent days, in which case our baseline prediction may be an underestimate of the true number of cases in Wuhan.
• We assume all cases in travellers flying to destinations outside mainland China are being detected at those destinations. This may well not be the case. If cases are being missed in other countries, our baseline prediction will underestimate the true number of cases in Wuhan.[/i]

There is suspicion among many in China that officials may be downplaying the number of cases recorded over recent weeks, recalling the government’s reluctance to disclose the full scale of the 2002-03 Sars outbreak, which killed almost 800 people

[vox_mundi]

If You've Been Waiting for Your 21st Century Version of the 1918 Spanish Flu Pandemic; Your Ship Has Come In! ...

-----------------------------------

https://www.who.int/news-room/detail/23-01-2020-statement-on-the-meeting-of-the-international-health-regulations-(2005)-emergency-committee-regarding-the-outbreak-of-novel-coronavirus-(2019-ncov)

... Chinese authorities presented new epidemiological information that revealed an increase in the number of cases, of suspected cases, of affected provinces, and the proportion of deaths in currently reported cases of 4% (17 of 557). They reported fourth-generation cases in Wuhan and second-generation cases outside Wuhan, as well as some clusters outside Hubei province.

... Human-to-human transmission is occurring and a preliminary R0 estimate of 1.4-2.5 was presented. Amplification has occurred in one health care facility. Of confirmed cases, 25% are reported to be severe. (... requires ICU)

4% of 7.75 Billion = 310 Million = entire population of U.S. - just sayin'

http://www.influenzavirusnet.com/1918-flu-pandemic/mortality.html

--------------------------------------

Man Diagnosed With Wuhan Coronavirus Near Seattle Being Treated Largely by Robot
https://www.cnn.com/2020/01/23/health/us-wuhan-coronavirus-doctor-interview/index.html

The first person diagnosed with the Wuhan coronavirus in the United States is being treated by a few medical workers and a robot.

The robot, equipped with a stethoscope, is helping doctors take the man's vitals and communicate with him through a large screen, said Dr. George Diaz, chief of the infectious disease division at the Providence Regional Medical Center in Everett, Washington.

The man arrived at Seattle-Tacoma International Airport on January 15, before any health screenings began at US airports, the US Centers for Disease Control and Prevention has said.

Washington state health officials confirmed Thursday that they have reached out to 43 people considered "close contacts" of the 30-year-old man, who identified the people he had interacted with since returning from Wuhan, China.

... It's unclear when the patient will be released because the CDC, which is set to provide the discharge details, has recommended additional testing. "They're looking for ongoing presence of the virus," Diaz told CNN on Thursday. "They're looking to see when the patient is no longer contagious."



Any air travel from Wuhan is being funneled through Chicago, Atlanta, Los Angeles, San Francisco and New York.

------------------------------------

Texas A&M Confirms Student Has Possible Case of Coronavirus
https://www.theeagle.com/news/local/update-texas-a-m-confirms-student-has-possible-case-of/article_eb23c5e2-3e14-11ea-b1d8-5b0421665a06.html
https://www.theeagle.com/news/local/texas-a-m-student-may-have-coronavirus-brazos-county-health/article_467bf8b4-3e2a-11ea-833c-f38385dcfca8.html

Texas A&M has confirmed a student at the university may have a possible case of novel coronavirus. (... positive screening test)

A sample from the student was obtained and sent to a CDC facility in Atlanta, which Wilke said has the proper equipment to confirm whether this is a case of the novel coronavirus. The sample is expected to reach the facility today, and the local health district should be made aware of the results by Saturday at the earliest, he said.

... Until that confirmation, officials cannot share what airline the student flew, cities the student traveled through or other details about possible points of exposure, Wilke said.

--------------------------------

A Second Third US Case of Deadly Coronavirus Has Been Confirmed, This Time in Illinois
https://www.usatoday.com/story/news/health/2020/01/24/coronavirus-wuhan-china-lockdown-quarantine-us-cases/4562257002/

The deadly coronavirus has afflicted another person in the United States, health officials confirmed Friday, bringing the total number of U.S. cases to two as Chinese health officials scramble to contain the outbreak that has killed 26 people.

A Chicago woman returned Jan. 13 from Wuhan, the epicenter of the outbreak, and began experiencing symptoms a few days after arriving home, said Dr. Allison Arwady, commissioner of the Chicago Department of Public Health.

... At least 63 potential cases are under investigation in 22 states, and 11 were confirmed negative, Messonnier said. The other potential cases are being tested, she said.

-----------------------------------------

On January 23, 2020, CDC again raised its travel alert for the coronavirus outbreak. The travel notice for Wuhan City was raised from Level 2: Practice Enhanced Precautions to Level 3: Avoid Nonessential Travel.

... CDC has developed a real time Reverse Transcription-Polymerase Chain Reaction (rRT-PCR) test that can diagnose 2019-nCoV. Currently, testing for this virus must take place at CDC

CDC advisors are concerned about the lack of data coming out of Wuhan and worry that Chinese health officials still have not released basic epidemiological data more than three weeks into the outbreak.

-------------------------------------------


https://en.wikipedia.org/wiki/Contagion_(2011_film)

------------------------------------------

... A young, previously healthy man died in Wuhan, raising concerns about the deadliness of the virus. Until now, the vast majority of victims have been older than 60 with preexisting conditions.

------------------------------------------

Republican Senator Calls on Trump to Declare Coronavirus a Public Health Emergency
https://www.washingtonpost.com/world/coronavirus-china-live-updates/2020/01/24/4e678f9c-3e03-11ea-afe2-090eb37b60b1_story.html

WASHINGTON — Senator Rick Scott (R-Fla.) called on President Trump on Friday to declare the coronavirus outbreak a public health emergency after senators received a briefing from top health officials and a second case of the virus was confirmed in the United States.

“We have to get serious about the threat of coronavirus coming from China. I don’t trust Communist China to coordinate in a transparent and efficient manner,” Scott said in a statement. “I’m calling on the administration to declare a national public health emergency to stop the coronavirus from spreading within the United States.”

[vox_mundi]

Map Tracks Coronavirus Outbreak in Near Real-Time
https://hub.jhu.edu/2020/01/23/coronavirus-outbreak-mapping-tool-649-em1-art1-dtd-health/


https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

The Johns Hopkins Center for Systems Science and Engineering has built and is regularly updating an online dashboard for tracking the worldwide spread of the coronavirus outbreak that began in the Chinese city of Wuhan.

The site displays statistics about deaths and confirmed cases of coronavirus, or 2019-nCoV, across a worldwide map. It also allows visitors to download the data for free.

"We built this dashboard because we think it is important for the public to have an understanding of the outbreak situation as it unfolds with transparent data sources," Gardner said. "For the research community, this data will become more valuable as we continue to collect it over time."

Making the data available for download is "critical" for researchers, she added.

... The website provides a link to a downloadable Google Sheet that contains information on confirmed and suspected cases in more than 30 Chinese locations as well as for the nations of Japan, Thailand, South Korea, Vietnam, Singapore, Colombia, Brazil, Australia, Mexico, and the United States. One case has been confirmed in Washington state.

https://gisanddata.maps.arcgis.com/apps/opsdashboard/index.html#/bda7594740fd40299423467b48e9ecf6

---------------------------------------

Up to 70 Percent Chance of Chinese Virus Reaching Europe: Analysis
https://medicalxpress.com/news/2020-01-percent-chance-chinese-virus-europe.html

There is up to a 70 percent chance of a patient carrying the deadly coronavirus that originated in China arriving in Europe, according to calculations released Friday by French researchers.

The National Institute of Health and Medical Research (Inserm) analysed flight paths between Europe and China, where hundreds of people have contracted the previously unseen virus.

Iserm concluded that there was a 33-70 percent risk of a patient arriving in Europe by air.

"Given air traffic patterns, the countries most exposed are Germany and Britain," it said in a statement.

[Tom_Mazanec]

Can anyone tell me if this is tinfoil hat fakenews, or if this is true (just because it is on Zero Hedge doesn't necessarily mean it's a hoax):

The Real Umbrella Corp: Wuhan Ultra Biohazard Lab Was Studying "The World's Most Dangerous Pathogens"
by Tyler Durden
Fri, 01/24/2020 - 03:10

https://www.zerohedge.com/economics/real-umbrella-corp-wuhan-ultra-biohazard-lab-was-studying-worlds-most-dangerous-pathogens

A quick read of what this lab was meant to do, prompts the immediate question whether the coronavirus epidemic isn't a weaponized virus that just happened to escape the lab:

If this is the real deal, and this outbreak gets as bad as the Spanish Flu, I could see this becoming a casus belli vis-a-vis China.

[blumenkraft]

This is a mixture of anti-china propaganda and fear-mongering IMHO.

[kassy]

It is a Coranavirus and we had trouble with those before like MERS and SARS but if you look at numbers our seasonal flue kills more people.

Don´t think it is from the lab just a result from China´s suboptimal way of keeping lifestock.

[Tom_Mazanec]

This is a mixture of anti-china propaganda and fear-mongering IMHO.

Probably.
But if this goes Spanish Flu I could see the meme, if you'll pardon the expression, "going viral".

[vox_mundi]

Using the logic implied by your article suggests that any disease encountered in the following cities should immediately be blamed on the BSL-4 labs; skipping over available science on the subject.

Atlanta , GA
Galveston, TX
San Antonio, TX
Hamilton, MT
Fredrick, MD
Manhattan, KS
Boston, MA
Richmond, VA

https://fas.org/programs/bio/research.html

The issue is moot. The virus is out and humans are hosts.

Nature has plenty of surprises waiting for us.

------------------------------

Researchers Trace Coronavirus Outbreak in China to Snakes
https://medicalxpress.com/news/2020-01-coronavirus-outbreak-china-snakes.html

The study notes that patients who became infected with the virus—which is a type of virus called a coronavirus and was named 2019-nCoV by the World Health Organization—were exposed to wildlife animals at a wholesale market, where seafood, poultry, snake, bats, and farm animals were sold.

By conducting a detailed genetic analysis of the virus and comparing it with available genetic information on different viruses from various geographic locations and host species, the investigators concluded that the 2019-nCoV appears to be a virus that formed from a combination of a coronavirus found in bats and another coronavirus of unknown origin. The resulting virus developed a mix or "recombination" of a viral protein that recognizes and binds to receptors on host cells. Such recognition is key to allowing viruses to enter host cells, which can lead to infection and disease.

Finally, the team uncovered evidence that the 2019-nCoV likely resided in snakes before being transmitted to humans. Recombination within the viral receptor-binding protein may have allowed for cross-species transmission from snake to humans.

Wei Ji et al, Homologous recombination within the spike glycoprotein of the newly identified coronavirus may boost cross‐species transmission from snake to human, Journal of Medical Virology (2020). https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.25682

Guangxiang (George) Luo et al. Global Health Concern Stirred by Emerging Viral Infections, Journal of Medical Virology (2020) https://onlinelibrary.wiley.com/doi/abs/10.1002/jmv.25683

---------------------------------

First Clinical Studies Find Wuhan Virus Closely Resembles SARS
https://medicalxpress.com/news/2020-01-clinical-wuhan-virus-resembles-sars.html

The new coronavirus rapidly spreading in China and nearby countries seems to trigger symptoms similar to those seen in the severe acute respiratory distress syndrome (SARS) coronavirus outbreak in 2003, two new studies show.

... Similar to the 2003 SARS outbreak in China, most patients who came down with the Wuhan coronavirus were healthy, without any chronic underlying health issues. And symptoms also resembled those of SARS, said Chinese researchers led by Bin Cao, from the China-Japan Friendship Hospital and Capital Medical University, both in Beijing.

All of the hospitalized patients had developed pneumonia, nearly all (98%) had a fever, three-quarters developed a cough, 44% felt fatigued, and 55% had some shortness of breath. Symptoms such as headache or diarrhea were rare, however.

Severe illness—enough to require admittance to the ICU—occurred in about a third of the hospitalized patients, Cao's team said, and six patients died.

A condition involving immune system dysfunction known as a "cytokine storm" occurred in some of these very ill patients, but it's not yet clear how the new virus affects the immune system, the researchers said.

... "Because asymptomatic infection appears possible, controlling the epidemic will also rely on isolating patients, tracing and quarantining contacts as early as possible, educating the public on both food and personal hygiene, and ensuring health care workers comply with infection control."

https://jamanetwork.com/journals/jama/fullarticle/2759815?guestAccessKey=da12c4d9-bed5-4c36-88cf-4db717115947&utm_source=For_The_Media&utm_medium=referral&utm_campaign=ftm_links&utm_content=tfl&utm_term=012320

---------------------------------

Marburg Virus Found in Sierra Leone Bats
https://medicalxpress.com/news/2020-01-marburg-virus-sierra-leone.html

Scientists have detected Marburg virus in fruit bats in Sierra Leone, marking the first time the deadly virus has been found in West Africa. Eleven Egyptian rousette fruit bats tested positive for active Marburg virus infection. Research teams caught the bats separately in three health districts.

The presence of Marburg virus, a close relative to Ebola virus that also causes hemorrhagic disease in people, was detected in advance of any reported cases of human illness in Sierra Leone. However, the virus's presence in bats means people who live nearby could be at risk for becoming infected. No outbreaks have been reported to date.

----------------------------------

https://www.nature.com/news/inside-the-chinese-lab-poised-to-study-world-s-most-dangerous-pathogens-1.21487
https://wwwnc.cdc.gov/eid/article/25/5/18-0220_article

The facility, known as the Wuhan National Biosafety Laboratory, is housed within the Wuhan branch of the Chinese Academy of Sciences and was specifically designed to help Chinese scientists "prepare for and respond to future infectious disease outbreaks," according to a 2019 report published by the U.S. Centers for Disease Control and Prevention (CDC).

The Chinese government moved to construct such a lab following the 2003 SARS (severe acute respiratory syndrome) epidemic, during which more than 8,000 people caught the infection and more than 750 died worldwide, according to the CDC. Laboratories that handle pathogens receive a rating of 1 to 4, depending on what class of microbe they can feasibly contain, with 1 representing the lowest risk and 4 representing the highest risk. Designated at Biosafety Level 4 (BSL-4), the Wuhan lab can hold the world's most dangerous pathogens at maximum biocontainment levels.

Although China intends to build five to seven high-containment laboratories by 2025, as of now, only the Wuhan lab can currently contain pathogens of this nature, according to the 2019 CDC report.

Chinese health officials have classified the new coronavirus as a Class B infectious disease, placing the illness in the same category as SARS and HIV/AIDS, The Washington Post reported. However, the Chinese government announced that it will institute Class A controls — which are usually reserved for more dangerous diseases, like cholera and the plague — in an attempt to contain the outbreak.

Open Access: Han Xia, Yi Huang, et.al. Biosafety Level 4 Laboratory User Training Program, China, Volume 25, Number 5—May 2019 CDC Online Report

[Tom_Mazanec]

Using the logic implied by your article suggests that any disease encountered in the following cities should immediately be blamed on the BSL-4 labs; skipping over available science on the subject.

Atlanta , GA
Galveston, TX
San Antonio, TX
Hamilton, MT
Fredrick, MD
Manhattan, KS
Boston, MA
Richmond, VA

If the disease originates in one of those cities, I could see panic beginning about the BSL-4 labs. People are Earthlings, not Vulcans. When scared we do not react rationally.
If the coronavirus originated at any of scores, if not hundreds, of locations it could have in China besides Wuhan there would be no question. But with the New Cold War with China it is different, because it did originate in Wuhan.

[vox_mundi]

Big Pharma's Bottom Line is Leaving the World Vulnerable to Pandemics
https://www.axios.com/big-pharma-research-pandemics-vaccines-antibiotics-3671a700-9dee-43a7-9494-ed98523d379d.html

Drug companies don't have much financial incentive to invest research and development dollars into new vaccines and antibiotics, leaving the world vulnerable to future pandemics.

Between the lines: The best-case scenario for these kinds of drugs is that they're lightly or never used. That doesn't sound very good to companies when their R&D dollars could alternatively go to diseases like cancer (... or erectile dysfunction), which are much more likely to turn a sizable profit.

... The possibility for blockbuster sales motivates large drugmakers; little else moves the needle. The revenue potential for many infectious disease drugs is likely to remain limited, so other serious incentives are required (... I say we infect the CEO, management, Board of Directors and their families - put a little skin in the game)

20 drug companies spent more than $2 billion on R&D over the last year, but only four of them have major vaccine units, per Bloomberg Opinion. Some drug companies have also stepped away from antibiotic development.

First vaccines a year away – drugs companies

The first version of a vaccine has already entered laboratories at the global pharmaceutical firm Johnson & Johnson but it will be close to year before vaccines are available publicly from drugs companies.

That’s according to Paul Stoffels, chief scientific officer at Johnson & Johnson, and Richard Hatchett, ceo of the Coalition for Epidemic Preparedness Innovations (CEPI), which is funding two of projects and co-funding the third to develop vaccines.

Speaking in Davos, Hatchett told the BBC’s Today programme that CEPI hoped the vaccines it had announced partnerships for could enter clinical trials in the summer.

It would be close to a year before they were available, however, he added, and this was a very ambitious timeline. He also said that restrictions on air travel into countries such as the UK would not keep the virus out and for now the only means of responding were via public health interventions.

Companies were also looking at progressing the manufacture and release of protective equipment for hospital workers and others, said Stoffels, who added: “We know that this could become a very big global epidemic.”

---------------------------------

https://thebulletin.org/2020/01/outbreaks-of-lethal-diseases-like-ebola-and-the-wuhan-coronavirus-happen-regularly-the-us-government-just-cut-funding-for-the-hospitals-that-deal-with-them/

When a Liberian man named Thomas Duncan first showed up at a Dallas hospital in September 2014 with a fever and abdominal pain, he was sent home with some antibiotics. Days later, Duncan was dead from Ebola.

... After Duncan died, US health officials put in place a strategy to prepare hospitals to deal with patients who had diseases like Ebola, caused by so-called special pathogens. This tiered response system consists of frontline and assessment hospitals that determine whether or not patients have a serious infectious disease and higher-level hospitals that can treat patients with these dire infections. The tiered approach has significant flaws, but it’s a whole lot better than the haphazard structure that was previously in place. Unfortunately, federal funding for the program is set to expire this year, and save for a small number of specialized treatment facilities and an Ebola education center, Congress did not include funding for the program in the 2020 budget.

...  “Funding is running out in 2020, and this creates a real risk of decreasing our national preparedness,” Jennifer Andonian, a project manager for Massachusetts General Hospital’s Center for Disaster Medicine, says. ­­“Even after hospitals have developed good … plans and facilities, there are ongoing costs to keep staff trained and to use their equipment in practice.”

----------------------------------

A crucial question for how the outbreak will unfold is how contagious the virus is. Scientists around the world are trying to establish how many people, on average, each infected person will pass the virus on to, a number known as R0 in epidemiology. If this number is more than one, an epidemic will grow and if less than one it will fizzle out.

An analysis posted online on Friday by scientists from Lancaster University puts R0 for the new coronavirus at 3.8 and estimates that should the epidemic continue unabated, there could be 191,529 infections by 4 February.

The paper also suggests that travel restrictions from and to Wuhan city are unlikely to be effective in halting transmission across China. The analysis assumes that only 5% of infections in Wuhan have been identified, which would imply a far larger pool of people whose symptoms have been mild and who have not attended hospital.

Novel coronavirus 2019-nCoV: early estimation of epidemiological parameters and epidemic predictions
https://www.medrxiv.org/content/10.1101/2020.01.23.20018549v1.

-----------------------

Scientists Predict Wuhan's Outbreak Will Get Much Worse
https://www.wired.com/story/scientists-predict-wuhans-outbreak-will-get-much-worse/



https://www.medrxiv.org/content/10.1101/2020.01.23.20018549v1.full.pdf+html

Summary estimates:
- early basic reproduction number (R0), i.e. the average number of persons that a new case will infect in a fully susceptible population, is 3.6-4.0. This is higher than the @WHO
estimate of 1.4-2.5, but within the range reported for #SARS in 2002/3 (R0 2-5)



- Assuming no control interventions or change in transmission, further outbreaks in Chinese cities outside of Wuhan and increasing rates of exported cases to other countries are likely. >250,000 infected cases predicted in 2 weeks’ time.

---------------------------------

France Confirms First Two Cases of Wuhan Coronavirus
https://amp.france24.com/en/20200124-france-confirms-first-two-cases-of-wuhan-coronavirus-china-bordeaux-paris

Two cases of the coronavirus have been "confirmed" in France, the first in Europe, French Health Minister Agnès Buzyn said on Friday.

"We have today the first European cases probably because we developed the test very quickly and we are capable of identifying them."

[vox_mundi]

Chinese health authorities reported at least 15 new deaths in one day, raising the death toll to 41 — all in China. A second case was confirmed in the United States and three cases were confirmed in France, as health officials were preparing for an outbreak that could last months.

The new figures, announced early Saturday, represented a nearly 60 percent jump from the previous death toll of 26, yesterday.

There were also 180 new cases of the virus diagnosed in Hubei between 4 a.m. and midnight on Friday, the authorities said, bringing the total number of confirmed cases worldwide to more than 1,280.

All but two of China’s 31 provinces and municipalities had reported cases by Friday.

https://mobile.twitter.com/xinyanyu/status/1220344021329072129



In response to the spread of the virus, airports worldwide have stepped up screening of passengers arriving from China, conducting temperature checks that would indicate fever and looking for other symptoms, including cough and difficulty breathing.

In other developments, the State Council, China's cabinet, has taken direct control of response measures. Also on Friday, the Ministry of Science and Technology appointed Zhong Nanshan, a key figure in the country's response to SARS, to head a group of scientists to develop a "joint prevention and control working mechanism" to control the virus.





--------------------------

China Coronavirus: Wuhan Medical Staff Being Infected at Much Faster Pace than Reported by Officials
https://www.scmp.com/news/china/society/article/3047441/wuhan-medical-staff-being-infected-virus-much-faster-pace

Fifteen cases of the coronavirus have been officially reported among medical staff in the city, but doctors say the true number is far higher.

One says that ‘even now we don’t have enough protective gear’ but hospital workers have ‘no option’ but to carry on.

A Wuhan doctor said at least one dormitory building at a hospital in the city was being used to house quarantined medical workers. ... “Definitely more than 15 medical workers are infected”

Another doctor, who helped treat Sars patients in Wuhan 17 years ago, said many of his former colleagues and classmates in medical school had fallen ill.

“You can find infected medical practitioners in almost all major hospitals in Wuhan. The number is certainly far higher than 15,” said the doctor, who also declined to be named. The doctor is still in Wuhan but no longer practises medicine.



https://www.scmp.com/news/china/society/article/3047613/china-coronavirus-wuhan-residents-describe-doomsday-scenes

--------------------------

The virus, which began in the central city of Wuhan, has now spread to much of east and south-east Asia, including South Korea, Japan, Hong Kong, Thailand and Vietnam.

In the UK, 2,000 travellers who have arrived recently from Wuhan are being sought. Fourteen people tested negative for the virus.

U.K. Health Secretary, Matt Hancock, chaired an emergency meeting of the Cobra committee to ensure appropriate measures were in place should the virus reach the UK.

Leaving Whitehall after the meeting, chief medical officer Prof Chris Whitty cautioned that it was “highly likely” that cases would be seen in the UK. But he stressed that contingency plans were ready for that eventuality.

--------------------------

U.S. State Department China Travel Advisory Update: Level 4 – Do Not Travel to Hubei Province
https://china.usembassy-china.org.cn/health-alert-012420/

... There is an ongoing outbreak of pneumonia first identified in Wuhan, China, caused by a novel (new) coronavirus.  In an effort to contain the novel coronavirus, the Chinese authorities have suspended air and rail travel in the area around Wuhan.  On January 23, 2020, the Department of State ordered the departure of all non-emergency U.S. personnel and their family members. The U.S. government has limited ability to provide emergency services to U.S. citizens in Hubei province.

Chinese authorities have imposed strict travel restrictions in the area around Wuhan.  Travelers should be aware that the Chinese government could prevent them from entering or exiting parts of Hubei province.  Travelers should be prepared for travel restrictions to be put into effect with little or no advance notice.

-----------------------------

... The State Department notice was a Level 4 advisory, the sternest warning the United States government issues regarding travel. Other Level 4 warnings issued by the State Department cover travel to Syria, North Korea, Afghanistan, Iraq, Venezuela and Yemen, among other places. The warning is a step up from Washington’s earlier cautions. Just a day before, the American government had been advising travelers to “exercise extreme caution” when traveling to the Wuhan area.

-----------------------------

...The Economist Intelligence Unit projects that the coronavirus could reduce China’s growth by 0.5 percent to 1 percent, compared with its projected growth rate of 5.9 percent before the outbreak, if the disease worsens on the level of SARS, the outbreak that killed hundreds in 2003.

[Tom_Mazanec]

You know, one difference between 1918 and 2020 is that we have a much higher tower of cards for global civilization. In 1918 most people could live for a week or two when the Flu disrupted the machinery of society. In 2020, with just-in-time deliveries to stores and most people living in cities instead of farms, that is no longer true. Half a billion people got sick in 2018 (and as many as 100 million died) and if that proportion is laid up for a week or two a lot of people aren't going to eat for a week or two.

[bluice]

We also have superior level of hygiene, medical care and overall health of populations. In 1918 they didn’t even have antibiotics to treat the sequelas following the flu. Not to mention knowledge and understanding of such things.

Biggest stress will obviously be on people working in healthcare. If large enough proportion of medical staff gets ill some patients won’t receive the treatment they need. The situation will become more difficult in less developed countries. Richer ones will once again be better off.

[TerryM]

I linked to an updating news blog about the coronavirus on the China, China, China thread,


This subject probably needs a dedicated thread - especially if it proceeds as expected.
Terry

[Tom_Mazanec]

I linked to an updating news blog about the coronavirus on the China, China, China thread,


This subject probably needs a dedicated thread - especially if it proceeds as expected.
Terry

Thanks for the blog, TerryM.
I started a dedicated thread here:
https://forum.arctic-sea-ice.net/index.php/topic,2996.0.html

[TerryM]

^^
Great Tom!!
Terry

[vox_mundi]

Artificial Intelligence Yields New Antibiotic
https://phys.org/news/2020-02-artificial-intelligence-yields-antibiotic.html

Using a machine-learning algorithm, MIT researchers have identified a powerful new antibiotic compound. In laboratory tests, the drug killed many of the world's most problematic disease-causing bacteria, including some strains that are resistant to all known antibiotics. It also cleared infections in two different mouse models.

... This molecule, which the researchers decided to call halicin, after the fictional artificial intelligence system from "2001: A Space Odyssey," has been previously investigated as possible diabetes drug. The researchers tested it against dozens of bacterial strains isolated from patients and grown in lab dishes, and found that it was able to kill many that are resistant to treatment, including Clostridium difficile, Acinetobacter baumannii, and Mycobacterium tuberculosis. The drug worked against every species that they tested, with the exception of Pseudomonas aeruginosa, a difficult-to-treat lung pathogen.

To test halicin's effectiveness in living animals, the researchers used it to treat mice infected with A. baumannii, a bacterium that has infected many U.S. soldiers stationed in Iraq and Afghanistan. The strain of A. baumannii that they used is resistant to all known antibiotics, but application of a halicin-containing ointment completely cleared the infections within 24 hours.

... After identifying halicin, the researchers also used their model to screen more than 100 million molecules selected from the ZINC15 database, an online collection of about 1.5 billion chemical compounds. This screen, which took only three days, identified 23 candidates that were structurally dissimilar from existing antibiotics and predicted to be nontoxic to human cells.

In laboratory tests against five species of bacteria, the researchers found that eight of the molecules showed antibacterial activity, and two were particularly powerful. The researchers now plan to test these molecules further, and also to screen more of the ZINC15 database.

[Tom_Mazanec]

There are other pathogens besides SARS-CoV-2

An Emerging Ebola-Like Virus in Bolivia Can Spread Between Humans, Scientists Find
https://gizmodo.com/an-emerging-ebola-like-virus-in-bolivia-can-spread-betw-1845697716

Scientists are urging caution over a mysterious, Ebola-like viral disease that appears to have spread from person to person during a small outbreak in Bolivia last year. The disease, caused by the Chapare virus, killed three people and is thought to have sickened at least five during the outbreak, including three healthcare workers who came into contact with patients. Its symptoms include internal bleeding, fever, and widespread organ damage.

[kassy]

The mystery virus was discovered to be a member of the arenavirus family, a group of viruses that commonly infect rodents and sometimes humans. Its relatives include the more well-known Lassa virus and other viruses first found in South America, such as Machupo virus in Bolivia and Junin virus in Argentina. Many of these viruses can cause hemorrhagic fever in people.

So ebola-like is a shorthand for hemorrhagic fever.

[Tom_Mazanec]

As if covid is not bad enough, is this what is next?

Over 700 people infected with mysterious disease in Senegal
https://www.afrinik.com/over-700-people-infected-with-mysterious-disease-senegal/

The mysterious dermatological disease detected a few days ago among fishermen in Thiaroye-sur-Mer, Senegal, is taking on worrying proportions, with more than 700 people infected as of today.

[Tom_Mazanec]

Yet another new outbreak:

Unidentified illness hospitalizes more than 300 people in India
https://www.cnn.com/2020/12/07/asia/india-mystery-illness-intl-hnk-scli/index.html

An unidentified illness has hospitalized more than 300 people in southeastern India, including one who has died, according to local officials investigating the cases.
Patients in the city of Eluru, in the state of Andhra Pradesh, reported a range of symptoms including seizures, loss of consciousness and some nausea over the weekend, said Dolla Joshi Roy, the district surveillance officer of Eluru's West Godavari District.

[morganism]

a little historical plague epidemi for your reading pleasure. A historical analysis of the fear of a global disease in Justinian. (late antiquity) There is supposed to be a great book on this, see  bottom

The Justinianic Plague and Global Pandemics: The Making of the Plague Concept

https://academic.oup.com/ahr/article/125/5/1632/6040961

"This article explores how plague—as an idea—became an ahistorical independent agent of historical change. It focuses on the case of the Justinianic Plague (ca. 541–750 c.e.), the first major recorded plague pandemic in Mediterranean history, which has increasingly been used to explain significant demographic, political, social, economic, and cultural change during late antiquity (ca. 300–800 c.e.). We argue that the Justinianic Plague retains its great historiographic power—namely, its supposed destructive impact over two centuries—because it evokes a terrifying myth of what plague should do rather than because of conclusive evidence of what it did."


These trees are reconstructed “stemma” type graphs (see Figure 3) that establish the evolutionary connections between Y. pestis genomes based on genetic composition, allowing scholars to establish the genetic and temporal relationship between different bacteria strains.147 Once this data is coupled with geographic data (i.e., where each specimen on the tree was found) and temporal data (i.e., the dating of each specimen based on archaeological or radiocarbon data), it is possible to follow Monica H. Green’s lead and ask new questions that “real epidemiologists do: ‘Why is this specific disease presenting here? Why in these populations? Where did it come from in the first place, and by what pathways did it (will it) spread?’” More research is required for the first two questions—since scientific evidence cannot alone answer them with certainty even for present-day plague—so most historians have focused on the latter two, which focus on one aspect: establishing plague transmission routes.

The phylogenetic evidence offers the beginning of an answer to these two questions. A recent paper revealed that the plague specimen from late antique Britain was basal (i.e., earlier in evolutionary terms) to other known late antique specimens from Europe. These specific finds suggest that plague made its way into Britain early in the first pandemic.149

Viewed from a broader perspective, however, the paleogenetics turn is reminiscent of earlier truisms that promised to “solve” plague questions without rethinking the plague concept. The ability of paleogenetics to answer these questions is also constrained by practical, financial, and even legal and ethical challenges. For example, geneticists have prioritized searching for late antique plague in mass graves, where medieval plague victims were often buried. Yet to date scholars have found plague in less than fifty individuals in such burials from late antiquity across Western Eurasia."


Justinian's flea : plague, empire, and the birth of Europe
Author:
Rosen, William, 1955-2016

" Abstract:
Weaving together evolutionary microbiology, economics, military strategy, ecology, and ancient and modern medicine, author Rosen tells of history's first pandemic--a plague seven centuries before the Black Death that killed tens of millions, devastated the empires of Persia and Rome, left victims from Ireland to Iraq, and opened the way for the armies of Islam. Emperor Justinian had reunified Rome's fractured empire by defeating the Goths and Vandals who had separated Italy, Spain, and North Africa from imperial rule. In his capital at Constantinople he built the world's most beautiful building, married its most powerful empress, and wrote its most enduring legal code, seemingly restoring Rome's fortunes. Then, in the summer of 542, he encountered a flea. The ensuing outbreak of bubonic plague killed five thousand people a day in Constantinople and nearly killed Justinian himself, bringing about one of the great hinge moments in history"

for current outbreaks, look to the forums on FluTrackers