Day 17: The Germ Boats Take Flight

The New York Post reports 99 new cases aboard Germ Boat #2, the Diamond Princess, for a total of 454. The jump seems to be due to testing of asymptomatic passengers for the sake of evacuation; some American cases were confirmed during the evac flight(s). (The food tweeter remained aboard and tweets on.)

The AP reports more details about Germ Boat #4, the MS Westerdam:

News over the weekend that an 83-year-old American woman who was on the ship and flew from Cambodia to Malaysia was found to be carrying the virus froze further movement of the passengers and crew of the MS Westerdam. Some are now in hotels in Cambodia’s capital, Phnom Penh, while others are still aboard the ship.

The American woman was among several hundred passengers who were flown out of Cambodia on Friday and Saturday. According to authorities in Malaysia, 143 continued their flights home from that country, while the woman and her 84-year-old husband, who was diagnosed with pneumonia, remained behind for treatment.

P.S. People's Daily (China) reports the death of Liu Zhiming, director of Wuhan Wuchang Hospital and the first hospital director to die of COVID-19.

Day 16: The Germ Boats Strike Again

CNN reports that the US is planning to evacuate passengers from Germ Boat #2, the Diamond Princess. The current case count is 356, perhaps because at least one "quarantine worker” was infected, not to mention that

[...] some 1,000 crew on board the ship had not been kept in quarantine, eating meals together with masks off and working side by side.

Also, the Washington Post reports that an 83-year-old American off the MS Westerdam who flew to Malaysia after disembarking and being cleared in Cambodia has now been diagnosed, calling into question the entire now-dispersed passenger complement of Germ Boat #4.

P.S. The confirmed case count has now exceeded 71,000.

Day 14: Nosocomial Infections Day

Via Xinhua: China has reported a COVID-19 case count of 1716 among health care workers, including six deaths so far.

Kyodo News reports a farmer has tested positive for COVID-19 in Wakayama Prefecture (Japan). He had visited the hospital where the surgeon who was confirmed infected yesterday practiced; however, he had symptoms before he visited the hospital. The surgeon himself still has no known Chinese contacts, and another doctor and patient there have also come down with pneumonia and are being screened.

Nikkei reports a general pattern of Japanese cases that have not been traced back to China yet, including Japan's first death, an 80-year-old Kanagawa Prefecture woman, her son-in-law who is also infected, a confirmed case in Chiba Prefecture, and the Tokyo taxi driver who, despite rumors to the contrary, did not recall transporting any foreign passengers.

On the lighter side, CNN reports on a crafty Russian woman who escaped quarantine in St. Petersburg by short-circuiting the lock on her hospital room. She had tested negative several times and her 14-day quarantine period was up, so it's unclear why she felt the need to break out, or why the government feels the need to prosecute her.

P.S. The Straits Times reports that an anaesthesiologist is Singapore's first healthcare worker to be diagnosed with COVID-19:

The day before he had a fever, the general anaesthesiologist was working in an operating theatre and was feeling perfectly well.

Day 13: Germ Boat #5

The AIDA Cruises ship AIDAvita, under an Italian flag but owned by a German company and apparently full of Germans, started out of Bali on January 17th, but has been denied docking at its next Vietnamese port. (This is the fifth cruise ship to appear in the epidemic news.)

Stories about the AIDAvita tend to also report that Germ Boat #4, the MS Westerdam, expected to dock in Thailand when last PlagueBlog reported on it, actually docked in Preah Sihanouk, Cambodia today.

Reuters reports that Singapore is still looking for their "patient zero" who brought COVID-19 to a conference there, eventually infecting Malaysia and Europe.

Reuters also reports a confirmed case in a Tokyo taxi driver in his 70's, as well as a doctor in central Japan. On the bright side, Japan intends to start letting elderly and interior passengers of Germ Boat #2, the Diamond Princess, come ashore beginning tomorrow to complete their quarantine on dry land.

A second evacuee case has been confirmed in San Diego, bringing the US total to 14.

P.S. A third evacuee case has been confirmed at Lackland AFB in Texas, bringing the US total to 15.

Day 12: One Bad Bug, Two Bad Names

PlagueBlog apologizes for misreporting the naming of SARS-CoV-2 as COVID-19. In fact, the virus is now officially named SARS-CoV-2, and the disease it causes is now officially named COVID-19. PlagueBlog prefers the Internet's names (#RatBatVirus and Wuhan Disease), but you can't win them all.

In a surprise move, and despite rumors that China would no longer be reporting asymptomatic confirmed cases, Hubei has reported almost 15,000 new cases, pushing the world total over 60,000.

CNN explains the details of the strange focus on dry traps as a COVID-19 vector in Hong Kong, although the reason some Hong Kong residents hack their own toilet pipes remains unexplained.

P.S. On the bright side, there are now over 6,000 recovered.

P.P.S. In Japan, where it's tomorrow (Thursday) already, Forbes reports that the Germ Boat case count has jumped again to 218. Yet the food tweeter tweets on.

Day 11: The First and Fourth Germ Boats

For those playing the home game, the first germ boat was the World Dream, on a five-day cruise starting January 19th from Guangzhou to Vietnam to Hong Kong. Eventually eight cases were identified from this cruise, and as a consequence a later batch of tourists have been quarantined off Hong Kong out of concern that the crew may have been infected. Those 3,600 passengers were just released on Sunday, despite not having completed fourteen days of quarantine (because the crew were cleared).

The second germ boat is the Diamond Princess, quarantined for an ever-restarting 14 days off Yokohama, where the food tweeter tweets on.

The third germ boat was the Anthem of the Seas out of Bayonne, NJ, which had no actual cases.

The fourth germ boat is the Holland America ship the MS Westerdam, originally meant to dock in Yokohama on Valentine's Day (this coming Friday).

According to passengers on board, they’ve been denied at “every port” since leaving Hong Kong in early February.

Fox reports that, fortunately for them, Thailand has agreed to let them dock in Laem Chabang on Thursday.

PlagueBlog prefers the term "germ boat", though, in deference to common parlance, germ boat posts have been tagged "plague ships".

In other coronavirus news, a lucky thirteenth case has been confirmed in the US: an evacuee in San Diego who, despite testing positive, was initially released by the CDC into the wild quarantine quarters, but has since been returned to hospital.

P.S. The WHO has finally named the virus "COVID-19". While we understand that "Please stop eating the bats already, folks" was not an option, PlagueBlog maintains that "Wuhan coronavirus" could hardly do Wuhan's reputation or China's face any additional damage at this point. You'd have to go with something like "Wenliang coronavirus" to manage that.

P.P.S. COVID-19 celebrated its new name with a record 45,000 cases, as well as an additional 39 cases on the Germ Boat (for a total of 174 cases, but the food tweeter tweets on).

Day 10: Not Our Brighton

The Argus reports that a medical center in Brighton, England has closed due to a GP being confirmed to have coronavirus. He was apparently part of the ski cluster and caught it in France, despite being from the same part of England as the postulated super-spreader from Hove. The claim is that the GP only went in to work at the medical center for one day, during which he did paperwork and saw no patients.

The pangolin theory has reached Nature.

Caixin Global reported Saturday that the nucleic acid test (NAT) for coronavirus has a high false negative rate. (NAT is the cheaper, more convenient test.)

In a Wednesday interview with state broadcaster CCTV, Wang Chen, an expert in critical diseases and director of the Chinese Academy of Medical Sciences, said one characteristic of the virus was that "not all of those infected by it return positive NATs."

"Even patients who definitely have the disease only come back positive 30%-50% of the time," Wang said.

[...]

A doctor in the imaging department of another major Wuhan hospital, who spoke on condition of anonymity, told Caixin said that previously some patients whose CT scans clearly showed signs of viral infection but whose NATs tested negative were "released" back into their communities due to a shortage of hospital berths.

Genetic testing is more accurate but more expensive and not available everywhere. This has led to some changes in the official diagnostic criteria:

In response to calls from medical professionals on the frontlines of the epidemic, the NHC on Tuesday relaxed the clinical criteria for reporting suspected coronavirus cases, with extra leeway granted to people in Hubei. Outside the stricken province, medical professionals should now suspect coronavirus infection in patients with radiographic evidence of pneumonia, fever, and/or breathing problems, and a low-to-normal white blood cell count or a low lymphocyte count. Within Hubei, only 2 of the 3 criteria are required.

P.S. Later in the day, cases exceeded 43,000, deaths exceeded 1,000, and confirmed cases aboard the Germ Boat rose to 135, among them 10 crew (though the food tweeter tweets on).

Day 9: The Real Numbers

Via ProMED-mail: In the Swiss Medical Weekly, researchers estimate the real case and fatality numbers based on various possible rates of misreporting, underreporting, and overreporting (of both cases and deaths). While a good overview of the possible sources of error, the math itself seems less useful.

The five British cases in the French ski chalet were infected by a sixth Brit who brought the disease back from Singapore, another case of country-to-country-to-country transmission of Wuhan coronavirus.

The Washington Post reports that "lawyer and citizen journalist" Chen Qiushi who had been reporting on the epidemic from Wuhan has been missing since Thursday. The Chinese government claims to have him in quarantine, where PlagueBlog hopes he will receive better care than Li Wenliang.

Citizens of Hong Kong are encouraged to keep their drain traps wet and put down the toilet seat before flushing, as well as to practice more obvious hygienic precautions. PlagueBlog hopes they will take the advice to avoid wet markets to heart.

The South China Morning Post also reports that a 7-year-old Hong Kong boy has been diagnosed with an "imported" case of H9 (subtype unspecified) bird flu (emphasis added):

According to the centre's preliminary investigations, the patient had visited his grandparents' home in Shenzhen at the incubation stage of his viral infection. Although the family kept poultry in their house, the boy had not come into direct contact with the birds. His family members have not reported any symptoms.

P.S. Cases exceeded 40,000 by the end of the day, and cases aboard the quarantined cruise ship reached 70 (though the food tweeter tweets on). Cases in Singapore reached 40 and the French chalet ex-Singapore cluster also continues to grow.

Day 8: Death Toll Exceeds SARS

The death toll from novel coronavirus exceeded that of SARS (774) earlier today and as of this typing stands at 813. Also, a Chinese-American man died in Wuhan earlier this week but the news only broke today. The case count is at 37,525.

Aboard the Germ Boat, three new cases have been reported in the Japanese press but haven't been added to the official Others numbers yet. Li Wenliang's death yesterday continues to spark controversy.

The rumored unusual susceptibility of East Asian males to Wuhan coronavirus (which seems to be what the cool kids are calling it) and SARS actually does have a scientific explanation, the ACE2 virus receptor.

Day 7: The Germ Boat Enters International Waters

I reported the sharp jump in Japanese cases yesterday, but today Japan dropped back down to 25 patients, while the 61 unfortunate cruise ship passengers off Yokohama became their own category, Others, in the coronavirus app.

If you prefer your news in video form, the US Department of Health held a press conference today.

P.S. USA Today reports that a third suspected germ ship, Royal Caribbean's Anthem of the Seas out of Bayonne, NJ, has been cleared of any infection.

P.P.S. RIP Li Wenliang.

Day 6: 30,000 and Rising

As of this typing, the confirmed case count is 31,472, with 638 deaths and 1,551 recovered. Japan's count has shot up to 86.

Day 5: In the Gray Zone

According to the WHO (via CNN), the ongoing coronavirus epidemic is not a pandemic:

"We are not in a pandemic," Dr. Sylvie Briand, director of the World Health Organization's Infectious Hazards Management Department said in a press conference on Tuesday, explaining that the virus is currently considered to be an epidemic with multiple locations.

"We will try to extinguish the transmission in each of these," she said, adding that the agency believes this "can be done with containment measures currently in place."

Not everyone agrees, however:

Dr. Anthony Fauci, director of the National Institute of Allergy and Infectious Disease in the United States, believes we could be heading toward a pandemic.

"My bottom line is the way this is continuing to evolve every day, it looks like it's heading towards what we would call a pandemic," Fauci said.

But Fauci also said the term itself comes down to semantics -- it "means different things to different people," and that we're in a "gray zone."

One important bit of daily evolution is how the disease made its way through Singapore into Malaysia (via MalayMail) last month:

A Malaysian man has tested positive for the Wuhan virus, the first local to date, said Health Minister Datuk Seri Dzulkefly Ahmad at a press conference today.

Dzulkefly said the man travelled to Singapore from January 16 to 23 to attend a meeting which had several foreign delegates, including from China.

“He returned to Malaysia on January 23, and on January 29, he received treatment at a private hospital because of fever and cough.

P.S. The United Press reports a twelfth US case in Wisconsin (ex China).

P.P.S. Reuters reports that ten more passengers aboard the Diamond Princess, the cruise ship currently quarantined off Yokohama, have tested positive for novel coronavirus.

Day 4: The Germ Boats

Remember when norovirus was the biggest risk of taking a cruise? Well, now it's novel coronavirus. The South China Morning Post reports that 4000 passengers on a five-day cruise from Guangzhou to Vietnam to Hong Kong may have been exposed. Three cases are already known (though only one is officially confirmed) and two more are suspected.

“There was a clear risk of cross-contagion on board the cruise ship,” said the doctor, who declined to be named as they are not authorised to speak to the media. But the doctor said she decided to disclose the information out of concern that thousands of passengers from the same cruise were at large, even though it has not been confirmed that there was an outbreak on board.

P.S. The suspected NYC case is still not confirmed. You can keep an eye out for it at the live Johns Hopkins CSSE site (or the mobile version).

P.P.S. Another cruise ship story broke later in the day: Princess Cruises quarantines 3,700 on the Diamond Princess out of Yokohama, Japan after ten passengers tested positive.

The company confirmed to CNBC that one of the passengers who tested positive for the coronavirus is from the United States. The others are two passengers from Australia, three from Japan and three from Hong Kong and one Filipino crew member.

The company said it will continue to provide guests with complimentary internet and phone service. The ship will go out to sea to “perform normal marine operations,” the company said, such as “the production of fresh water and ballast operations before proceeding alongside in Yokohama where food, provisions, and other supplies will be brought onboard.”

Boston Day 2 (NYC Day 1)

According to MSN (via ProMED), our Boston patient has recovered and is voluntarily quarantined at home. Oh, and there's a suspected case in NYC.

Yesterday r/askscience on Reddit had an AMA (ask me anything) "about the novel coronavirus". (I'm hoping the WHO comes out with a handier name than 2019-nCoV soon.) In that haystack I found links to nice infographics at the New York Times.

The bats come home to roost

One of many rumors about novel coronavirus involves bats as snacks. Various vaguely described birds and "wild animals" from the epicentric "seafood" market have tested positive, though others have cleared the market of guilt on account of earlier patients who hadn't been there.

But my bigger concern right now is the nascent epidemic's sudden appearance just down the road:

A man in his 20s has the first case of coronavirus in Massachusetts, the Boston Public Health Commission announced Saturday. The man attends UMass Boston and lives in the city. He returned from Wuhan, China on Jan. 28 through Logan Airport.

He is being isolated at his home, which is not a dorm, and health officials say he is doing well.

DFTD2: The Sequel

Tasmanian devil disease recently got curiouser when a graduate student identified a second cell line:

In March 2014, Murchison’s colleague Ruth Pye, a graduate student at the University of Tasmania, noticed something weird about a facial tumor taken from a devil captured just north of Hobart. Physically, it looked like DFTD; genetically, it was clearly something different. For example, DFTD cells have lost their X and Y sex chromosomes, both of which were present in the new tumor. Pye reasoned that this particular devil had spontaneously developed its own type of facial tumor that looked like DFTD, but wasn’t. It was a one-off.
Except, a few months later, she found the same genetically distinct tumor in a second devil from the same area. In both cases, the tumors bore absolutely no genetic resemblance to either DFTD or their respective hosts. These devils had developed a second type of contagious cancer.

They've found a total of eight infected devils and published their results this January.

The Bubonic Plague of Justinian

In The Guardian and elsewhere: a new journal article in the Lancet identifies the sixth-century Plague of Justinian as Yersinia pestis.

Professor Edward Holmes, from the University of Sydney, was one of the authors of the study, and said it was the oldest pathogen ever sequenced.
"This is the first complete genome from one of the most significant disease events in human history," he said.
The results showed the strains from the plague victims were distinct from those involved in the Black Death, the later pandemic which killed an estimated 60% of the European population.
The Justinianic strains appear to be an evolutionary “dead end” when compared with modern strains, and most likely originated from Asia and then spread to Europe along trade routes such as the Silk Road.

Plague and Hemochromatosis

I tweeted this a few days back, but today everyone decided to tell me about it. So here's the latest story about the scientist with undiagnosed hemochromatosis who died of the attenuated plague virus he was working with, a year and a half ago now.

Casadaban was conducting laboratory research on the bacterium that causes the plague when he became sick. The germ was genetically weakened and considered harmless to humans. It was considered so safe, Casadaban’s work with the live plague bacteria wasn’t noted when he fell ill, according to the CDC. A professor at the university for 30 years, by all accounts he had followed the proper safety protocols, the report said.
[...] An autopsy found the researcher had a medical condition called hemochromatosis, which causes an excessive buildup of iron in the body, according to the CDC report. The disorder affects about 1 in 400 people and goes unnoticed in about half of patients.
Casadaban’s illness is important because of the way the plague bacterium had been weakened. Yersinia pestis needs iron to survive. Normally it gets this iron by stealing it from a host’s body with proteins that bind to it and help break it down. To make the bacterium harmless, scientists genetically stripped it of the proteins needed to consume iron.

It seems hemochromatosis may not be the protection against Yersinia pestis its been made out to be.

Mmm-mmm Melamine, Part MII

In the wake of the latest incident of melamine-contaminated milk in China, the Epoch Times reports that wealthy Chinese are now growing their own vegetables to ensure food safety.

In recent years, Chinese people have fought hard but ineffectively against poor food safety standards. There are simply too many tainted foods, from raw food products to cooking oil and food utensils. Waste oil, toxic chopsticks, and toxic lunch boxes can still be cleaned up, but there are three sources of poisoning which are most difficult to handle.

The three areas are: pesticides, food "additives" like melamine, and pollution.

The End of Rinderpest

Via twitter: The Food and Agricultural Organization of the UN reports the likely eradication of rinderpest, a disease of cattle.

"The disease has affected Europe, Asia and Africa for centuries and has caused widespread famine and decimated millions of animals, both domestic and wild. In the 1880s, rinderpest caused losses of up to one million head of cattle in Russia and central Europe," said Diouf.
When it entered Africa in the nineteenth century, it decimated millions of heads of livestock and wildlife and triggered widespread famine. It is estimated that in that pandemic alone, up to one-third of the human population of Ethiopia died of starvation as a result. The last known outbreak of rinderpest occurred in 2001 in Kenya.
A joint FAO/OIE announcement of global rinderpest eradication is expected in mid-2011, pending a review of final official disease status reports from a handful of countries to the World Organisation for Animal Health (OIE).

Wikipedia is already referring to rinderpest in the past tense. PlagueBlog, however, cannot help wondering whether there's still some stashed in a freezer somewhere...