Day 35: 100,000 Strong

Today the worldwide case count hit 100,000, with over 55,000 recovered and almost 3,400 dead. PlagueBlog will be at an inadvisable public gathering on the NH/MA border this weekend and will be unable to provide our usual level of gory detail. Just one note: Biogen maintains that its three infected employees are all out of state, even though they seem to have infected one another here in Massachusetts, meaning that the ex Italy case in their county is not an employee. PlagueBlog reserves judgement for the moment.

One other point of information: you may have heard about two strains, L and S, one nastier than the other, of SARS-Cov-2. The paper the media picked this up from is pretty baseless and has already been debunked in the literature, so ignore.

P.S. Channel 4 reports 3 Massachusetts cases from Biogen’s what-were-you-thinking conference last week, and 2 more out-of-state cases.

Day 34: Ex Boston

Channel 5 reports that we may have exported coronavirus to Tennessee in the person of a Williamson County (TN) man who flew from Nashville to Logan and back. Channel 10 reports he came to Boston for an international meeting "at Biogen" in Cambridge [reddit speculates this meeting was actually at the Boston Marriott Copley Square in the heart of Boston] last week, from which attendees took home both flu and COVID-19 (three positives so far). Our third Massachusetts case, also in Middlesex County (location of both Cambridge and yours truly) has been reported by the state as ex Italy but by NBC as ex Biogen, is awaiting confirmation by the CDC. PlagueBlog would like to thank you now for reading, because posting may come to an abrupt and possibly permanent halt at any time now.

Boston.com reports that the wayward New Hampshire medical worker "is now complying" with quarantine after exposing a bunch of Dartmouth Tuck Business School students at a mixer. One Tuck student "estimated that about a hundred business school students attended, along with 30 or 40 resident physicians associated with Dartmouth-Hitchcock, an academic medical center located near Dartmouth College."

In other local news, Governor Cuomo tweets that there are 5 new confirmed cases in New Rochelle, a couple in their 40's with three children who were friends of the previous family. There are also two untraced cases in New York City. New Jersey has two presumptive cases.

Texas has three new cases, two of them in Harris County (i.e., Houston). California is lousy with cases, but a notable one is one of the medical screeners from LAX. The CDC state-by-state map is updating daily again, possibly due to agitation from reddit. In less official but more accurate news-based counting, the US is up to 221 cases and 12 deaths.

An eight-month-old baby is a new Australian case, ex Iran. South Africa's first case is ex Italy.

On the bright side, the Diamond Princess has been downgraded to 696 cases and 6 deaths, due to some double-counting of cases.

P.S. Germ Boat #6 is another Princess Cruises ship, the Grand Princess. The story is similar to that of previous Germ Boats: passengers on a prior cruise later tested positive (including one death; these are some of the California mainland cases), so the current passengers have been condemned to a slow death by quarantine off the coast near San Francisco. Test kits are being flown in by helicopter.

Day 33: Biden Our Time

Iran has leapt ahead of Italy, with 2,922 cases (including 23 members of parliament) and 92 deaths. The Ayatollah was seen wearing gloves. Germany and France have each exceeded 200 cases and Spain is not far behind. Case counts are rising across Europe, with notable jumps in the UK, Switzerland, Norway, and the Netherlands. Portugal now has five cases (the fifth ex Italy, and the third and fourth connected to the initial two). Poland, famed for its resistance to the Black Death, has reported its first case.

Here in the New World, Canada is up to 33 cases, with several new cases ex Iran, while Mexico is holding at 5 and Brazil at 2. (The low case count in South America is the only thing between us and the WHO declaring this a pandemic.) The US has reached 132 cases, with 9 deaths (all in Washington State). CNN is tracking cases state-by-state. Most of today's new cases are in California and associated with travel, though at least one is untraced.

Governor Cuomo announced that many suspected New York State cases, including those in Buffalo and Oneida, tested negative. On the downside, the 50-year-old Westchester County case managed to super-spread the virus to his wife, a son (20), a daughter (14), and a neighbor. The children's schools (including Yeshiva University) will be closed today. He also announced that SUNY/CUNY students studying abroad in certain countries will be flown home and quarantined.

Day 32: Don't Lick the Shrine

The official case count is now over 92,000 cases. While Italy has exceeded 2,000 cases and South Korea 5,000, Iran (2,336) continues to be the most infectious, with almost as many new cases per day (835 today) as South Korea and the only significant death rate (11 today) outside of China (33 today). Notable figures in society continue to fall ill; the head of emergency services is now a confirmed case, and Mohammad Mirmohammadi, member of the Expediency Council and advisor to Khamenei, reportedly died of COVID-19 yesterday. The situation in Iran may have something to do with the government's failure to keep people from licking shrines—or, more likely, the very fact that they needed to tell people not to lick shrines in the first place. PlagueBlog also recommends you don't lick the shrine.

Back on the home front, Boston.com reports some more details about the first Rhode Island case, a school administrator. The second official case is one of the students from that trip to Italy. The article mentions that another chaperone is a suspected case; this suspected case may be Massachusetts' second case, a 27-year-old Cohasset woman who was on the same school trip. Whether a Massachusetts school was involved is still unclear.

Two cases have been confirmed in New York state. The first, a 39-year-old NYC health care worker, was ex Iran, but the second one is suspected local, untraced transmission to a Westchester County man in his 50's over whom not one but two local schools have already closed. Governor Kemp of Georgia reported two confirmed cases there ex Italy.

An unspecified foreigner in his 30's is the 706th case confirmed (yesterday) aboard the Diamond Princess. It's apparently a crew member, not the food blogger, who has escaped confinement (though not Japan) and is still food blogging while waiting to be readmitted to the US.

In non-humanitarian news, a stowaway cat at the port of Chennai is facing deportation over coronavirus fears. PETA India is concerned about its fate if returned to China and has offered to adopt it out.

Cancellations: The Louvre apparently remained closed today, though whether solely through worker action or now officially is unclear. The Japanese government is planning to cancel the annual Fukushima Memorial. The Chicago Tribune reports a major local trade show cancellation as well as other cancellations and postponements across the country. Twitter, Facebook, and Intel have pulled out of the SXSW conference in Austin.

P.S. The AP reports three new deaths in Washington State. Two seem to be posthumous confirmation of deaths from last week, and the third may be yet another nursing home resident from the Life Care Center of Kirkland, WA.

P.P.S. There's a second case in New Hampshire, a close contact of the first patient, though apparently not a result of the first patient breaking quarantine on Friday to attend a social event.

Day 31: The Accusations Fly

The official case count is over 89,000 cases, with over 3,000 dead and over 45,000 recovered. PlagueBlog cannot vouch for the Chinese number, which exceeds 80,000 cases with 2,912 deaths. South Korea now has 4,335 cases with 26 deaths. Iran has surged to 1,501 cases with 66 deaths. Italy is still slightly ahead at 1,696 cases and 34 deaths. Germany has hit 150 cases, France 130, and Spain 120.

Portugal has finally reported cases, both males in Porto, though only one is ex Spain. The 60-year-old doctor vacationed in Italy, while the 33-year-old construction worker worked in Spain and had some connection to Valência. Scotland has also reported its first case, ex Italy.

The US now has 88 cases, but no new deaths since yesterday. CNBC and MSN report on doctors' and suspected patients' lack of access to COVID-19 tests, despite CDC claims to the contrary. The New York Times also links CDC testing restrictions to weeks of covert spread of the virus in the Pacific Northwest. In other news, the CDC once again accidentally released an infected quarantined evacuee in San Antonio, but the patient was quickly recaptured.

The Bangkok Post reports that Thailand's first death, a 35-year-old sales clerk who dealt with Chinese tourists and passed away on Saturday, did not actually have an underlying condition; his dengue fever was a misdiagnosis and his only known disease was COVID-19. He had been in hospital since January 27th, stopped testing positive for coronavirus on February 16th, and succumbed to multiple-organ failure on February 29th.

And lastly, a cool toy: Genomic epidemiology of novel coronavirus (HCoV-19)

P.S. Steve Wozniak theorizes on Twitter that he was the American Patient Zero.

P.P.S. The Washington State cluster has now brought the US death count to 6.

P.P.P.S. New Hampshire has confirmed a case, in a hospital employee, ex Italy. Rumor has it he's been working since he returned from Italy. The nationwide case count is up to 100 as of 9pm EST.

Day 30: Looking Fully Incubated Now

NBC News reports that yesterday's death in Washington State turned out to be not just a domestic case, but also another unsourced infection in a non-traveller. In more disturbing news (from the same source), the CDC is responding to "the first possible outbreak" in a long-term care facility, the Life Care Center of Kirkland, WA.

In local news, the first Rhode Island "presumptive" case has been confirmed, a man in his 40's who'd travelled to Italy in February. Forty of his contacts are being monitored and/or quarantined at home by the RI Department of Health, but the patient himself is in an undisclosed hospital "nearby".

The US stands at 73 cases with one death. Canada has 20 cases. Mexico has 4, the fourth is ex Italy. Italy has jumped to 1,694 cases, though only 34 deaths. Unfortunate neighbors Germany and France are at or above 100 cases. Spain is at 76, the UK at 35, and Sweden, Austria, Switzerland, and the Netherlands have at least 10 cases each.

Iran reported 11 new deaths today, bringing their total to 978 cases with 54 deaths. Kuwait and Bahrain are now in the 40's, although Bahrain has only a quarter the population of Singapore.

South Korea has 3,736 with 21 deaths. Japan has 241 cases with 5 deaths. Hong Kong and Singapore have at least 100 cases each. Thailand, currently at 42 cases, has reported their first death.

P.S. PlagueBlog neglected to mention a canine case identified on Thursday: a pet Pomeranian in Hong Kong tested positive for the disease after her owner, Yvonne Chow Hau Yee, fell ill. The dog initially showed no symptoms; PlagueBlog has been unable to find any updates on its disease status, but Hong Kong is now quarantining pets.

P.P.S. New York has reported a case, and Washington State a second death.

P.P.P.S. Another Washington State case is a postal worker. PlagueBlog will refrain from "going postal" puns.

Day 29: Notable Deaths

The first US death is rumored, in Washington State. PlagueBlog has also not confirmed the rumored death of an Iranian MP.

Day 28: Poetic Justice

Poetic justice continues mowing down Iranian officials; reported cases now include (Ms.) Massoumeh Ebtekar, women's affairs, and Mojtaba Zolnour, national security and foreign affairs. Both are self-quarantined. For the country as a whole, the case count stands at 388 with 34 deaths.

Italy stands at 655 cases with 17 deaths, and has infected most of Europe at this point. More disturbingly, an Italian citizen in Nigeria has fallen ill, for that country's first case. The case was caught early on the patient's return to Nigeria, so the other 205 million Nigerians may be safe for the moment. Switzerland has banned large public events.

Germ Boat #2's case count does not include passengers falling ill after evac so remains steady at 705, but does include passenger deaths in Japanese hospitals, which have risen to 6. In other Japanese news, the governor of Hokkaido (a prefecture including the northernmost large island of Japan as well as some smaller islands) has declared a state of emergency over the local case count (54).

South Korea is now at 2,337 cases with 13 deaths. China continues to claim recovery with only 327 new cases.

Day 27: The Bats Come Home Again

Topping the coronavirus news is our 60th case, a patient at UC Davis medical center in Sacramento, with no known links to travelers. The San Francisco Chronicle reports the patient was apparently transferred there from somewhere in Solano County, California while already intubated. The CDC initially refused to test the patient due to their lack of contacts, and still hopes to find the missing link to China. Several health care workers are under voluntary quarantine.

CoronaChan never sleeps, and there are plenty of other developments to report. Reuters reports Japan will closed all primary and secondary schools for the month of March. With 505 cases yesterday, South Korea has taken over China in daily reported cases (though what is actually going on with China's numbers is unclear) and has hit 1766 cases as of this blogging. The virus is also spreading among the South Korean military, though the case count among the US forces permanently encamped there remains at 2.

The case count for Germ Ship #2, the Diamond Princess, has risen to 705 with 4 deaths.

Italy's count has gone up to 528 cases with 14 deaths. The rumored 50 Iranian deaths have still not shown up in their case counts, which currently stand at 275 cases with 26 deaths. Ilna news reports the sad passing of a 23-year-old women's soccer player from Qom.

Day 26: Coronival

Brazil has confirmed the first Latin American coronavirus case, ex Italy (which now has over 450 cases). South Korea is at 1,261 cases. US cases have gone up by about 15 (rather unspecified) travelers and their contacts; President Trump is attempting to throw fistfuls of money at the problem.

Iran's project to infect the entire Middle East proceeds apace, and their deputy health minister has tested positive.

Day 25: Just Saying No to Bats

The Daily Mail reports that China is turning its wildlife-eating ban permanent. PlagueBlog can only hope that it sticks. China also seems to have stopped reporting case numbers, making the worldwide stats rather inaccurate.

Day 24: Iran Makes China Look Good

Iran continues to make China look open and responsible; most Middle Eastern cases have already been traced back to Iran, and the AP reports on some fudgy numbers:

A staggering 50 people have died in the Iranian city of Qom from the new coronavirus this month, a lawmaker was quoted as saying on Monday, even as the Health Ministry insisted only 12 deaths have been recorded nationwide.

The new death toll reported by the Qom representative, Ahmad Amirabadi Farahani, is significantly higher than the 47 total cases of infections state TV had reported just hours earlier. Iran’s health ministry now says total infections have risen to 61, but a spokesman said deaths remained at 12.

Still, questions of transparency are being raised as the number of deaths compared to the number of confirmed infections from the virus is higher in Iran than in any other country, including China and South Korea, where the outbreak is far more widespread.

Rumor has it that the Qom representative then left the parliament feeling ill and the staff sterilized his chair.

It's tough to top that one, but the WHO is trying; Reuters reports they no longer use the classification "pandemic". In other words, no pandemic for you!

In less laughable news, Italy reports 38 new cases, for a total of 223 cases with 7 deaths. (Some reports have 229 with 6 deaths.) South Korea is at 833 cases with 8 deaths.

In Germ Boat #2 news, a third passenger of the Diamond Princess died yesterday (an 80-year-old Japanese man), and the case count has risen to 691, apparently due at least in part to ongoing testing of the largely Filipino crew, though some ex-plague-ship cases that have been popping up post-evac may also have been counted.

The JHU CSSE app seems to be struggling under the load of cases today, so I've added another source of COVID-19 numbers the sidebar, BNO News.

P.S. A 900-point plunge in Dow futures has been attributed to coronavirus fears.

P.P.S. The worldwide case count has exceeded 80,000.

Day 23: Italy Takes the Lead

The AP reports that "coronavirus infections in Italy are now the largest outbreak outside Asia" (which isn't saying much) with 132 cases. More notably, Carnevale has been cancelled in Venice and schools shut down in Lombardy. As mentioned yesterday, these case remain untraced:

Authorities expressed frustration they haven’t been able to track down the source of the virus spread in the north, which surfaced last week when an Italian man in Codogno in his late 30s became critically ill.

“The health officials haven’t been yet able to pinpoint patient zero,” Angelo Borrelli, head of the national Civil Protection agency, told reporters in Rome.

At first, it was widely presumed that the man was infected by an Italian friend he dined with and who recently returned from his job, based in Shanghai. When the friend tested negative for the virus, attention turned to several Chinese people who live in town and who frequent the same cafe visited by the stricken man. But Lombardy Gov. Attilio Fontana told reporters all of those Chinese residents have tested negative, too.

Back in Asia, South Korea has firmed up its lead with 602 cases, while two young Chinese doctors have died in the past 24 hours. Reports continue to circulate about relapses; the South China Morning Post reports new quarantine restrictions for recovered patients:

The authorities in Wuhan on Saturday introduced 14 days’ mandatory quarantine for recovered coronavirus patients, after some discharged patients again tested positive.

From Saturday, all patients who had recovered and been discharged had to be sent to designated places for two weeks of quarantine and medical observation, the city’s coronavirus treatment and control command centre said on Weibo, China’s equivalent of Twitter.

P.S. Bloomberg reports on the potential significance of the fecal-oral route.

P.P.S. Iran has increased to 43 cases and 8 deaths. Several neighboring states have closed the border, and the government is already making noise about reducing New Year travel. (Nowruz, the Zoroastrian New Year, falls on the vernal equinox.)

Day 22: Untraceable Clusters

There are now 556 cases in South Korea and 79 in Italy. The AP reports on untraceable clusters in Singapore and Iran as well.

Business Insider has a nice writeup about asymptomatic spread in China.

Day 21: Oh, Shi'ite

While the official count remains at 5, Reuters reports two more deaths and 13 more cases in Iran, for a total of 18 cases and four deaths. Coronavirus has spread from the Shi'ite "Vatican" of Qom to Tehran and several other cities. Reuters also reports an exported case from Iran is Lebanon's first case. Another exported case has appeared in British Columbia (Canada).

P.S. I forgot to mention the spike of 100 new cases in South Korea, which is now at 204 confirmed. Also, Israel has confirmed a case off the Diamond Princess. (It was otherwise a quiet day for Germ Boat #2.)

Day 20: China Still Closed

Reuters reports that the closure of schools and non-essential businesses in Hubei has been extended from the original deadline of tomorrow to March 11th. Also, South Korea shoots up by 53 new cases to a total of 104, and has delayed school opening in Daegu. Iran has added 3 more confirmed cases.

In general the confirmed case counts seem to be falling, but this seems to be more an artifact of changed reporting standards in China than any real peak to the pandemic.

In a mixed day for Germ Boat #2, the Diamond Princess count went up only 13 cases to 634, but two of the infected passengers have now died.

P.S. China has hit 75,000 cases.

Day 19: Bigger and Germier

The numbers hit over 75,000 cases, 2,000 deaths, and 15,000 recovered today. A new country has reported cases, Iran with 2 confirmed cases in Qom and apparently more suspected. South Korea reports 20 more cases in one day, most related to a super-spreader at a church, for a total of 51. Japan's count for the day is at 10 and still climbing. I've seen some reports that today's count includes an Okinawa taxi driver who drove passengers from Germ Boat #2 (the Diamond Princess) at their previous port of call (Naha), but this particular case seems to have been confirmed last week. It remains unclear whether the passengers infected the driver or vice versa.

Germ Boat #2 has 79 more cases, bringing the total to 621. The Irish Examiner reports that, in addition to his SARS-CoV-2 infection and Type II diabetes, Germ Boat celebrity David Abel also suffers from early-onset dementia (which, along with an initial diagnosis by a Japanese-speaking doctor, explains some confusion in the reporting of his case). But the food tweeter tweets on about the ongoing evacuations.

BBC News reports (in Chinese) on a postulated Patient Zero in his seventies who lived near the suspect wet market, but was already ill and did not actually visit the market before becoming sick(er) around December 1st.

P.S. Reuters reports that the two Iranian patients have already died.

Day 18: The Germ Boat Dives Deeper

The Diamond Princess (Germ Boat #2) has jumped another 88 cases, to 542 cases. The food tweeter seems to be tweeting on, but another celebrity passenger, David Abel, and his wife have tested positive. The Daily Mail reports that the airlift has been cut short and a hundred Germ Boat Americans still in Japan will need to remain their for their quarantine period (an additional 14 days).

P.S. The COVID-19 death toll has now exceeded 2,000.

Interlude: What Killed the Wampanoag

This is an accidental interlude in the coronavirus news inspired by Taki Magazine columnist David Cole, who has paused his extremely spicy politico-disease commentary (e.g., Crazy Rich Asians Will Kill Us All) to reflect on the far older epidemiological mystery of what killed the natives of New England four centuries ago now. Cole cites a Slate article making seasonal hay of the story circa Thanksgiving 2012:

The Pilgrim leader William Bradford was already aware of the death toll from “Indean fever.” His scouts had ventured inland and noted “sculs and bones were found in many places lying still above ground, where their houses and dwellings had been; a very sad spectackle to behould.” It’s estimated as many as nine out of 10 coastal Indians were killed in the epidemic between 1616 and 1619.

What killed so many people so quickly? The symptoms were a yellowing of the skin, pain and cramping, and profuse bleeding, especially from the nose. A recent analysis concludes the culprit was a disease called leptospirosis, caused by leptospira bacteria. Spread by rat urine.

That "recent analysis" had been published in the CDC's monthly journal in February of 2010; it postulates "incremental, episodic, and continuous" exposure to leptospirosis introduced by Old World Rattus rattus as the most likely source of the deadly epidemic. PlagueBlog regrets having overlooked the theory at the time, but 2010 was a busy year of crazy Asians killing one another with melamine, and the mainstream press also seems to have missed it.

In defense of the natives contra Cole, PlagueBlog notes that though they eschewed hard-soled shoes, they did bathe far more than the invaders; this otherwise laudable practice was just as likely to give them a cryptic disease invisibly imported into their "sweet brook" as was their semi-shoelessness. It was a lose-lose situation, and not an appropriate metaphor for dangerous modern-day African or Asian superstitions.

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...

New Prion Disease Discovered

Via ProMED-mail: last month ScienceDaily reported the publication of a journal article on a new spontaneous prion disease:

In 2008, Pierluigi Gambetti, MD, and Wen-Quan Zou, MD, PhD, with collaborators, reported the discovery of this novel disease, which affected patients who exhibit only one of the three types of the prion protein gene. In this follow-up study, they discovered that all three genetic groups can be affected also by this novel disease which now joins sCJD in displaying this feature. However, VPSPr is associated with an abnormal prion protein that exhibits characteristics very different from those of sCJD, as well as other prion diseases, suggesting that it may be caused by a different mechanism, perhaps more akin to other neurodegenerative diseases, such as Alzheimer's disease. This finding may exemplify, for the first time, the possibility that the prion protein affects the brain with different mechanisms.

Some claim there's a smoking cow behind this new variant.

Childhood Schizophrenia

Via twitter: the LA Times reports on a tragic case of childhood schizophrenia.

Doctors and other mental health experts don't fully understand the disease, which has no cure. Jani's extreme early onset has left them almost helpless. The rate of onset in children 13 and under is about one in 30,000 to 50,000. In a national study of 110 children, only one was diagnosed as young as age 6.
"Child-onset schizophrenia is 20 to 30 times more severe than adult-onset schizophrenia," says Dr. Nitin Gogtay, a neurologist at the National Institute of Mental Health who helps direct the children's study, the largest such study in the world on the illness.
"Ninety-five percent of the time they are awake these kids are actively hallucinating," Gogtay says. "I don't think I've seen anything more devastating in all of medicine."
For Jani's parents, the most pressing issue is where Jani should live. She has been on the UCLA psych ward -- where she was placed during an emergency -- since Jan. 16. The ward is not designed for long-term care.

Abortive Rabies

Via ProMED-mail: the CDC reports on a rabies case from last year in which the victim was intermittently symptomatic ("severe frontal headache, photophobia, emesis, neck pain, dizziness, and paresthesia of face and forearms") for two and a half weeks before rabies vaccine and immune globulin were administered. She soon appeared to recover without intensive care.

This is the first reported case in which certain clinical and serologic findings indicate abortive human rabies and in which, despite an extensive medical investigation, no alternate etiology for the illness was determined. The patient's positive serologic results offer evidence of rabies virus infection; IFA and Western blot assays indicated the presence of antibodies capable of binding to rabies virus antigens before the patient received rabies PEP. Rabies virus can crossreact serologically with other members of the Lyssavirus genus, distributed in Australia, Eurasia, and Africa (5) or, theoretically, with as yet uncharacterized rhabdoviruses. However, this patient had no history of foreign travel and no evidence of infection with KCV, the only other rhabdovirus associated with bats in North America.
[...]
Certain other clinical and laboratory findings also support a diagnosis of abortive rabies in the patient described in this report. First, the onset of acute encephalopathy approximately 2 months after exposure to bats is compatible with documented incubation periods after rabies virus exposure. Second, central nervous system (CNS) findings (e.g., fever, photophobia, emesis, neck pain, dizziness, paresthesia, limitation of visual field, and altered behavior with agitation and combativeness) are compatible with clinical aspects of rabies. Although this patient did not have classic symptoms such as laryngeal spasms (manifested as hydrophobia) or autonomic instability, the lack of such symptoms has been documented in other rabies patients (1,2,6). Finally, despite an extensive medical workup, no alternate infectious etiology was identified for the patient's neurologic symptoms, increased intracranial pressure, and CSF pleocytosis.

I should note that, after her apparent recovery, the patient returned to the hospital two more times complaining of headaches, and afterwards went missing. ("The current clinical status of the patient or [sic] her boyfriend is unknown.") Judging from the reporting state, the patient was probably in the country illegally. PlagueBlog would not jump to the conclusion that she is still here, or still alive.

Mumps in NYC Update

Via ProMED-mail: the CDC reports that the mumps outbreak in New York/New Jersey has reached 1,521 reported cases, with no apparent end in sight. They also speculate about possible demographic causes of the outbreak in a relatively well-vaccinated community:

Like the mumps outbreaks that occurred in 2006 (2), much of the current outbreak is occurring in congregate settings, where prolonged, close contact among persons might be facilitating transmission. Within the affected religious community, cases have occurred predominantly among school-aged boys, who attend separate schools from girls. The higher rate among boys might be a result of the additional hours that boys in this community spend in school compared with girls, including long periods in large study halls, often face-to-face with a study partner.
In addition, transmission in the community overall might be facilitated by relatively large household sizes. According to the 2000 U.S. Census, the mean household size in one of the affected communities was 5.7, compared with a mean U.S. household size of 2.6. The limited transmission to persons outside the community might be a result of the relatively less interpersonal contact between persons inside and outside the community.
Although the school settings and large household sizes might be promoting transmission, the high vaccination coverage in the affected community likely is limiting the size of the outbreak. In addition, high vaccination coverage in surrounding communities is the most plausible reason that the few cases outside of the affected community have not caused other outbreaks.

PlagueBlog recommends letting the boys out for recess more frequently and sending them home earlier, poor things.

Mumps in NYC

Via ProMED-mail: the mumps outbreak in New York City continues, with over 900 cases identified so far. See the link for MMR clinics serving the apparently under-vaccinated population. The NYC Department of Health notes that:

Each site will have separate entrances for women and men and will have separate staff members to vaccinate them. The staff will be culturally sensitive and respectful.

At the risk of sounding culturally insensitive, PlagueBlog must state that there are worse things than getting an MMR shot from a member of the opposite sex who's just doing their job--for example, orchitis.

Mmm-mmm Melamine, Part MI

Via ProMED-mail: melamine has once again been detected in milk products in China. AsiaNews reports that the scandal has widened to six dairy companies, one of which was still in operation as of Friday.

China has also banned independent reporting of the scandal and jailed a food-safety activist:

Zhao Lianhai is a 37 year old former government employee from Beijing, who was recently arrested and charged with provoking social disorder.
His son was one of 300,000 kids poisoned by contaminated milk across China.
Mr Zhao used to work for the country's food quality and safety authority, so he started a website advising parents of affected children and campaigned to take responsible companies to court.

In other melamine news, on Friday a federal court sentenced the Chinese-American couple for importing the melamine-tainted wheat gluten from the 2007 pet-food scandal.

Mmm-mmm Cadmium, Part I

Via ProMED-mail: the Associated Press found cadmium in children's jewelry imported to the US from China. The LA Times reports:

For China's low-cost jewelry makers, it was an open trade secret: The metal cadmium is shiny, strong and malleable at low temperatures, regardless of its health hazards. And it's cheap.
Despite the risks, manufacturers in factories ringing this city on China's east coast say their top priority is profit. So offering cut-rate goods often means using lower quality materials, including cadmium, which is known to cause cancer.
"Business is business, and it's all up to our client," said He Huihua, manager of the Suiyuan Jewelry Shop at International Trade City in Yiwu[...]
Asked what he thought about the health risks associated with cadmium and other toxic metals, He said: "I can't be overly concerned about that."

PlagueBlog recommends a trade embargo.

Mmm-mmm Melamine, Part M

Via ProMED-mail: another melamine scandal has broken in China, once again belatedly, and once again involving tainted milk. The Wall Street Journal reports that the two-month investigation of Shanghai Panda Dairy Company began almost a year ago.

Shanghai Panda, one of the nation's smaller dairies, was among 22 companies originally implicated in the 2008 scandal and was briefly shut by quality inspectors.
Now, among the allegations against the company are that instead of destroying its melamine-tainted product that had been recalled in 2008, Shanghai Panda reconstituted the milk into new products.

Lovely.

Prion Evolution

Ed Yong discusses prion evolution in his blog at ScienceBlogs:

Jiali Li from the Scripps Institute in Florida has found that prions - the infectious proteins behind mad cow disease, CJD and kuru - are capable of Darwinian evolution, all without a single strand of DNA or its sister molecule RNA.
Prions are rogue version of a protein called PrP. Like all proteins, they are made up of chains of amino acids that fold into a complex three-dimensional structure. Prions are versions of PrP that have folded incorrectly and this misfolded form, called PrPSc, is social, evangelical and murderous. It converts normal prion proteins into a likeness of its abnormal self, and it rapidly gathers together in large clumps that damage and kill surrounding tissues.
Li has found that variation can creep into populations of initially identical prions. Their amino acid sequence stays the same but their already abnormal structures become increasingly twisted. These "mutant" forms have varying degrees of success in different environments. Some do well in brain tissue; others thrive in other types of cell. In each case, natural selection culls the least successful ones. The survivors pass on their structure to the "next generation", by altering the folds of normal prion proteins.

Marburg Reaches the US

Via ProMED-mail: the CDC reports on an imported case of Marburg hemorrhagic fever in Colorado last year. A bat-cave tourist came home from Uganda in January 2008 and exhibited the less dramatic symptoms of Marburg. Tests for Marburg came back negative, but she was retested six months later at her own request and Marburg was confirmed, both then and in the original sample. (It seems the CDC has a big freezer.)

On January 22, 2009, CDC notified the World Health Organization and Uganda Ministry of Health of the imported MHF case. The Python Cave had already been closed to visitors in July 2008, during the response to the Dutch MHF case. CDPHE and CDC conducted a public health investigation during January--February 2009. Interviews were conducted with the patient and her spouse, the patient's medical records were reviewed, and a retrospective contact investigation was conducted to identify possible secondary transmission. A contact was defined as a person who had physical contact with the patient, her body fluids, or contaminated materials or was in the same room as the patient during her acute illness (January 4--19, 2008). Contacts included health-care workers (including health-care providers, housekeeping staff, and hospital laboratory staff), commercial laboratory staff, and social contacts.

No explanation for the six month delay in reporting to the WHO was provided, nor for the further year it took this information to appear on the CDC site. One imagines that it may be due to the fact that the victim, though now recovered, was quite ill with Marburg, including eleven days of hospitalization in "a community hospital," and no notable precautions were taken. The story has medical thriller written all over it. Or perhaps the bird flu/H1N1 story was considered to be enough for the public to panic about at the time.

PlagueBlog recommends against bat-cave tourism of any sort, locally or in Africa.

Tis the Season

It's time again for ProMED-mail's Internet-a-thon. You can make donations at their website.

Non-Plushy Giant Virus

Via twitter: the AFP reports that French scientists have discovered a (non-plushy) giant virus.

With a genome of 368,000 basic pairs, Marseillevirus is the fifth biggest virus ever sequenced and has a diametre of 250 nanometres (around 250 millionth of a millimetre, according the a report by Raoult's for the French National Centre for Scientific Research (CNRS).
The DNA of the giant virus contains material from different sources including plant and animal matter, bacteria and other giant viruses such as the Mimivirus, the report said.
"There is a mechanism of permanent creation going on in amoeba producing a new repertoire of viruses and predisposing giant viruses to become pathogens once they specialise", Raoult said.

Some interesting statements about Darwin follow, which one hopes are merely mistranslated.

Microevolutionary Defenses against Kuru

Via Twitter: Razib at ScienceBlogs reports on cannibals, kuru, and microevolution.

127V is extremely efficacious against fatality due to kuru. Looking through the pedigrees in a region of very high kuru exposure the researchers found that of the individuals who carried 127V, only 1 out of 36 in the parent generation died of kuru. By contrast, 33 of 218 parents from those carrying 127G only (the modal allele) had died of kuru (some of these presumably would also have carried the protective variant of 129). When the researchers looked at the 127V haplotype, the nature of the variation around this mutation implied that a common ancestor existed ~10 generations ago, with a 95% confidence interval 7 to 15 generations. That means that all of the copies of 127V extant today in the Fore descend from one particular copy present on the order of 250 years in the past within the population.

Double Dipping

Via ProMED-mail: the Charleston Daily Mail reports on a pediatrician who came down with swine flu twice.

Parsons says she's spoken with CDC representatives about the results, and they said the double infection isn't all that unbelievable.
"They said this happens every year with seasonal flu, so there's no reason to expect that it wouldn't happen with swine flu," Parsons said. "Every flu strain can change a little bit."
The pediatrician says there may have been a tiny change in the virus that stopped her immune system from recognizing it or her body never built up immunity to it.

Iron and MS

Via Twitter: The Globe and Mail reports on a researcher's personal obsession that led to an unexpected treatment for multiple sclerosis.

Fighting for his wife's health, Dr. Zamboni looked for answers in the medical literature. He found repeated references, dating back a century, to excess iron as a possible cause of MS. The heavy metal can cause inflammation and cell death, hallmarks of the disease. The vascular surgeon was intrigued – coincidentally, he had been researching how iron buildup damages blood vessels in the legs, and wondered if there could be a similar problem in the blood vessels of the brain.
Using ultrasound to examine the vessels leading in and out of the brain, Dr. Zamboni made a startling find: In more than 90 per cent of people with multiple sclerosis, including his spouse, the veins draining blood from the brain were malformed or blocked. In people without MS, they were not.
He hypothesized that iron was damaging the blood vessels and allowing the heavy metal, along with other unwelcome cells, to cross the crucial brain-blood barrier. (The barrier keeps blood and cerebrospinal fluid separate. In MS, immune cells cross the blood-brain barrier, where they destroy myelin, a crucial sheathing on nerves.)
More striking still was that, when Dr. Zamboni performed a simple operation to unclog veins and get blood flowing normally again, many of the symptoms of MS disappeared.

BU's Leaky Biolabs

Via ProMED-mail: the Boston Globe reports on another BU researcher who accidentally brought his work home with him.

The genetic tests, conducted at the state laboratory in Jamaica Plain, compared a blood sample from the researcher with bacterial matter recovered from the lab where he was working on BU’s South End campus. “The bottom line,’’ said Dr. Anita Barry, top disease tracker at the Boston Public Health Commission, “is they matched.’’
The analysis erased any doubt about what caused the researcher to become sick last month and intensified investigations into precisely how he was exposed to a germ known as Neisseria meningitidis, which can cause meningitis.
The city’s biological lab safety division will review safety procedures in BU’s medical labs, to ensure that the school is doing everything possible to minimize researchers’ exposure to pathogens, Barry said.

I thought they did that last time.

PlagueBlog recommends moving to the suburbs before the new BU biolab opens downtown. And by "suburbs" I mean Maine.

Accidental Vaccinia

Via ProMED-mail: the CDC reports on a case of vaccinia infection in an immunocompromised woman who handled rabies vaccine bait, in which a genetically modified version of variola's little sister is used. There's much more on the story and the history of vaccinia at ScienceBlogs.

Atypical Scrapie

Via ProMED-mail: the New Zealand Ministry of Agriculture and Forestry reports on a case of atypical scrapie.

MAFBNZ Principal International Adviser Dr Stuart MacDiarmid says global knowledge about atypical scrapie/Nor 98 is evolving. The widely accepted mainstream scientific view is that it occurs spontaneously or naturally in very small numbers of older sheep in all sheep populations around the world.
"This positive detection of atypical scrapie/Nor 98 in a sheep from New Zealand's national flock reinforces that view. Every country that has conducted sufficient surveillance for atypical scrapie/Nor 98 has found it in their flocks. This includes most Scandinavian and EU countries, the UK, the USA and Canada," he says.
The detection does not change New Zealand's status as free from scrapie.

Mad Elk and Mad Fish

Via ProMED-mail: last month, the New York Times reported on the spread of CWD among elk via fecal-oral transmission, due to preclinical shedding of prions.

Dr. Aiken said prions tended to bind to clay in soil and to persist indefinitely. When deer graze on infected dirt, prions that are tightly bound to clay will persist for long periods in their intestinal regions. So there is no chance chronic wasting disease will be eradicated, he said. Outside the laboratory, nothing can inactivate prions bound to soil. They are also impervious to radiation.

Also, Practical Fish Keeping reported last month on a study of mad cow and scrapie transmissibility to fish:

The authors found that while the bream never displayed clinical signs of spongiform encephelopathies during the study period, the brains of TSE-fed fish sampled two years after challenge showed signs of neurodegeneration and accumulation of deposits that reacted positively with antibodies raised against sea bream PrP. The control groups, fed with brains from uninfected animals, showed no such signs.

Swine Flu Shots vs. Seasonal Flu Shots

Via ProMED-mail: temperatures are still high in Canada, where the Globe and Mail reports that two and a half provinces have rebelled against seasonal flu shots in reaction to as-yet-unpublished research showing that a seasonal flu shot makes people more susceptible to swine flu.

The hodge-podge of vaccination strategies comes after a controversial, unpublished study suggested that people under 50 are twice as likely to contract the H1N1 virus if they have received a seasonal flu shot compared to unvaccinated people.
With no data revealing the optimal way of rolling out vaccines against the looming double threat of seasonal flu and the pandemic swine flu virus, the abrupt changes by provinces and territories could create disarray in inoculation programs, with fewer people turning up for either shot, potentially resulting in more cases of severe illness.
New Brunswick's public health authorities, skeptical about the science behind the Canadian study, have moved up seasonal flu shots for all their residents to October before proceeding to the pandemic vaccine campaign. Meanwhile, Quebec and Nunavut are deferring their seasonal flu campaigns until after their H1N1 mass vaccination clinics.

Shaken Baby Syndrome

Radley Balko at Reason Online reports on growing doubts about "shaken baby syndrome":

The phrase shaken baby syndrome entered the pop culture lexicon in 1997, when British au pair Louise Woodward was convicted of involuntary manslaughter in the death of Massachusetts infant Matthew Eappen. At the time, the medical community almost universally agreed on the symptoms of SBS. But starting around 1999, a fringe group of SBS skeptics began growing into a powerful reform movement. The Woodward case brought additional attention to the issue, inviting new research into the legitimacy of SBS. Today, as reflected in the Edmunds case, there are significant doubts about both the diagnosis of SBS and how it's being used in court.
In a compelling article published this month in the Washington University Law Review, DePaul University law professor Deborah Teurkheimer argues that the medical research has now shifted to the point where U.S. courts must conduct a major review of most SBS cases from the last 20 years. The problem, Teurkheimer explains, is that the presence of three symptoms in an infant victim—bleeding at the back of the eye, bleeding in the protective area of the brain, and brain swelling—have led doctors and child protective workers to immediately reach a conclusion of SBS. These symptoms have long been considered pathognomic, or exclusive, to SBS.

If you're really interested, you can dig up some ideas about alternate causes of SBS at this blog.

Mattel Exempted Itself from Lead Testing

Via Purple Pawn: The LA Times reported late last month that Mattel had lobbied itself out of third-party lead testing of its products.

"It's really ironic that the company that was a principal source of the problem" is now getting favorable treatment from the government, said Michael Green, executive director of the Center for Environmental Health in Oakland.
Mattel is getting a competitive advantage, Green said, because smaller companies must pay independent labs to do the tests. Testing costs can run from several hundred dollars to many thousands.

Medical Isotope Shortage

Via Orthoprax: the Journal of the American Medical Association reports on the ongoing "critical" shortage of medical isotopes (^99mTc) due to a reactor shutdown in Canada.

The shortage was expected to be exacerbated by the temporary closing of the Netherlands reactor for a month-long maintenance inspection from July 18 to August 18. Because the isotopes have a relatively short half life, they cannot be stockpiled.
Canadian authorities said they were working with medical isotope distributors and others to maximize the use of existing isotope supplies and with other international producers to increase isotope production and to coordinate shutdowns and other operations.

Since the journal article was written, the reopening of the Ontario reactor has been pushed into 2010, causing some trouble for the company that sells the isotopes, the Canwest news service reports:

Life sciences company MDS Inc. said Wednesday it has agreed to sell its analytical technologies division to Danaher Corp. for $650 million in cash and is also looking to unload its pharma business.
The Mississauga, Ont.-based company cited the recession and the prolonged shutdown of the National Research Universal reactor in Chalk River, Ont., as its reasons for the sales, which will allow MDS to focus on its isotope business, MDS Nordion.
Stephen DeFalco, chief executive at MDS, said the company still expects the reactor to restart in spring 2010.

A Cure for MS?

Via a mailing list: Science Daily reports that multiple sclerosis has been reversed in mice.

The new treatment, appropriately named GIFT15, puts MS into remission by suppressing the immune response. This means it might also be effective against other autoimmune disorders like Crohn's disease, lupus and arthritis, the researchers said, and could theoretically also control immune responses in organ transplant patients. Moreover, unlike earlier immune-supppressing therapies which rely on chemical pharamaceuticals, this approach is a personalized form of cellular therapy which utilizes the body's own cells to suppress immunity in a much more targeted way.
GIFT15 was discovered by a team led by Dr. Jacques Galipeau of the JGH Lady Davis Institute and McGill's Faculty of Medicine. The results were published August 9 in the prestigious journal Nature Medicine.
GIFT15 is composed of two proteins, GSM-CSF and interleukin-15, fused together artificially in the lab. Under normal circumstances, the individual proteins usually act to stimulate the immune system, but in their fused form, the equation reverses itself.

A caveat: this appears to be an early-stage treatment that may not reverse existing damage to the nerves.

Not Your Grandfather's Influenza After All

Via ProMED: News1130 reports that swine flu may not be coming back in a more virulent form in the fall, because the Spanish Flu may not have done so.

Virologist Dr. Jeffery Taubenberger, along with co-author and medical historian Dr. David Morens, argues there is no firm evidence that the 1918 virus ratchetted up in virulence in a fall wave - because there is no solid proof outbreaks of illness in the U.S. in the spring of 1918 were caused by the same virus.
Their commentary, published in this week's issue of the Journal of the American Medical Association, suggested changes in virulence or transmissibility of the current pandemic virus are not inevitable. In fact, they wrote, there are reasons to hope for "a more indolent pandemic course and fewer deaths" than seen in many previous pandemics.

Superbug Enzyme in Britain

Via an unnamed source: the BBC reports on a new "superbug" in the UK, a shared antibiotic-eating enzyme imported from India.

The enzyme, called New Delhi Metallo-1, has so far been found attached to bacteria that has caused urinary tract infections and respiratory infections.
It is of particular concern because it can jump from one strain of bacteria to another meaning it could attach itself to more dangerous infections that can cause severe illnesses and blood poisoning making them almost impossible to treat.
The NDM-1 enzyme destroys a group of antibiotics called carbapenems which are mainly used in Britain for severe infections and are tightly controlled because they are one of the few groups of antibiotics that remain useful against bacteria that have already developed resistance to the commonly used drugs.

Plague in China

Via an unnamed source: the BBC reported last week on the rising plague death toll in China.

A BBC correspondent in Beijing, Michael Bristow, says that unlike in the past the authorities are being very open about this outbreak.
Local officials in north-western China have told the BBC that the situation is under control, and that schools and offices are open as usual.
But to prevent the plague spreading, the authorities have sealed off Ziketan.

Today the WHO reported on the situation, which seems to be under control:

According to the epidemiological investigation, the source of this outbreak was a wild marmot, which had contact with the dog of the index case. Ziketan is in an area of natural plague bacteria circulation amongst animals and at the present time it is the active season for plague transmission amongst animals. No drug resistance of the bacterium has been found so far and the 3 death cases have been attributed largely to delayed treatment.

Beware the Bitter Lupini

Via ProMED-mail: the Brisbane Times reports on two cases of lupini bean poisoning in Australia.

They suffered blurred vision, light-headedness, lethargy and had difficultly walking.
"Fortunately, neither of the two women who presented to hospital became seriously ill," says Nevada Pingault, an epidemiologist at WA Health's Communicable Disease Control Directorate.
"But lupin poisoning can be fatal."
An investigation revealed a quantity of bitter lupins had been milled into flour to meet a local shortage in supply.

Flu Ship

On the Typhoid Traveller front, via an unnamed source, the BBC reported on Friday that large numbers of crew on a cruise ship in the south of France were suffering from a flu-like illness.

It has now gone on to Marseille. The authorities there say neither passengers nor crew will be allowed to disembark until further tests have been carried out on their health.
"Based on the results, a decision will be made on whether or not passengers can disembark," a statement from the local prefecture, or local government, said.

Refrigerate After Opening

Via twitter: Wired reports on a company that's making beer from Eocene yeast recovered from amber.

Lambert and Cano had toyed with the idea for 12 years. Before Ambergene went under, the company made a batch on a lark. "We called it Jurassic Amber Ale or T-Rex Lager or something, and it was pretty good," Cano says. It was served at his daughter's wedding, and they even sent some to the Jurassic Park 2 cast party. That experiment had Cano and Lambert itching to release a beverage commercially. But they wanted it to be something respectable.

Needless to say, PlagueBlog recommends against eating anything that's over 40 million years old. In fact, only under the most extraordinary circumstances should you eat anything over 4 years old.

Fido Fricassee

ProMED-mail reports five recent cases of trichinosis "due to consumption of stray dog meat," with a total of nine cases this year.

PlagueBlog recommends against eating housepets, and especially not strays. You don't know where they've been.

Rabid Foxes

Via an unnamed source: WBZ reported a rabid fox attack Tuesday in Worcester. The victim was a 76-year-old woman who'd been gardening. The good Samaritan who held off the fox until the police shot him was also bitten. The fox was apparently known to police:

They believe this was the same fox that had been seen in the neighborhood the night before. One man was bitten, and two cats were also attacked.

There was a similar fox showdown in Pennsylvania in May.

More Recalls

Via an unnamed source: WBZ reports that Dunkin Donuts is temporarily cutting off the Dunkaccinos due to salmonella contamination at their chocolate supplier.

Via twitter: the AP reports that Shaws, Star, and Big Y are recalling some tuna steaks sold last week due to histamine.

Symptoms may include tingling or burning sensation in the mouth, rash on the face and upper body, hives and itching of skin, nausea, vomiting or diarrhea.