HK19
Colors of the mountain will never leave our door
Sounds of the river will linger forever in our ears

Colors of the Mountain
Da CHEN


The onset of COVID-19

For COVID-19 note that the figures provided are purely indicative and changing fast

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arrow 29 february 2020. The epidemic triggers irrational behaviours. « What the monkey sees, the monkey does » this is the saying describing the panic behavior of some people. There is considerable variation in the public behaviour in different places in the world. State of emergency in the northern island of Hokkaido in Japan, where the number of cases now reached 242.  This country does not have a centre for disease control, leaving management of the epidemic to the administration. It is important to remember that the letality of this disease is limited, but that the simultaneous presence of serious cases poses difficult problems to the health care systems, and this triggers more panic in people around patients than epidemics of influenza (which have also significant consequences in terms of fatalities, but more evenly spread). 85,955 cases worldwide, 79,251 cases in China, 95 in Hong Kong, 102 in Singapore and 2,934 deaths. The number of cases in South Korea reaches now 3,150 with 17 deaths. The role of the SCJ sect (which appears to have a delegation in Hong Kong) appears progressively more important in the dissemination of the disease. Iran declares 593 cases and 43 fatalities. In Italy 1,128 cases and 29 deaths. France has 100 cases. The United States have recorded 62 cases and one death. In this country a first case of pharmaceutical ingredient (made in China) shortage has been identified. Several coronaviruses are responsible of common colds resulting in a sizeable proportion (1-2%) of the severe pneumonia cases. They were never put under control and there is, as yet, no vaccine against these infections. This implies that if the present epidemic is not contained before summer, it will remain present in the future. Alternatively, if it is controlled, as SARS was, then it will disappear.
arrow 28 february 2020. Group gatherings, where people share common premises are frequently a major source of the epidemic. This comprises group tourism and cult practices. One case in Nigeria (coming from Italy), and one case in New Zealand (from Iran). The four main sources of contamination are China, Italy, Iran and South Korea. Most of the cases that are now present in the majority of countries come from these sources. The first imported case in China comes from Iran. 84,131 cases worldwide, 78,824 cases in China, 94 in Hong Kong, 98 in Singapore and 2,876 deaths. The number of cases in South Korea reaches now 2,337 with 16 deaths. Iran declares 388 cases and 34 fatalities. In Italy 888 cases and 21 deaths. The United States have recorded 60 cases. The number of affected passengers from the Diamond Princess remained at 705 but with now six fatalities. The lack of propagation of the epidemy in sub-saharan Africa is puzzling. It could be due to some genetic resistance setup (and this will be seen if Americans from African origin are less affected), or, more likely to the double epidemic scenario, witnessed during the SARS episode. Pet owners in Hong Kong are worried after a weak response against SARS-CoV-2 has been found in the dog of a patient. It should be stressed that, exactly as common cold happens in humans, coronaviruses also infect pets (sometimes, also as with SARS, with highly virulent forms.) Authorities recommend quarantine for such pets. The obscure and secretive practice of the sect Shincheonji Church of Jesus the Temple of the Tabernacle of the Testimony (SCJ) may have been important in the first dissemination of COVID-19. The Shanghai laboratory where researchers published—before the authorities—the first genome sequence of the SARS-CoV-2 that causes Covid-19 has been shut down. No reason for closing has been communicated.
arrow 27 february 2020. As it spreads in the world the SARS-CoV-2 keeps evolving. The first patient of the disease is still unknown. There are now cases in several South America's countries. It will be interesting to follow how the virus evolves in Sao Paulo, as this will give an idea of how the outbreak will evolve when spring comes. Argentina is also important to monitor the future as it lies in the southern hemisphere, and has tight relations with Italy. Among the countries important to monitor is also South Africa. Australia and New Zealand being quite isolated, they are more likely to contain any epidemic. 82,456 cases worldwide, 78,659 cases in China, 93 in Hong Kong, 96 in Singapore and 2,814 deaths. The number of cases in South Korea reaches now 1,766 with 13 deaths. Iran declares only 245 cases (after 141 this morning) and now 26 fatalities. In Italy 650 cases and 17 deaths. The United States have now recorded 60 cases. The number of affected passengers from the Diamond Princess reached 705. It seems that immunization of some recovered patients may be temporary, which is a negative prospect for vaccination.
arrow 26 february 2020. Two thirds of all workers have come back to work in China. Only five new cases outside the Hubei province in China. By contrast, the disease spreads in Europe with Italy a major source of contamination for other countries. China has updated the clinical definition of the disease, which may change the number of Chinese cases in the next disclosure. 81,248 cases worldwide, 78,064 cases in China, 91 in Hong Kong (as expected, the contribution of passengers from the Diamond Princess is showing up), 93 in Singapore and 2,770 deaths. The number of cases in South Korea reaches now 1,261 with 12 deaths. Iran declares 139 cases at this time and now records 19 fatalities. In Italy 374 cases and 12 deaths. The United States have now recorded 59 cases. One case in Algeria of a person coming from Italy. One case in Brasil (also coming from Italy). For those who wish to see how the virus is travelling GISAID has constructed a site with interesting information showing the world-wide spread of the virus (colors show the various places of identification).
note In the present context it may be interesting to note that the company Tonix has synthesized de novo a copy of the vaccinia virus, without any official reaction, despite the fact that this opens up a very dangerous Pandora box.
arrow 25 february 2020. COVID-19 is still on the increase outside of China. Outside Hubei, where it took time to recognize the disease and which takes the brunt of the number of patients and deaths, it seems that as soon as the disease is identified, the measures put in place allow it to be contained fairly quickly. 80,382 cases worldwide, 77,658 cases in China, 85 in Hong Kong, 91 in Singapore and 2,710 deaths. In Hong Kong, a change in the regulation controlling sewage systems, introduced in 2016 may have increased the risk of oro-fecal contamination via sewage. The northern province of Heilongjiang, next to Russia, has 480 cases and 12 deaths. The number of cases in South Korea reaches now 977 with 11 deaths. This sect-originating outbreak may have started with proselyt members of the sect who met in Wuhan in january or exchanges between Wuhan and Daegu. Iran still does not report any reliable number of patients—95 at this time—but records officially 16 fatalities. In Italy 322 cases and 11 deaths. The United States have now recorded 53 cases. Finally 691 cases and 4 deaths were related to the Diamond Princess cruise.
arrow 24 february 2020. Scientists are reluctant to share their data on the SARS-CoV-2 because they hope to hit high Impact Factor journals. A very unfortunate habit at this time makes that people try publishing in scientific journals with high "impact factor (IF)". As an illustration, I received this mail: "the samples are only for detection. Not allowed to do research if the hospitals did not want to do it now. […] It is really a shame to me anyway. Please understand that it is the situation now and here. I assure you that we, together with the clinicians, will publish many sequences very soon." The reason is that fashionable journals (with high IFs) usually put an embargo on the data associated to the articles they will publish, and, in most countries, this is counted for scientists recruitment and even salaries! This is despite the fact that these journals publish a considerable amount of fake or unreproducible research, selected by editors trained for advertisements, who have as only target the commercial impact or otherwise visibility of the journal they manage. For true scientists this is a nightmare, and in cases like what happens now, this is a crime, because it is essential that the data about the epidemic is shared worldwide, and immediately. A number of academic structures have signed the San Francisco Declaration (DORA) seeking to impose that the evaluation of research rests on its content and not on the reputation of journals whose objectives are very questionable, but it is still far from being generalized (in France researchers continue, for example, to be assessed on the fact that they have published in journals with a high impact factor, which also leads to repeated scandals!) 79,444 cases worldwide, 77,150 cases in China, 81 in Hong Kong, 90 in Singapore and 2,627 deaths. In Wuhan, the epidemic has peaked. The number of cases in South Korea reaches now 833 with 8 deaths. Iran does not report any reliable number of patients—61 at this time—but suggests that there is now 50 fatalities in the city of Qom. Some change in Italy at this hour: possibly as many as 215 cases and 7 deaths. Multiple cases in Middle East, substantiating the unknown character of the situation in the region. Fortunately, as seen with MERS—which is not spreading as an epidemic—temperature appears to prevent the spread of the virus. Yet, it seems important to monitor places where the weather will remain cold. This comprises Russia, central Asia and mountainous regions.
arrow 23 february 2020. More than 9,000 members of a 200,000 followers evangelist cult are tested for SARS-CoV-19 as the disease explodes in South Korea. At least nine members of a South Korean group that toured Israel and Cisjordania tested positive for the virus and the presence of some 1,000 tourists of this country in the region suggests that they may have created new foci of the epidemic. These tourists are requested to self-quarantine. 78,959 cases worldwide, 76,936 cases in China, 74 in Hong Kong, 89 in Singapore and 2,465 deaths. The number of cases in South Korea reaches now 602 with 6 deaths. Iran now reports 43 patients and 6 fatalities. A cluster in northern Italy brought the number of cases in this country to 155 and 3 deaths. Several cities have been quarantined and it has been decided to cancel the carnival of Venice. The first patient in Italy has not yet been identified, which implies that the disease might be much more widespread than already observed. In this contest, the origin of the virus is still a matter of considerable debate. A study (not peer reviewed) suggests that the virus did not originate in Hua Nan market in Wuhan, but rather from southern China.
arrow 22 february 2020. Several clusters out of China. China has implemented an AI surveillance analysis approach allowing people to know whether they are permitted to travel (red, green and yellow pass, on their cell phones). The increase of the COVID-19 spread out of China is worrying, in particular at places where the temperature will remain low for some time. 77,953 cases worldwide, 76,288 cases in China, 70 in Hong Kong, 89 in Singapore and 2,364 deaths. The number of cases in South Korea reaches now 433 with two deaths. Iran now reports 28 patients and 6 fatalities. A cluster in northern Italy brought the number of cases in this country to 51 and two deaths. Identification of authentic cases is essential and the difficulty of the process, coupled to local political worries, explains much of the uncertainty of the number of cases. The BGI has interrupted its normal activity to work 7/7 on the construction of assay kits for the virus (more than 420,000 at this time) and on assays for isolates coming from all China (more than 170,000 at this time), also building 3 large facilities at designed places to perform the assays locally.
note An invasion of locusts is affecting the Horn of Africa, Yemen and neighbour countries, with dire consequences on staple food supplies. Despite the COVID-19 epidemic, China succeeds in producing a considerable amount of spores of Metarhizium fungi that kill locusts as a control of this ancient plague.
arrow 21 february 2020. Multiple cases in Chinese prisons. South Korea meets an « emergency » situation and steps up measures as the number of cases keep rising fast in the cities of Daegu and Cheongdo. Monitoring the situation in Iran seems important, as a Canadian who never visited China but returned from Iran is possibly infected by the SARS-CoV-2. Another possible place where the disease could develop unchecked is North Korea, knowing the thriving smuggling at the border with China. To understand the propagation of the disease it is essential to be confident in the figures provided by authorities. The very fact that there was a sudden increase in cases on february 13th, right at the moment when local governmental authorities were changed casts some doubt on actual numbers. 76,794 cases worldwide, 75,465 cases in China, 69 in Hong Kong, 86 in Singapore and 2,250 deaths. The Ministry of Justice of China informed that more than 500 prisoners in five prisons in three provinces had been infected by the virus. At  least 200 prisoners interned in two jails in Shandong province and 34 in a jail of the Zhejiang province were infected by the SARS-CoV-2. The number of cases in South Korea reaches now 208. This is apparently due to a « superspreader » member of a religious evangelist sect who infected a large number of members of her community. Together with the Diamond Princess cruise ship this demonstrates that confined environments are prone to propagate the disease fast. Iran now reports some 18 patients (15 more than previously) and 4 fatalities. Lebanon reports a positive case from a traveler just returning from Iran. Recovering patients who have been let back to standard life conditions may be still carrying the virus for some time and might therefore contribute to propagate the COVID-19. Finally, the severity of the disease is higher in men than in women, like for SARS and MERS. Aboard Westerdam, it seems that the apparent contamination of a passenger was a false positive alert.
arrow 20 february 2020. The 3D structure of the spike protein of the virus is solved using cryoelectron microscopy. As expected, this technical feat is interpreted as leading directly to new drugs and vaccines. It is still another demonstration of the power of cryoelectron microscopy. This emphasis on structure is a follow up of a long tradition that is, unfortunately and contrary to much advertisement, seldom followed by real rapid successes in terms of applications. China ASEAN emergency meeting on the COVID-19 epidemic. 75,773 cases worldwide, 74,576 cases in China, 69 in Hong Kong (2 deaths), 85 in Singapore and 2,129 deaths. The  number of cases in South Korea reaches now 104. The sudden decrease in Mainland China is somewhat puzzling. It reflects the difficulty in precise clinical identification of cases of COVID-19. Among the 621 infected patients on the Diamond Princess two passed away. Iran reported three new cases of patients affected by the disease. A letter to the NEJM compares the effects of the new virus to that of SARS and notes both that the contagion mainly seems to appear at the same time as the symptoms and that one significantly infected patient was asymptomatic the day when the analysis was conducted.
arrow 19 february 2020. Russia has closed its eastern border with China. It was somewhat of a surprise that no concern about COVID-19 appeared in Russia, as its eastern border is quite permeable and that many Chinese citizens do all sorts of trade in this region. 75,291 cases worldwide, 74,185 cases in China, 65 in Hong Kong (2 deaths), 84 in Singapore and 2,010 deaths. A cluster of patients related to an sectarian church in South Korea witnesses a sudden increase of 5 more patients (now 15), bringing the number of cases in South Korea to 51. Showing that the spread of the disease is not entirely clear yet, two cases have been diagnosed in Iran and both passed away. This suggests that the actual number of contaminated persons in this country is significantly higher.
arrow 18 february 2020. Assays combining anti-flu and anti-HIV drugs against SARS-CoV-2 infection are ongoing. The Chinese Journal of Epidemiology summarizes the situation, which shows an excess of deaths in Hubei province as compared to the rest of China. Older people or people with other illnesses are most at risk. 73,429 cases worldwide, 72,436 cases in China, 61 in Hong Kong, 81 in Singapore and 1,873 deaths. The 350 persons on board Diamond Princess are expected to be flown to Hong Kong. They will be placed in quarantine at the Chun Yeung Estate and its inhabitants are opposed to their coming. With 88 new cases the number of infected persons on the Diamond Princess reaches 542. Our model of the propagation of the epidemic is on line in MedRxiv. A small minority of the virus isolates display a remarkably long incubation period (from 14 to 24 days).
arrow 17 february 2020. There may be asymptomatic cases of SARS-CoV-2 infection.
If this is the case, it is almost impossible that the outbreak is contained and there is a great risk that COVID-19 becomes endemic. 71,440 cases worldwide, 70,548 cases in China, 60 in Hong Kong, 77 in Singapore and 1,775 deaths. To contain panic behaviour, Taiwan Health Authorities have created a cartoon with the dog Zongchai to display messages such as "Leave face masks for the people who need them, frequently wash your hands with soap, refrain from touching your eyes, nose and mouth with your hands". It will be of much interest to see the fate of passengers of the Westerdam cruise ship after a passenger has been found carrying the virus. This is particularly important as 99 new cases have been identified among the Diamond Princess passengers.
Alert on another positive RNA virus that infects plants, the Tomato rugose brown fruit virus (ToBRFV) is enforced in France, where a first case of infection might have been identified.
arrow 16 february 2020. The pace of COVID-19 is slowing down.
All the population of the Hubei province (58 million, among which 24 million from rural areas) have been requested to stay home until further notice. In Hong Kong some 2,000 protesters demonstrated against plans to set up quarantine centres near the estates where they live. 69,278 cases worldwide, 68,500 cases in mainland China, 57 in Hong Kong, 75 in Singapore and 1,670 deaths. While the origin of the outbreak remains unknown (an article was published suggesting that the contaminating animal was a pangolin) the Wuhan Institute of Virology (a safety level 4 laboratory, the highest possible security level) denies that "patient zero" was one of its employees. With the continuous propagation of COVID-19  aboard the Diamond Princess cruise ship (355 persons are infected including 21 from Hong Kong, to compare with the situation in the city that hosts 7 million inhabitants), we witness how « floating Petri dishes », may be involved in the propagation of epidemics.
arrow 15 february 2020. While there are still no case of SARS-CoV-2 infection in Indonesia, people react by panic buying of face masks and basic goods.
67,187 cases worldwide, 66,492 cases in mainland China, 56 in Hong Kong, 72 in Singapore and 1,527 deaths. At least one passenger on the Westerdam cruise ship, which had struggled to dock somewhere to end up in Cambodia, was infected with the virus and flew to Malaysia.
arrow 14 february 2020. The extent of COVID-19 resumes a standard course.
Winter is in the northern hemisphere the time for peaks of pneumonia. Identifying the specific cause of a disease of this type requires a heavy infrastructure. However  the combination of clinical signs as precise as possible may be sufficient to characterize a disease, and this is now what takes precedence when molecular identification of the  genome of the virus is not possible. It seems however difficult to monitor correctly the situation in a country where authorities control upstream all information sources. 64,452 cases worldwide, 63,851 cases in mainland China, 56 in Hong Kong and 1,383 deaths. At least 1,716 medical staff have been infected in China. The serum of recovered patients seems to have some protective effect. 67 persons have now been infected in Singapore. First identified case in Egypt.
arrow 13 february 2020. An apparent surge of COVID-19 cases reflects a lag in counting.
Modelling heavily depends on the way authorities communicate the number of cases. From previous numbers it was clear that there was something unusual going on. This seems to be now corrected, with 60,386 cases worldwide, 59,804 cases in mainland China, 53 in Hong Kong and 1,370 deaths. 10,000 persons are quarantined in Vietnam. 2,600 military medical staff arrived in Wuhan, putting the total to 6,600 persons. This is much higher than during the SARS episode in 2003.
arrow 12 february 2020. The economic consequences of the epidemic appear to be more important than those during the SARS episode.
The name of 2019-nCoV has been changed by the international Committee on Taxonomy of Viruses to SARS-CoV-2. Until now, more than 80% of the COVID-19 clusters occur within families. 45,175 cases worldwide, 44,653 cases in mainland China, 50 in Hong Kong and 1,117 deaths. The questions of the transmission mode and incubation time are not clearly answered. An important point which is not yet understood is the number of very mild or asymptomatic cases.
arrow 11 february 2020. The epidemic seems to slow down in Wuhan and the Hubei region.
The disease caused by the 2019-nCoV has been given an official name: COVID-19
, CoronaVIrus Disease 2019. It appears that at least 500 members of the health personnel have been infected by the 2019-nCoV. Hong Kong health authorities are looking for nine households from the Cheung Hong Estate in Tsing Yi to monitor their health status. The sewage system of that complex is certainly less prone to contamination than that of the Amoy Gardens Estate, but, together with the episode of the Diamond Princess cruise ship it appears that contamination via the oro-fecal route is quite significant. 43,114 cases worldwide, 42,638 cases in mainland China, 49 in Hong Kong and 1,018 deaths. The question of the origin of the virus remains open and subject to a variety of rumors.
arrow 10 february 2020. The number of people recovering from « Novel Coronavirus Pneumonia » (NCP) becomes significant.
Hong Kong police is on the hunt to find two people who escaped from quarantine. 3,344 have recovered from the disease. 40,631 cases worldwide, 40,171 cases in mainland China, 43 in Hong Kong, including 10 members of the same family, and 910 deaths. The situation in Tsing Yi, a suburb of Hong Kong, seems to be similar to that of Amoy Gardens during the episode of SARS (contamination by the liquid effluent evacuation system). In line with the oro-fecal contamination route 65 more people aboard the Diamond Princess, the cruise ship currently under quarantine in Japan’s Yokohama harbor, have tested positive for 2019-nCoV, bringing the total to 136 passengers infected.
arrow 9 february 2020. Modeling trends of epidemics between different locations is essential to understand the propagation of a disease (and whether numbers can be trusted).
The quarantine imposed on the Hong Kong cruise ship ends and passengers and crew can now leave the ship. 37,580 cases worldwide, 37,198 cases in mainland China, 36 in Hong Kong (with eight cases belonging to one whole family of an infected patient) and 813 deaths. The tentative name of the disease is « Novel Coronavirus Pneumonia » (NCP). The Chinese Ambassador to the US reacts against fake news related to the origin of the Wuhan-nCoV virus.
arrow 8 february 2020. Lack of transparency increases the spread of dangerous fake news.
The best way to explore the spread of the epidemic and its real cost in terms of lives, it seems important to monitor what happens in open countries. 34,898 cases worldwide, 34,546 cases in mainland China, 26 in Hong Kong and 725 deaths. Again, understanding the origin of the virus should trigger a worldwide ban on importation of wild animals.
arrow 7 february 2020. Waves of anger in China after the announcement of the death of WenLiang Li. The illegal wildlife trade in China is no doubt responsible for the epidemic. At this stage, research leads to suspect that the pangolin, unfortunately subject to this traffic despite its rarity, could be the intermediate host of 2019-nCoV. Hopefully the Chinese government will learn from it and severely punish the use of wild animals in the country. The epidemic spreads in a quarantined cruise ship near Tokyo with 61 identified cases. 31,527 cases worldwide, 31,203 cases in mainland China, 26 in Hong Kong and 638 deaths.
arrow 6 february 2020. Community outbreak declared in Hong Kong.
It seems that WenLiang Li, the doctor who alerted Wuhan authorities on December 30 of the outbreak, and was reprimanded by the police, is dead. He was 34 years old. At this point, Chinese health officials say he is still alive. Hygiene reminder: having hands and face uncontaminated is essential to prevent the spread of the virus. The use of masks is therefore often less useful than harmful (because there is a risk of touching your face) in spaces where the confined air is recycled after correct filtration. Many of the 24 hongkongers who have been infected did not recently visit the Mainland, demonstrating local transmission chain. 28,403 cases worldwide, 28,130 cases in mainland China, 24 in Hong Kong and 567 deaths. Fierce quarantine measures are implemented in the Zhejiang province. Cruise ships are common reservoir for gut viruses epidemics. Thousands more people than previously thought might have been exposed to the 2019-nCoV, after a cruise line admitted one of its ships had sailed four times (Nansha-Vietnam-Guangzhou-Hong Kong, where 8 infected patients were disembarked) since carrying the Chinese passengers infected with the disease. The vessel is at present quarantined (other cruise ships are also quarantined elsewhere in the world).
arrow 5 february 2020. The Chinese government has deployed a BSL-3 mobile biosafety laboratory in Wuhan.
24,648 cases worldwide, 24,405 cases in mainland China, 21 in Hong Kong and 494 deaths. The number of people who have recovered has now exceeded 1000. Hong Kong is extending the authorization to work from home. University staff in Shenzhen are invited to stay home until February 24. Chinese public health officials have added some respiratory problems to the symptom list of suspected cases, expanding the classification of coronavirus patients from three to four, adding a category for "mild" cases. Those in the mild category who have symptoms of fever, fatigue, cough or breathing problems but no lung infection should be quarantined.
arrow 4 february 2020. All other things being equal, the number of cases outside China is not increasing very significantly
20,702 cases worldwide, 20,492 cases in mainland China, 18 in Hong Kong and 427 deaths. Singapore reports six new cases among which four are person to person contamination. Many drug trials are underway in China. Several groups used AI approaches to explore the potential of existing drugs. The medical personnel is on strike in Hong Kong to protest against the management of the crisis and in particular the maintenance of a certain opening of the border with mainland China.
arrow 3 february 2020. The likely double route of contagion will modify the course of the epidemic, hopefully for the best
17,491 cases worldwide, 17,307 cases in Mainland China, 15 in Hong Kong and 362 deaths. Contagion via the oro-fecal route, as witnessed already for SARS limits considerably the usage of face masks. People should avoid touching their face.
arrow 2 february 2020. In parallel with the 2019-nCoV epidemic, an outbreak of H5N1 flu in Hunan province.
Winter time is a common period for respiratory diseases. As during the SARS episode H5N1 flu is lingering. However it now appears that flu viruses of the H5 or H7 descent, while causing severe infections to people in direct contact with infected animals are not prone to cause epidemics. This is in contrast with H1 and H3 descent viruses. In particular H3N8, that infects dogs, horses and seals should be monitored carefully. 14,556 cases worldwide, 14,380 cases in Mainland China, 14 in Hong Kong and 305 deaths. The evolution of the disease in Hong Kong may give us ways to predict how the epidemic will fare in the future. It is likely that it has common features with the double type of spread witnessed in the case of SARS, that we summarized as « the double epidemic ».
arrow 1 february 2020. Public Health Emergency in the USA.
12,031 cases worldwide, 11,860 cases in Mainland China, 14 in Hong Kong and 259 deaths. Johnson and Johnson plan to develop a vaccine. In Hong Kong medical personnel threaten to go on strike if the border with mainland China is not closed.
arrow 31 january 2020. A name for the disease: 2019-nCoV Acute Respiratory Disease. The final name will be given at the International Committee on Taxonomy of Viruses. 9,910 cases worldwide, 9,783 cases in Mainland China, 13 in Hong Kong and 213 deaths. Several sources suggest that the actual number of cases is lower than published. Remember that at this season there are many respiratory diseases in the Northern Hemisphere. For the time being the vast majority of patients out of China have an history of recent contacts with Wuhan. Russia closes its border with China. Lack of transparency about the person-to-person contagion of the first cases mid-december in Wuhan triggers a social media storm in China.
arrow 30 january 2020. Several large foundations contribute to financing research on the virus. The WHO declares that the epidemic is a PHEIC. The average incubation period of the disease is around five days. All Chinese provinces are now affected. 8,265 cases worldwide, 8,144 cases in Mainland China, 12 in Hong Kong and 171 deaths. Hong Kong universities stop courses until march. A study showed that person to person transmission began mid-december 2019. "The infection of 2019-nCoV was of clustering onset, is more likely to infect older men with comorbidities, and can result in severe and even fatal respiratory diseases such as [ARDS]". Facing grave limitation of supply, Hong Kong's prison authority has asked prisoners to produce facial masks 24/24.
arrow 29 january 2020. Controversy about the future of the Wuhan epidemic. In view of the lack of proper communication during the very first phases of the epidemic, the WHO will reevaluate its status as a public health emergency of international concern (PHEIC). The Chinese state media say that the disease will last less than SARS, while Hong Kong doctors say the opposite. A family cluster in Vietnam confirms person to person contagion but with no further contagion at this time. Phylogenetic analyses show that the first case dates probably from the end of last november. 6,154 cases, 6,061 in Mainland China and 132 deaths. In an interesting development, the Supreme People's Court ruled that police should not have censored an exchange of chats led by a medical doctor who discussed unusual cases of pneumonia in Wuhan, very early on (the doctor was himself contaminated by a patient). This demonstrates in a vivid way the importance of a significant level of transparency in the exchanges between ordinary citizens. An unfortunate feature of the epidemic is that it spreads anti-Chinese racism as a disease, especially in Asia.
arrow 28 janvier 2020 Significant increase of the number of persons infected by the Wuhan CoV. 4,607 cases in China (4,682 world wide) and 106 fatalities (see with some lag a map of East Asia and the WHO report page). Two new cases in Japan, including a bus driver who transported Chinese tourists in Nara prefecture, showing a clear case of person to person contamination. Another case in France, this time severe. Civil servants in Hong Kong are asked to work from home. Stock exchange worldwide begin to react negatively as the economic impact of the disease will probably be considerable. Of the 13M residents in Wuhan, 5M left the city for New Year travel before they walled in the whole city not allowing anyone out. Importantly, many of those outside of Wuhan are in Beijing, Shanghai, Guangzhou etc, and many of them, together with local residents in Guangdong and elsewhere catching the virus will likely come to HK for treatment. The Dean of the Faculty of Medicine at HKU has asked the HK Government to close the HK borders because it will overwhelm the medical system here, but the Government has initially refused to do so. So the hospital staff has threatened to go on strike unless the Government closes the border, which is now almost accepted. The 1,000 places hospital created for the SARS epidemic reopens in Beijing. In order to place figures in perspective remember that the flu epidemic caused each year from 250,000 to 500,000 extra deaths worldwide as compared to seasons without flu, and note that many people are reluctant to be vaccinated, in sharp contrast with the present pre-panic situation. This does not mean that the epidemic is not serious, but it is important not to relay fake news and understand why, in general, vaccination is a useful practice. If the disease reached the proportions of flu, then it is likely that it would remain endemic at least for some time. The main problem with any new contagious disease is that it creates locally large numbers of cases because their is no previous immunity. This triggers panic, which make people move away and spread the disease, with enormous economic consequences...
arrow 27 january 2020 The pace of the epidemic does not slow down. Standard information about the epidemic is now widely avaible. The WHO chief arrives in Beijing to discuss ways to contain the epidemic. The main questions are those related to the origin of the virus and the future trends of its contagion and virulence. We will here follow scientific trends in this direction, remembering for example that, during the SARS episode it was at a time suspected that the source was a snake. Foreigners try to escape China with the help of their own authorities. In any event, if governments accept to move some of their citizens out of a contaminated region it is essential that these persons are confined to a quarantine zone for at least two weeks when they arrive. 2,839 cases in Mainland China (2,901 worldwide) and 82 deaths (see with some lag a map of East Asia), that is 769 cases on Sunday compared to 688 the day before. The virus has adapted to man and is still evolving fast. Incubation depends on the viral load of contamination, from one to 14 days (10 days on average).
arrow 26 january 2020 The epidemic potential of the Wuhan CoV disease appears to be quite high (2.6, range 1.5-3.5). As in the case of influenza, the virus is contagious even during the incubation time (which may last at least 14 days).
The length of the contagious incubation period makes the disease much more difficult to contain. 2,034 cases in Mainland China (2,084 worldwide) and 56 deaths (see with some lag a map of East Asia). Tibet is the only province without any identifed case of the disease. There are now six cases in Hong Kong. As many as 5 million inhabitants of Wuhan appear to have left the city before lockdown, and this will likely create foci of the disease everywhere. Premier Li Keqiang will head the high-level group to fight the coronavirus epidemic. More than an extra 1,000 doctors and nurses will join the relief effort in Hubei. 2,400 hospital beds have been added in Wuhan, and the government is planning to add 5,000 more over the next three days. Here is an example of the reaction of the highest authorities in China. Antiviral compounds, including those against HIV are assayed to alleviate the development of the virus. It is obvious that this interferes with its mutagenesis profile, which is not necessarily a positive outcome. The scenario of the origin of the disease remains fairly elusive. The phylogeny of the virus makes it similar to a bat coronavirus, as in the case of SARS. Note however that the fairly distant MERS coronavirus, usually found to infect camels, is also related to bat viruses. There are signs that the virus may become more contagious as time passes. It may be interesting to note that biological intuition can be quite early (we noted the possibility of an SARS-type epidemic on January 1, as we can see in the present record, even if an artificial intelligence approach was able to get ahead of us: the BlueDot platform seems to have perceived the danger from December 31. The WHO notified the general public on january 9th of a disease possibly originating at the Huanan Seafood Market in Wuhan. In Hong Kong, the population is violently trying to prevent the transformation of a recently completed building complex (Fai Ming Estate) into a quarantine zone.
arrow 25 january 2020. Normal operations of the 6,000 taxis services have been suspended in Wuhan, diverting them for medical and logistics activities. China deploys 1,230 doctors and nurses to help fight the disease.
Experts, including some who were involved in fight against SARS, from Guangdong, Shanghai and other places move to Wuhan. There appears to be no connection between the first patient (identified on december first, much earlier than previously communicated) and the seafood market initially incriminated in Wuhan. Hong Kong declares highest level of emergency (five cases), where schools are closed. 1459 cases in Mainland China (1497 worldwide) and 42 deaths, including a doctor in Wuhan: three cases in France (two in Paris, one in Bordeaux);
7 cases in Thailand, 4 in Australia, 3 in Japan, 2 in South Korea, 2 in Vietnam and one in Nepal. An image, slightly lagging behind, gives the situation in China. The youngest patient is a two-year-old girl. The authorities are seeking to increase the number of machines allowing to re-oxygenate and remove carbon dioxide (Extra Corporal Membrane Oxygenation) from intensive care patients, as suffocation is the major cause of death for this disease. 81 of these machines were shipped from Shanghai. It is now likely that some people infected with the coronavirus show no symptoms but that they were indeed infected, showing that, contrary to some affirmations, our immune system can protect us. Whether they can transmit the disease is open to question. Many articles are already out describing the disease and its propagation and that lower virulence increases danger of propagation. For those interested see for example a study from Shenzhen and HKU. The fact that there may be latent immunity should lead to looking for places where the disease, unexpectedly, does not develop. There is currently no indication to that effect, unlike the situation that prevailed in 2003, where Shanghai was remarkably spared.
arrow 24 january 2020. Quarantine is failing: most counties of Hubei province as well as 29 out of 31 provinces have now cases of Wuhan nCoV infection.
910 cases and 26 fatalities in mainland China; a second patient in the USA. From now on, we will no longer provide details of the spread of Wuhan's pneumonia because mass media are well informed. However we will discuss the scientific and socio-political questions asked by the spread of the disease. In collaboration with Fudan University in Shanghai several American Universities are working on the development of a vaccine with the US NIH, aiming at having vaccine trials in three months time. The WHO stopped short of declaring and advice of Public Health Emergency of International Concern (PHEIC) after heated debates, in particular because there is as yet no indication of a super-spreader form of the disease. It will be important to explore the evolution of the genome, in particular in terms of its G+C content (see our study). For the time being Chinese Health Authorities have fixed the containment level for studies of the virus to level 3 (BSL3). The risk of fatality among hospitalized cases is approximately 14%. The Wuhan authorities aim at building up a health facility for hundreds of patients within a week. Workers are paid three times their usual wage to build up this facility. 40 officers from the PLA with specialists in intensive care are now working in Wuhan. More to follow. The origin of the virus remains an enigma (see how things unfolded during the SARS episode in 2003).

note According to the FAO the current desert locust situation is extremely alarming and represents an unprecedented threat to food security in the Horn of Africa. In addition, important swarms continue to form along both sides of the Red Sea, in Oman and in southern Iran. Important earthquake in East Turkey.
arrow 23 january 2020. The city of Wuhan - including the close city of Huanggang, then Ezhou, Chibi, Xiantao, Qianjiang, Zhijiang and Lichuan - are quarantined. However it seems obvious that preventing movements from a city of 11 million people is not really possible.
The Year of the Golden Rat begins in two days time. This will be marked by huge movements of population within China and worldwide as well. However many celebrations are cancelled throughout China. Some people even try—and succeed—to avoid detection at temperature control at airports, which should be severely punished. A person with this profile has arrived in France, and can therefore be considered as a suspect case. It can thus be predicted that the present epidemic will develop further and likely become a pandemic. It is therefore essential that development of a vaccine is rapidly undergoing. It can be noticed that Wuhan is the place in China of a maximum confinement laboratory (P4, in the Jiangxia district), that was put into operation just one year ago, so that proper facilities should be available locally. At this time there have been 647 cases (634 cases in mainland China) and 18 deaths, 17 in Wuhan and one in the Hebei province. The figures are increasing at a steady pace. A first case is diagnosed in Singapore. Proper updates are now found at the Centre for Health Protection in Hong Kong.
arrow 22 january 2020. First case of Wuhan-nCoV in Hong Kong, 106 suspected cases.
Furious guests leave the hotel in Tsim Sha Tsui where the patient with the first case in Hong Kong stayed. Note that this is a very dangerous attitude as panic is the best way to propagate the disease. The SARS epidemic was stopped after strict quarantine measures were established. A fourth patient dies in Wuhan, triggering fear of emergence of a 'super-spreader' form of the virus. More suspected cases are reported in Shanghai, Qingdao, Chengdu and the provinces of Yunnan and Guangxi. This indicates that a large part of China is likely contaminated. Many people who got infected are now discharged from hospital, indicating that they are protected against the disease, showing that vaccination will be possible (but this ask for significant time).
arrow 21 january 2020. A possible case of Wuhan-CoV infection in Australia, one in Taiwan, one in the USA, more than 300 cases in China and six deaths, and 15 health personnel affected in Wuhan.
The origin of the disease is puzzling, but it is now established that it is contagious from person to person. The most curious feature is that it comes from a seafood market in Wuhan. Yet mollusks concentrate bacteria and viruses, and certain coronavirus infect the gut. A shift in tropism from gut to lung as in the swine epidemic of 1984 (in French) may open up an explanation for this new epidemic.
arrow 20 january 2020. The Wuhan-CoV seems to be spreading right before the Lunar Year Festival.
The authorities in Hong Kong provide a validated information about WuhanCoV. Statistics are about 24 h late but fairly accurate (discontinued). The total number of cases is now 198, 136 new cases over the week end with three deaths. Two patients are identified in Beijing. Many more suspected cases, with quarantine for five in the province of Zhejiang and eight in Shenzhen. South Korea reports first case.
arrow 19 january 2020. At least three patients (two in quarantine) in Shenzhen and one in Shanghai are suspected to be infected with Wuhan-CoV.
The total number of cases in Wuhan is now at least 62, eight in serious condition. In Hong Kong at least 90 persons are monitored for related pneumonia. People in China begin to be worried, as seen on Weibo, China's Twitter equivalent: “all the information we see has been filtered […] the real situation could be worse”; “How infectious the virus is, how serious it is and if it can spread from person to person – the poster [displayed by health authorities] just keeps people guessing”. People are adviced, just for sake of protecting themselves, to wear masks, wash their hands often and avoid crowded places.
arrow 18 january 2020. The Wuhan n-coronavirus may have spread much more than expected.
The total number of cases in Wuhan is 45, but the real number may have been much higher. Thailand confirmed a second case in a 74-old Chinese coming from Wuhan. The morbidity and letality of the virus being at this time significantly lower than that of SARS or MERS coronaviruses the importance of the disease might have been overlooked.
arrow 17 january 2020. While a second death marks the outbreak of the novel pneumonia coronavirus discovered in Wuhan, Hong Kong Health Authorities closed the poultry market for poultry coming from Poland.
Second death due to a novel coronavirus in  Wuhan and a first case in Japan. Person to person contagion seems possible. In parallel, animal flu caused by virus H5N8 spreads in many breeding centers in Poland and Hungary. HK authorities suspend import from these countries.
arrow 11 january 2020. The sequences of the coronavirus identified in Wuhan have been deposited at the GISAID.
First death due to this atypical pneumonia. Seven person, with two boys aged eight and 13, a 10-year-old girl, a man and three women, aged 38 to 67, returning to Hong Kong from Wuhan where they were in the past two weeks developed fever, respiratory infection or pneumonia symptoms, prompting more proactive measures.
arrow 9 january 2020. A coronavirus is identified in 15 among 59 patients affected by pneumonia in Wuhan.
The Wuhan based mysterious pneumonia is still active. Fortunately it did not causes deaths at this point. The origin of the novel coronavirus is still under investigation.
arrow 5 january 2020. The pneumonia outbreak in Wuhan unfolds in a way similar to what happened with SARS in 2002-2003.
Airports in China monitor the temperature of passengers coming from Wuhan. Hong Kong raised its response to outbreaks to the « serious » level, while a child in Singapore who came from Wuhan has severe pneumonia symptoms. As was the case with SARS, many different viruses were suspected, but subsequently found negative.
arrow 1 january 2020. Pneumonia outbreak in Wuhan, China.
An outbreak of atypical pneumonia affects the city of Wuhan. Health authorities and the WHO are monitoring the situation carefully as the pathogenic agent, possibly a virus, might be linked to consumption of wild animal meat.
arrow 27 december 2019. More than 200 scientists get infected by Brucella in China.
Lanzhou Biopharmaceutical Plant, in the Gansu province, did not properly decontaminate their premises while making its Brucella vaccines. People working at Lanzhou Veterinary Research Institute, downwind from the factory, developed antibodies from breathing in waste air in July and August, demonstrating that they got contaminated by the pathogen.
arrow 20 october 2019. A new class of viruses is found in the human respiratory tract.
A family of small circular DNA viruses—Redondoviridae—seem to be associated with human diseases. These small circular DNA viruses have only been found in human samples, mostly from respiratory tract and oro-pharyngeal sites, where they are the second most prevalent eukaryotic DNA virus family, associated with periodontal disease, and often in critically ill patients.
arrow 8 october 2019. A new dimorphic fungus is progressively spreading.
First identified in South Africa a new dimorphic fungus genus "Emergomyces" has been detected in many countries, including in Europe. We can note that the nomenclature does not follow good scientific rules (mixing up Latin and Greek),  reflecting a general spread of ignorance. The genus name should be Anadyomyces.
arrow 6 august 2019. Dogs as sentinels for Filovirus infections.
A study of the serum of dogs in regions infected with the Ebola virus has detected a high prevalence of Filovirus antibodies in dogs. Whether dogs can spread the disease is not yet known.
arrow 3 august 2019. The East maritime Arctic road is open.
As is now common observation the Arctic maritime road is open North of Russia. open-route
This coincides this year with huge fires in Siberia, melting of permafrost and a serious heatwave in western Europe.
arrow 25 january 2019. The H1N1 flu virus is at the origin of narcolepsy. 
The origin of narcolepsy, which leads to the uncontrolled onset of sleep, is now understood. It is an autoimmune disease that occurs in a part of the population (carrying a specific HLA marker). It appears as a result of infection by a flu virus strain, strain H1N1, now quite widespread. Since vaccination is not very effective the vaccine does not seem to cause the disease (but it does not protect efficiently). If it were to be improved, the possibility of narcolepsy should be taken into account by selecting vaccine variants, and it would be useful to perform HLA typing of the at-risk population.
arrow 24 january 2019. Misinformation about bats as propagating diseases is driving down important populations of these animals
Our general anthropocentrism is often misleading. While bats harbour many viruses (as we do), some of which able to cross the species barrier does not imply that these extremely useful animals should be hunted down to very small populations. For the time being, perhaps the most worrying family of viruses is that of influenza. There, two (perhaps three) immune groups are really significant: H1, H3 (and H2). While the other groups may lead to dangerous diseases upon heavy infection (H5N1, H7N7, H7N9, H9N2...), they are in fact unlikely sources of pandemics. By contrast, we still should monitor carefully the H3 viruses that infect our pets (H3N8) in particular.