biodiversity
The observable effects of climate, habit, diet, and other causes, on length of life, have furnished the pretext for asserting its indefinite extension; and the sandy foundation on which the argument rests is that, because the limit of human life is undefined, because you cannot mark its precise term, and say so far exactly shall it go no further, that therefore its extent may increase for ever, and be properly termed indefinite or unlimited.

An Essay on the Principle of Population
Thomas MALTHUS


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The course of COVID-19 in 2022, then a monkeypox outbreak


Because people tend to group indoors when it is cold or it rains COVID-19 is sensitive to climate
meteoblue

This page was initiated in Hong Kong in year 2000, when blogs did not exist yet, at the HKU-Pasteur Research Centre Ltd, established by Antoine Danchin. It does not compete with information provided by news agencies such as Agence France Presse or Reuters but selects information occasionally not discovered by the mainstream media. It also provides information on the History of Science and the creation of concepts used by modern biology. Access to the very nature of Science is discussed in a lecture given at Zhong Shan University (中山大學) in Guangzhou (广州). You can also follow our E-seminar for ongoing open discussions. Finally, the importance of China is stressed: the Western world is so dominant in its control of the mass media that it seems a necessity.

Many sites provide interesting information about the seasonal flu (type A H3N2 in particular), avian flu (H5N1) and swine influenza A (H1N1). Crawford Kilian's blog, which has now expanded to cover all sorts of other diseases and keeps a close eye on the Web, is highly recommended. The Center for Infectious Disease Research Policy (CIDRAP), University of Minnesota and the World Health Organization (WHO) websites are major sources of information. In contrast to the situation 10 years ago, when little information was available, there are now a multitude of data sources. We provide here only updated supplementary information. For H7N9 and H9N2 influenza, see the Hong Kong Health Authorities alerts. In general, new emerging pathogens are mainly viruses. Note that among the possible outbreaks that would have negative consequences (far more than the perhaps relatively benign COVID-19 episode, but which would have negative consequences as it progressed) are influenza outbreaks, particularly those related to the H2 serotype H2N2, which could be far more deadly. Let us hope that, unlike SARS, the current epidemic will have served as a lesson.

Continuous update of infection by the 2019-nCoV (from Johns Hopkins CCSE)

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

mobile-arrow General daily update
mobile-arrow Death rate analysis
mobile-arrow Forecast of the number of cases

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arrow 24 June 2022. With significant latency in reporting, the number of cases of the misnamed monkeypox now exceeds 5000 outside Africa.
The disease, which is only contagious through direct contact or a contaminated environment, mainly affects rodents in Africa. If the number of cases continues to rise elsewhere, it is feared that it will create an animal reservoir and become endemic in the areas where it has spread.
flu-covid

It currently exists in two forms, of different severity, and it is the less severe form that is spreading. Once the number of cases has increased significantly, it will explore other variants, possibly much more contagious and severe. Moreover, while, so far, the vast majority of infected people are men, a few female cases show that, as expected, the general public is susceptible to the disease. The number of cases is currently doubling every 10 days. Vaccination against smallpox provides some protection, but it was discontinued after 1972 almost everywhere in the world, so that people born before that date are less likely to develop the disease.
arrow 17 June 2022. North Korea reports an outbreak of a gastrointestinal disease in a southern city of the country.
The origin of the disease is not known, but it appears serious enough to have been noticed by authorities. As the tropism of sarbecoviruses (the family that comprises SARS-CoV-2) is prone to change tropism from lung to gut and vice versa this is a matter of concern and should be investigated carefully. Indeed, we should remember that the benign lung disease of pigs that prevailed for decades has transformed into SADS (Swine Acute Diarrhea Syndrome), a highly lethal disease with a gut tropism, only a few years ago.
arrow 8 June 2022. Dengue alert in Singapore.
And it is confirmed that COVID-19 is far more dangerous for children than influenza.
flu-covid

Singapore's health authorities are facing a dengue epidemic that far exceeds the epidemic that affected the entire year 2021. The disease is gradually spreading throughout the inter-tropical zone and is beginning to threaten temperate zones. The COVID pandemic is continuing with a slight rebound, and initial epidemiological analyses show that, contrary to the general impression due to the fact that the elderly are severely affected, the disease can be very serious in children. The number of reported cases of monkeypox worldwide exceeds 1,000, with over 300 cases in the UK.
arrow 3 June 2022. The synthetic RNAs used for the construction of vaccines against COVID-19 are remarkable examples of Synthetic Biology.
Among the many targets of Synthetic Biology, which aims at reconstructing life from scratch is the change of the chemical substrates of the genetic program, DNA or RNA molecules. This constitutes the field of « xenobiology ». We remarked some time ago that the RNA used as a translatable mimic in RNA vaccine was synthetic, assuming at the time that it used pseudouridine instead of uridine in its make up.
methyl-pseudouridine
The exact nature of the substitution is now known, it is not pseudouridine, but a nucleoside farther away from uridine, N1-methyl-pseudouridine! Hence the new vaccines that have helped us limit the lethal consequences of COVID-19 are a remarkable illustration of the power of Synthetic Biology. This nucleoside is not totally absent from life. It is present in rare species belonging to the domain of Archaea. In the genus Ignicoccus this modification replaces the usual modification of a thymidine residue (this is as such unusual because RNAs normally comprise uridine, not thymidine, but omnipresent in transfer RNAs) of a stem-loop structure that also usually contains a pseudoruridine, the T-loop of tRNA  — often with the sequence T PseU C G. It is also present in the ribosomal RNA of the small subunit of the ribosomes, under the action of an enzyme coded by the EMG1 gene in man.
arrow 21 May 2022. Against the backdrop of the resurgence of a more contagious but slightly more benign COVID-19, two contagious diseases are emerging.
North Korea has reported more than 200,000 new patients with « fever » for a fifth consecutive day, as it continues to battle its first confirmed outbreak of SARS-CoV-2. With the country refusing to vaccinate, the death toll is likely to be significant, but little is known about it. In Indonesia, an outbreak of acute or severe hepatitis of unknown origin in children began to cause worldwide concern in April. Today, at least 169 cases have been reported in 12 countries: the UK, Spain, Israel, the US, Denmark, Ireland, the Netherlands, Italy, Norway, France, Romania and Belgium. More than 70 cases from 13 countries are being tested and verified, and the World Health Organisation (WHO) has identified about 450 probable cases of the mystery disease in 20 countries. Indonesia, Malaysia and Singapore are awaiting official confirmation of acute hepatitis after a number of young children fell ill or died. Meanwhile, monkeypox, a known smallpox-like disease endemic to central Africa, is spreading, with a pattern very similar to that seen in the early days of AIDS, mainly infecting male homosexuals.
arrow 27 April 2022. A first case of human influenza H3N8 in a four-year-old boy is reported in Hunan province, China.
For years, we have said that the H3N8 variant of the influenza virus should be closely monitored. This virus is commonly found as a pathogen for dogs and horses, and has killed dozens of seals on several occasions. The very fact that it affects mammals in close contact with people is worrying. China continues to fight the COVID-19 outbreak in Shanghai and other cities and reports the first deaths after a long period.
arrow 19 April 2022. A top expert in epidemiology in China publishes that a zero-COVID policy is not sustainable.
In an editorial of the journal National Science Review well-known authorities propose Strategies for reopening in the forthcoming COVID-19 era in China, where they suggest that a zero-COVID policy may be disastrous. Initially translated into Chinese and available on social networks the article has since been deleted.
arrow 16 April 2022. Although the Shanghai authorities are not recording COVID-related deaths, this is unlikely.
The number of COVID-19 cases in Shanghai is increasing, with more and more cases becoming symptomatic. Health authorities have not recorded any deaths related to the outbreak, but this contradicts an apparent increase in the mortality rate of the elderly in the city. A correction in death figures can be expected in the coming weeks.
arrow 5 April 2022. As of today morning, Shanghai has the highest SARS-CoV-2 infection rate since the start of the pandemic.
On Tuesday, 13,354 new COVID-19 infections were recorded in Shanghai, bringing the number of cases nationwide to a record high since the outbreak of the disease, which explains why authorities in China's commercial hub are in no hurry to lift the city's lockdown. Authorities have maintained the lockdown in the city of 25 million people after mass tests revealed 73,000 infections since March 1. The local government reversed plans to lift the lockdown of Puxi on Tuesday. The vast majority of cases are asymptomatic.
France has by far the worst management of the disease among European countries, with an infection rate well above steady state (R0 ~1.12). As a result, hospitalisations  and deaths are increasing.
arrow 31 March 2022. Panicked Russian soldiers flee from Chernobyl.
According to the South China Morning Post, Russian troops began leaving the Chernobyl nuclear plant after soldiers got “significant doses” of radiation from digging trenches at the highly contaminated site, Ukraine’s state power company said Thursday as heavy fighting raged on the outskirts of Kyiv and other fronts. Energoatom, the operator, gave no immediate details on the condition of the troops or how many were affected. But it said the Russians had dug in in the forest inside the exclusion zone around the now-closed plant, the site in 1986 of the world’s worst nuclear disaster. The troops “panicked at the first sign of illness,” which “showed up very quickly”, and began to prepare to leave, Energoatom said.
arrow 11 March 2022. The COVID-19 epidemic is coming back in Europe while China gets more that 1,000 cases..
China reports its highest daily Covid-19 case count since its first national outbreak in 2020, with more than 1,000 locally acquired coronavirus cases detected on Thursday.
resurgence
Knowing how the epidemic develops in Hong Kong, it will be important to witness the way China reacts and tries to keep its zero COVID policy.

arrow 6 March 2022. Hong Kong failed to properly vaccinate its elderly population and the number of COVID-19 related deaths is soaring.
Less than 50% or the people aged 70 or older have been double vaccinated in Hong Kong. This is totally incompatible with a zero-COVID policy. This makes the city a dangerous hot spot for mainland China as any serious leakage from the city would lead to an uncontrolled situation there. Again, it is surprising that no information on the epidemic is coming out of the war in Ukraine. Soldiers are young, but the sheer density of troops, especially in cold weather suggests that there should be outbreaks there.
arrow 3 March 2022. The explosion of SARS-CoV-19 cases in Hong Kong is overloading its public hospitals.
As the Hong Kong authorities introduce mandatory SARS-CoV-2 testing for its entire population, the disease, which infects more than 30,000 people every day, is saturating public hospitals. Many residential areas are locked down. In this context, the war in Ukraine raises a question: crowded groups of soldiers are ideal places for the spread of infection. Do we have any idea what is happening to the Ukrainian population and the invading armies?
arrow 18 February 2022. Climate is a major drive of COVID-19 spread.
An Italian study explored the pattern of COVID-19 development and concludes that climate factors have a major impact. Temperature, humidity and UV indexes play a key role. This should be taken into account by health authorities to implement relevant policies. This suggests that the next few months should see a considerable attenuation of the epidemic, with a likely resurgence, possibly of a milder form, in the autumn in the Northern Hemisphere.
arrow 12 February 2022. COVID-19 is back with a vengeance in Hong Kong.
Hong Kong health authorities report a record 1,514 infections, 3 additional deaths and over 1,500 suspected cases. This shows that maintaining a zero COVID policy will be extremely difficult, and probably impossible in the medium term in China.
arrow 5 February 2022. Two villages on Java island are declared red zones, with livestock movement banned from the area after the deaths of several farm animals from anthrax.
Anthrax is caused by Bacillus anth­racis bacteria which are naturally found in soil and commonly affect animals that breathe in or ingest spores in contaminated soil, plants or water. It has been proposed as a biowarfare agent based on aerosols loaded with the bacteria spores, but it is not directly contagious from animal to person or person to person. It can be prevented in animals via regular vaccination. It can cause severe illness in both humans and animals, including skin blisters and black lesions (hence its name) that can become ulcerated and infected leading to swollen lymph nodes. If left untreated it can be fatal. Direct infection of the lungs is letal.
arrow 30 January 2022. The letality and morbidity of variant omicron can now be evaluated.
Variant omicron is certainly less dangerous than previous variants.However this observation must be placed in the context of vaccination.
before omicron
Indeed, the global mortality curve following the global invasion of this variant still shows an increase despite the high level of vaccination now known to protect against the most severe forms of the disease. Mortality has not yet reached its peak. Three main scenarios are to be expected: 1/ evolution of the virus towards a progressively attenuated highly contagious variant; 2/ evolution towards a more benign form but present for a long time in infected persons, or 3/ change of tropism of the virus, passing from the lung to the digestive tract. Hypothesis 1/ is the most desirable, as the infection would produce its own vaccine effect. However, as the infected population is huge it is likely that the disease would become endemic, as is influenza, with different variants each year. Hypothesis 2/ could have serious consequences for a part of the population, affected by long-lasting disorders (long COVID). Finally, hypothesis 3/ could lead to an extremely severe disease such as acute swine diarrhoea syndrome (SADS), often fatal. This is therefore what should be monitored continuously as a priority, in particular by analysing the forms present in wastewater.
arrow 13 January 2022. Variant omicron spreads like fire and reached China.
Central Henan province and Tianjin remain at the centre of the COVID-19 outbreak, with a total of 117 new cases in the two provinces on Thursday, while a city in the country's northeast reports its first infection with the omicron variant. Authorities in Henan province reported 76 new cases on Thursday, up from 118 the previous day, while the northern port city of Tianjin reported 41 new cases, up from 33 on Wednesday. While 40 of the new infections were detected in one district alone, the origin of the outbreak is still unknown. But the chain of transmission is clear, according to the local authorities, which still allows the "zero COVID" procedure to be applied.
arrow 6 January 2022. Several clusters of COVID-19 appear in China, including in Hong Kong.
China seems to be struggling to contain new outbreaks of COVID-19. The "zero COVID" policy reaches its limits. After more than two weeks of strict lockdown in Xi'an, several other large cities have also been submitted to this fierce rule. In Hong Kong it is suspected that a guest participating in a birthday party was infected by variant omicron. Several officials, tied with the Mainland, were present and are now quarantined. In parallel, a Hong Kong ship that left for a 'cruise to nowhere' is ordered to return back to port to test its passengers.
arrow 1 January 2022. A severe bird flu outbreak is affecting Europe.
675 influenza outbreaks in wild birds and 534 in poultry have been reported in Europe between the beginning of October and December 29, according to the Friedrich Loeffler Institute (FLI), Germany’s leading animal disease centre. Additional cases have also been detected in mammals, such as foxes in the Netherlands and Finland, grey seals in Sweden, harbour seals in Germany and otters in Finland. This is mainly due to the H5N1 virus, but there are also human infections with the H5N6 and H9N2 strains of the virus. The standard strains affecting people (H3N2 and H1N1) have also made a comeback.