Clouds of witness
Dorothy L. SAYERS
COVID-19 in 2022, then a monkeypox outbreak
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|30 December 2022. After
a 180° turn from its "zero-Covid" policy, China no longer
reports on Covid cases.
As has been widely reported, China suddenly stopped its "zero Covid" policy after witnessing unrest in several major cities. This triggered an upsurge in cases. Unfortunately, the authorities do not seem to be able to control the situation and do not report the nature of the emerging variants. It is only indirectly, and often by hearsay, that the world is aware of the situation. A random sampling of air travelers suggests that at least half of the population of major cities is or has been infected with the virus.
|17 December 2022. Details
of the origin of SARS-CoV-2 begin to emerge.
The COVID-19 etiological agent is a mix of several pieces that must have come from several viruses or artificially created nucleic acid sequences. The body of the virus genome is highly related to viruses that are found in caves in Laos and presumably in caves of the Yunnan province in China. The corresponding sequence from isolates collected by the Laos Institute Pasteur headed by Paul Brey in Vientiane spans the whole virus genome. It just misses a short RNA sequence that codes for a region of the spike protein which allows it to bind to its ACE2 receptor in human cells, and to enter them, starting the infection. This sequence is highly unusual, not only because it is exquisitely poised to infect human cells, but also because it codes for two arginine residues encoded by the rarest arginine codon (CGG) in the virus. Associated to epidemiological analyses this led the Senate of the USA to write a report suggesting that the virus is the result of an accident caused by an experiment of "gain of function" developed in low safety laboratories in Wuhan. This plausible conjecture is now further supported by the observation that the "parent" viruses from Laos infect the gut of bats, not their respiratory tract. It is only after the furin site has been introduced in the virus that it must have got its lung tropism. These observations are very important if we consider the future evolution of the virus. Indeed, while insertions are fairly rare events, deletions are very frequent and deletion of the furin region of SARS-CoV-2 would likely change its tropism to our gut, with possibly very dangerous consequences, as observed with the epidemic of SADS in pigs in recent years.
|20 November 2022. China
reports its first Covid-19 death in six months.
According to the Beijing Daily a 87-year-old man died in Beijing on Saturday. He was sick with the disease for a few days and then passed away from multiple organs failure. This happens as the country battles its worst outbreak for half a year and may mark a turning point in the spread of the disease in China.
|3 November 2022. Thousands
of fire ants, including four queens, were discovered in a
container at the port of Fukuyama port Japan.
The discovery of fire ants Solenopsis geminata in a container shipped from Vietnam and transiting through Hong Kong has reinforced the need for strict policies and constant vigilance to keep the invasive species from becoming established. More than 10,000 ants, including at least four queens, were discovered after a worker opened a container unloaded at the port of Fukuyama in Hiroshima Prefecture and then transported by road to Ibara in neighbouring Okayama Prefecture.
|29 October 2022. A
serious cholera epidemic is affecting Haiti.
At least 40 deaths and 1,700 suspected cases have been reported, but the numbers are likely to be much higher, in slums and crowded public shelters. Health officials say patients are dying because they cannot reach a hospital in time. The crisis is exacerbated by rising gang violence and a lack of fuel and clean water. The cholera bacillus is only contagious from highly polluted water or food, and the disease is treatable if patients are treated with effective intravenous rehydration, but this requires sufficient medical infrastructure.
|3 September 2022. Both
arctic sailing routes from Europe to Japan are open.
As happens more and more frequently western and eastern sailing routes to Japan are open
|26 August 2022. An
unexpected role of alcohol in plant resistance to drought.
This year is witnessing a severe drought situation worldwide. A lack of available water limits plant growth and photosynthetic capabilities, resulting in decreased crop yield and any type of remediation would be welcome. In plants, tiny holes in leaves, stomata regulate gaseous exchange, in particular evaporating water. Curiously, ethanol is produced under drought conditions and a study just appeared that showed protection against drought for plants spread with a limited amount of ethanol. Whether this can be extrapolated to fields remains to be seen, but if successful this would be a fast way to help plants to resist drought, for a minimal cost.
|11 August 2022. An
accumulation of observations suggests that the benefits of the
synthetic RNA vaccine against COVID-19 fades rapidly, even
after booster injections.
It is now proposed that mixing vaccine types has a much more effective long-term effect. Health authorities need to take this into account before the next wave of infections that may develop this fall. Vaccination is very important at a time when polio is re-emerging in countries where vaccination compliance has declined.
Monkeypox is slowing down in several countries but exploding in the United States. This is worrisome because the likelihood of the virus mutating into a more contagious form increases with the global viral load.
|10 July 2022. The
number of monkey pox cases reached 10,000 out of Africa.
Given the latency of case registration, it appears that the number of monkeypox cases has certainly doubled since 24 June. The European Centre for Disease Prevention and Control (ECDC) has published the first update of its rapid risk assessment on the outbreak, indicating that the likelihood of the disease spreading among people with multiple sexual partners in Europe is high, but the risk to the general population is very low. As with the origin of AIDS, superspreaders create multiple clusters, which will make it more difficult to control the disease. Monkeypox is not a sexually transmitted disease (it is spread by any type of close contact) and is more contagious than AIDS, which means that if it reaches the general population, it will be more difficult to contain. Fortunately, the smallpox vaccine is effective in preventing the spread of the infection. The US Department of Health and Human Services (HHS) announced on Thursday that it would distribute 144,000 doses of the two-dose Jynneos vaccine, approved for monkeypox and smallpox, to cities and states starting Monday to address the outbreak. These doses are in addition to the 56,000 doses the ministry made available last week, of which 41,000 have been delivered.
On the Covid-19 front, the new BA.2.75 variant, also known as Centaur, could well take hold and keep the epidemic active until this winter. Until the next one. The new BA.2.75 variant appeared in India. It has been found in at least 70 positive test sequences in the last few days, indicating the spread of a new lineage of Covid. This variant is in fact a new version of the Omicron BA.2 variant, which is currently dominating in Europe and driving the epidemic forward.
|8 July 2022. A
severe outbreak of foot and mouth disease is affecting
The outbreak, which began in May, is spreading fast. It has spread throughout the country's main islands Sumatra, Java, Borneo, the island-province Bangka-Belitung and the island Lombok of the province West Nusa Tenggara. As the epidemic now reached Bali, Australian health authorities are concerned because of the important number of their citizens taking holidays in Indonesia.
|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.
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.
|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.
|8 June 2022. Dengue
alert in Singapore.
And it is confirmed that COVID-19 is far more dangerous for children than influenza.
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.
|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.
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.
|21 May 2022. Against
the backdrop of the resurgence of a more contagious but
slightly more benign COVID-19, two contagious diseases are
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.
|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.
|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.
|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.
|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.
|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.
|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.
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.
|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.
|3 March 2022. The
explosion of SARS-CoV-19 cases in Hong Kong is overloading its
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?
|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.
|12 February 2022. COVID-19
is back with a vengeance in Hong
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.
|5 February 2022. Two
villages on Java island are declared red zones, with livestock
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.
|30 January 2022. The
letality and morbidity of variant omicron can now be
Variant omicron is certainly less dangerous than previous variants.However this observation must be placed in the context of vaccination.
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.
|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.
|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.
|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.
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