H5N1

‘It was all for nothing’: Chinese count cost of Xi’s snap decision to let Covid rip

Via The Guardian: ‘It was all for nothing’: Chinese count cost of Xi’s snap decision to let Covid rip | Coronavirus. Excerpt:

When Sunny[not her name] thinks back to March last year, she laughs ruefully at the ordeal. The 19-year-old Shanghai student spent that month locked in her dormitory, unable to shop for essentials or wash clothes, even banned from showering for two weeks over Covid fears. In April, the entire city locked down.  

It was the beginning of the chaos of 2022, as local Chinese authorities desperately tried to follow President Xi Jinping’s zero-Covid decree while facing the most virulent strain of the virus yet: Omicron. “Everyone was panicking, no one was ready,” she tells the Observer.  

By the end of the year, zero-Covid was gone. Sunny says she felt instantly “relieved” that lockdowns were over but her feelings soon turned to anger as it became clear China’s government had opened up the country, knowing it wasn’t ready. “I felt it was all for nothing,” Sunny says.  

Over the last two months, the virus has rapidly spread through the country. Up to 10,000 critical cases were registered in hospitals every day. Morgues were overwhelmed, pharmacies reported shortages of basic medications, and supply of antiviral drugs was held up by protracted negotiations with foreign suppliers. Online and in the streets, people spoke of almost everyone they knew having caught Covid, and of elderly relatives dying.  

Sunny’s grandfather was among those who died in that wave. “It was the morning, and my mum walked into my room and said: your grandpa is in the emergency room,” she recalls. “A few hours later, he passed away. My grandmother was in tears, saying he had left her behind.”  

Xi’s extraordinary backflip left analysts alarmed and confused. China was not the only country to choose a zero-Covid strategy, and certainly not the only one to “let it rip” once it dropped it. But it was the last, and global health experts say there were plenty of lessons it could have heeded – primarily, making sure vaccinations and health resources were high before the tsunami of cases hit.  

“All governments had to decide to open up at some stage or risk the consequences of lockdowns far outweighing the problems of Covid,” says Professor Emma McBryde, an epidemiologist at James Cook University, Townsville, Queensland, Australia. 

 “Most models suggest that it would be better for the health system to open up slowly. Although there would be little change in how many people get infected, it could mean some lives are saved if the health system can function well.”  

But Xi threw the gates open. Right up until the day of repeal, local governments were still developing and enforcing zero-Covid measures and infrastructure. The city of Chongqing was building a 21,000-bed quarantine centre.  

Experts on health and Chinese politics have told the Observer they believe the local authorities were hamstrung. Any preparations for ending zero-Covid would be seen as a vote of no confidence in both the policy and Xi – an act of political suicide.

China is flying blind as pandemic rages

Via Science: China is flying blind as pandemic rages. Excerpt:

Most scientists believe China’s decision to end its zero-COVID policy was long overdue. But now they have a new worry: that the country is collecting and sharing far too little data about the rough transition to a new coexistence with the virus.  

China abruptly dropped virtually all controls a month ago, after protests, a sagging economy, and the extreme transmissibility of the virus’ latest variants made clinging to zero COVID untenable. Now, “SARS-CoV-2 has an open goal in front of it: a population with very low levels of standing immunity,” says evolutionary biologist Edward Holmes of the University of Sydney. But how the epidemic is unfolding is a mystery because the country has practically stopped collecting basic epidemiological data.  

Models that predicted a massive wave of infection and death if China ended zero COVID appear to have been correct. Press reports and social media posts have shown intensive care units stretched beyond capacity, with crowds of patients in wheelchairs and on gurneys in hallways. Doctors and nurses are reportedly working while sick. Crematoriums are overwhelmed. 

But China’s official COVID-19 death toll is widely considered laughably low. And some scientists worry a genomic monitoring plan unveiled last month doesn’t have the power to detect new SARS-CoV-2 variants arising as the virus works its way through one-fifth of the world population.

Earlier in the pandemic China’s daily counts of COVID-19 cases and deaths, based partly on its exhaustive testing programs, were generally believed to be accurate. Now, they are anyone’s guess. Patients with mild symptoms are not encouraged to get tested, let alone those who are asymptomatic. People testing positive at home are not asked to report their results.  

The China Center for Disease Control and Prevention (China CDC) put the number of confirmed cases the last week of December 2022 at more than 35,000—a fraction of the official number in the United States. But leaked notes from an internal meeting suggest a very different reality: The agency was told that almost 250 million people in China—roughly 18% of the population—may have caught COVID-19 in the first 20 days of December. Some experts said the number is implausibly large, but Yanzhong Huang, a global health specialist at the Council on Foreign Relations, a U.S. think tank, says it’s “not unreasonable,” given credible reports that 80% of Beijing residents have been infected by now.  

As to the death toll, China’s reporting had long been inconsistent, Huang says, with some regions reporting all fatalities in which SARS-CoV-2 was a factor, as most countries do, and others excluding people who died from other conditions, such as heart attacks, even if they had COVID-19. In early December, China’s government decided the narrower definition should be used nationwide.  

Even then, the official count is astonishingly low: just eight deaths for the entire last week of December, which is “not matching media reports and what is being seen on social media,” says Louise Blair, who tracks China’s COVID-19 outbreak for Airfinity, a London-based health analytics firm that estimates about 9000 people were dying of COVID-19–related causes every day in late December.  

Also missing are data on case fatality rates, the average number of new infections stemming from each case, and hospital and intensive care admissions. “These are critical data” that would help health authorities get a handle on the surge and further the world’s understanding of the pandemic, says Xi Chen, a public health scientist at the Yale School of Public Health.

Up to 70% of Shanghai population infected with COVID-19: Top doctor

Via Channel NewsAsia: Up to 70% of Shanghai population infected with COVID-19: Top doctor. That means about 17.5 million people in Shanghai alone have COVID-19.

SHANGHAI: A senior doctor at one of Shanghai's top hospitals has said 70 per cent of the megacity's population may have been infected with COVID-19 during China's huge surge in cases, state media reported Tuesday (Jan 3).  

The steep rise in infections came after years of hardline restrictions were abruptly loosened last month with little warning or preparation, and quickly overwhelmed hospitals and crematoriums.  

Chen Erzhen, vice president at Ruijin Hospital and a member of Shanghai's COVID-19 expert advisory panel, estimated that the majority of the city's 25 million people may have been infected.  

"Now the spread of the epidemic in Shanghai is very wide, and it may have reached 70 per cent of the population, which is 20 to 30 times more than (in April and May)," he told Dajiangdong Studio, owned by the Communist Party mouthpiece People's Daily.  

Shanghai suffered a gruelling two-month lockdown from April, during which over 600,000 residents were infected and many were hauled to mass quarantine centres.  

But now, the Omicron variant is spreading rampantly across the city and experts predict infections there will peak in early 2023. In other major cities, including Beijing, Tianjin, Chongqing and Guangzhou, Chinese health officials have suggested that the wave has already peaked.  

In neighbouring Zhejiang province, disease control authorities said Tuesday that there had been one million new infections in recent days and that the province was entering a peak plateau for COVID-19.  

Chen added that his Shanghai hospital was seeing 1,600 emergency admissions daily - double the number prior to restrictions being lifted - with 80 per cent of them COVID-19 patients.  

"More than 100 ambulances arrive at the hospital every day," he was quoted as saying, adding that around half of emergency admissions were vulnerable people aged over 65.  

At Tongren Hospital in downtown Shanghai, AFP reporters saw patients receiving emergency medical attention outside the entrance of the overcrowded facility on Tuesday.  

The corridors overflowed with dozens of elderly patients lying on beds crammed together, hooked up to IV drips. Some patients wore oxygen masks attached to bedside canisters.

Impact of surge in China COVID-19 cases on epidemiological situation in EU/EEA

A news report from ECDC: Impact of surge in China COVID-19 cases on epidemiological situation in EU/EEA.

The number of COVID-19 cases has reached a record high in mainland China, peaking on 2 December 2022. In the past three weeks, incidence has fallen, likely also due to a lower number of tests being carried out, resulting in fewer infections being detected.  

ECDC, together with the EU/EEA Member States and the European Commission has increased its monitoring activities and will revise risk assessments and adjust actions if needed. ECDC is working closely with the World Health Organization (WHO)/Europe and WHO/Headquarters and is in regular contact with the Chinese Center for Disease Control and Prevention (China CDC) and major CDCs globally.  

ECDC continues to routinely monitor and report on emerging SARS-CoV-2 variant threats via its Strategic Analysis of Variants in Europe (SAVE) Working Group, where variants and epidemiological trends in countries neighbouring China as well as in the EU/EEA will continue to be evaluated.  

The number of COVID-19 cases has reached a record high in mainland China, peaking on 2 December 2022. In the past three weeks, incidence has fallen, likely also due to a lower number of tests being carried out, resulting in fewer infections being detected. There continues to be a lack of reliable data on COVID-19 cases, hospital admissions, deaths as well as Intensive Care Unit (ICU) capacity and occupancy in China.  

High levels of SARS-CoV-2 infections and increased pressure on healthcare services in China are expected in the coming weeks due to low population immunity and the relaxation of non-pharmaceutical interventions.  

China has started depositing SARS-CoV-2 sequences in GISAID EpiCoV[1] in higher numbers. From 1 to 30 December 2022, China has deposited 592 sequences, out of which 540 sequences were being deposited this week (from 25 December to 30 December 2022). As of 30 December 2022, of the total 592 sequences submitted from China, 437 had recent sample collection dates between 1 and 24 December 2022 in GISAID EpiCoV.  

These sequences mainly belonged to the lineages (including their sub-lineages) BA.5.2 (35%), BF.7 (24%), BQ.1 (18%), BA.2.75 (5%), XBB (4%), BA.2 (2%). In addition, from travel related cases, the variants BA.5.6, BA.4.6, BM.4.1.1 and BA.2.3.20 have also been detected to be circulating in China. No new variant has been detected.  

The variants circulating in China are already circulating in the EU, and as such are not challenging for the immune response of EU/EEA citizens. In addition, EU/EEA citizens have relatively high immunisation and vaccination levels.  

Given higher population immunity in the EU/EEA, as well as the prior emergence and subsequent replacement of variants currently circulating in China by other Omicron sub-lineages in the EU/EEA, a surge in cases in China is not expected to impact the COVID-19 epidemiological situation in the EU/EEA. This is based on the information available as of this week, and the ECDC assessment, as detailed in Communicable Diseases Threat Report of week 51, remains currently unchanged.

Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy

Via ScienceDirect, a report in Environmental Research that could change the origin story of SARS-CoV-2: Molecular evidence for SARS-CoV-2 in samples collected from patients with morbilliform eruptions since late 2019 in Lombardy, northern Italy. The abstract:

As a reference laboratory for measles and rubella surveillance in Lombardy, we evaluated the association between SARS-CoV-2 infection and measles-like syndromes, providing preliminary evidence for undetected early circulation of SARS-CoV-2. 

Overall, 435 samples from 156 cases were investigated. RNA from oropharyngeal swabs (N = 148) and urine (N = 141) was screened with four hemi-nested PCRs and molecular evidence for SARS-CoV-2 infection was found in 13 subjects. Two of the positive patients were from the pandemic period (2/12, 16.7%, March 2020–March 2021) and 11 were from the pre-pandemic period (11/44, 25%, August 2019–February 2020). 

Sera (N = 146) were tested for anti-SARS-CoV-2 IgG, IgM, and IgA antibodies. Five of the RNA-positive individuals also had detectable anti-SARS-CoV-2 antibodies. No strong evidence of infection was found in samples collected between August 2018 and July 2019 from 100 patients. 

The earliest sample with evidence of SARS-CoV-2 RNA was from September 12, 2019, and the positive patient was also positive for anti-SARS-CoV-2 antibodies (IgG and IgM). Mutations typical of B.1 strains previously reported to have emerged in January 2020 (C3037T, C14408T, and A23403G), were identified in samples collected as early as October 2019 in Lombardy. One of these mutations (C14408T) was also identified among sequences downloaded from public databases that were obtained by others from samples collected in Brazil in November 2019. 

We conclude that a SARS-CoV-2 progenitor capable of producing a measles-like syndrome may have emerged in late June-late July 2019 and that viruses with mutations characterizing B.1 strain may have been spreading globally before the first Wuhan outbreak. Our findings should be complemented by high-throughput sequencing to obtain additional sequence information. 

We highlight the importance of retrospective surveillance studies in understanding the early dynamics of COVID-19 spread and we encourage other groups to perform retrospective investigations to seek confirmatory proofs of early SARS-CoV-2 circulation.

Japan's daily COVID-19 tally hits record 250,000 cases

Via The Mainichi Shimbun: Japan's daily COVID-19 tally hits record 250,000 cases.

TOKYO (Kyodo) -- Japan's daily coronavirus tally soared to a record 250,403 cases on Wednesday, as Prime Minister Fumio Kishida's new Cabinet faces the challenge of tackling the seventh wave of the COVID-19 pandemic amid renewed concerns over a strain on the medical system.  

"We will move into a new phase toward" a life with COVID-19 without delay, Kishida said at a press conference after the new lineup for his Cabinet was announced the same day.  

Fueled by the highly transmissible Omicron BA.5 subvariant, Japan's new COVID-19 cases topped 250,000 for the first time, exceeding the previous record of around 249,800 on Aug. 3.  

New coronavirus cases had been increasing since June and in mid-July, the figure more than doubled from a week before. The number of deaths and of people suffering from severe conditions has also been quickly rising.  

Out of Japan's 47 prefectures, 20 reported a record number of cases on Wednesday, while Tokyo reported 34,243 cases and Osaka and Aichi prefectures saw 23,730 and 18,862 cases, respectively.

Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada

Via eLife: Genomic epidemiology of the first two waves of SARS-CoV-2 in Canada. The abstract:

Tracking the emergence and spread of SARS-CoV-2 lineages using phylogenetics has proven critical to inform the timing and stringency of COVID-19 public health interventions. We investigated the effectiveness of international travel restrictions at reducing SARS-CoV-2 importations and transmission in Canada in the first two waves of 2020 and early 2021. 

Maximum likelihood phylogenetic trees were used to infer viruses’ geographic origins, enabling identification of 2263 (95% confidence interval: 2159–2366) introductions, including 680 (658–703) Canadian sublineages, which are international introductions resulting in sampled Canadian descendants, and 1582 (1501–1663) singletons, introductions with no sampled descendants. 

Of the sublineages seeded during the first wave, 49% (46–52%) originated from the USA and were primarily introduced into Quebec (39%) and Ontario (36%), while in the second wave, the USA was still the predominant source (43%), alongside a larger contribution from India (16%) and the UK (7%). 

Following implementation of restrictions on the entry of foreign nationals on 21 March 2020, importations declined from 58.5 (50.4–66.5) sublineages per week to 10.3-fold (8.3–15.0) lower within 4 weeks. Despite the drastic reduction in viral importations following travel restrictions, newly seeded sublineages in summer and fall 2020 contributed to the persistence of COVID-19 cases in the second wave, highlighting the importance of sustained interventions to reduce transmission. Importations rebounded further in November, bringing newly emergent variants of concern (VOCs). 

By the end of February 2021, there had been an estimated 30 (19–41) B.1.1.7 sublineages imported into Canada, which increasingly displaced previously circulating sublineages by the end of the second wave. Although viral importations are nearly inevitable when global prevalence is high, with fewer importations there are fewer opportunities for novel variants to spark outbreaks or outcompete previously circulating lineages.

See also this CTV report on the study.

'Living with COVID': Where the pandemic could go next

Via Reuters: 'Living with COVID': Where the pandemic could go next. Excerpt:

LONDON/CHICAGO, Aug 1 (Reuters) - As the third winter of the coronavirus pandemic looms in the northern hemisphere, scientists are warning weary governments and populations alike to brace for more waves of COVID-19.  

In the United States alone, there could be up to a million infections a day this winter, Chris Murray, head of the Institute of Health Metrics and Evaluation (IHME), an independent modeling group at the University of Washington that has been tracking the pandemic, told Reuters. That would be around double the current daily tally.  

Across the United Kingdom and Europe, scientists predict a series of COVID waves, as people spend more time indoors during the colder months, this time with nearly no masking or social distancing restrictions in place.  

However, while cases may surge again in the coming months, deaths and hospitalizations are unlikely to rise with the same intensity, the experts said, helped by vaccination and booster drives, previous infection, milder variants and the availability of highly effective COVID treatments.  

"The people who are at greatest risk are those who have never seen the virus, and there's almost nobody left," said Murray.  

These forecasts raise new questions about when countries will move out of the COVID emergency phase and into a state of endemic disease, where communities with high vaccination rates see smaller outbreaks, possibly on a seasonal basis.  

Many experts had predicted that transition would begin in early 2022, but the arrival of the highly mutated Omicron variant of coronavirus disrupted those expectations.

"We need to set aside the idea of 'is the pandemic over?'" said Adam Kucharski, an epidemiologist at the London School of Hygiene and Tropical Medicine. He and others see COVID morphing into an endemic threat that still causes a high burden of disease.  

"Someone once told me the definition of endemicity is that life just gets a bit worse," he added.  

The potential wild card remains whether a new variant will emerge that out-competes currently dominant Omicron subvariants.  

If that variant also causes more severe disease and is better able to evade prior immunity, that would be the "worst-case scenario," according to a recent World Health Organization (WHO) Europe report.

COVID-19 cases in Japan top 200,000 for first time

Case counts up to July 22.

The surge in Japanese COVID cases has been sudden and alarming. Via The Japan Times: COVID-19 cases in Japan top 200,000 for first time. Excerpt:

Japan reported more than 200,000 new COVID-19 cases for the first time Saturday, shattering the daily record for the fourth straight day with 200,954 infections amid a seventh wave of infections driven by the BA.5 omicron subvariant.  

Single-day record caseloads were reported in 17 of the country's 47 prefectures, including Tokyo, which posted a daily figure above 30,000 for the third day in a row.  

The number of patients with severe symptoms rose by 12 from Friday to 203 across the country, the first figure at 200 or higher in three months, according to the health ministry. New deaths totaled 72, including nine each in Kanagawa, Osaka and Kumamoto prefectures.  

In Tokyo on Saturday, medical staff and elderly care workers also began receiving their fourth COVID-19 vaccinations after the government expanded its eligibility criteria in response to Japan's seventh wave of infections.  

Last week's decision to begin the vaccinations was aimed at ensuring enough medical and care workers are available when Japan is seeing record numbers of new cases driven by the BA.5 strain.  

Some medical institutions in the capital have been forced to limit the number of emergency patients they accept and scale back surgical procedures they conduct due to staff shortages caused by a spate of COVID-19 infections.  

Previously, the fourth dose was only available to people aged 60 and over and those between 18 and 59 with pre-existing conditions who are considered at higher risk of developing severe symptoms when infected with the virus.  

A study shows the fourth inoculation has relative efficacy for elderly people but may only provide marginal protection for younger people.  

The fourth vaccination is available at three mass vaccination sites, including the Tokyo Metropolitan Government building, for residents of the capital or people who commute into the city.  

A panel of health experts working under the health ministry said Friday fourth shots are effective to some extent in preventing the spread of the subvariant, citing clinical data.  

In the capital on Saturday, the daily count totaled 32,698 new cases, growing by 13,779 from a week before.  

The seven-day average of new infections rose to 23,068, the metropolitan government said. Seven deaths were reported.  

The number of coronavirus patients with severe symptoms under the metropolitan government's criteria came to 14, falling by one from the previous day.

Is the Covid pandemic finally nearing its end?

In The Guardian, Aris Katzourakis writes: Is the Covid pandemic finally nearing its end? Excerpt:

More than two years on from the realisation that we are dealing with a novel pandemic, we are still nervously wondering what comes next. In the UK, Covid infection rates appear to have fallen to their lowest level since the summer of 2021, as has the number of deaths the virus is causing, but we know that new variants are still likely to emerge. So when will the end of this pandemic come, and what might it look like?  

This is a very difficult question, because we won’t know we have passed the end of the pandemic until some time has elapsed. The expectation is that eventually the disease will reach endemic levels, meaning immunity in the population will balance out the reproduction of the virus, resulting in a stable level of infection year on year. That stability could include regular, repeatable fluctuations such as seasonality, but we won’t know that stability has been achieved unless the same pattern of infections is observed for more than one consecutive year.  

There are two big unknowns in attempting to determine how soon the end of the pandemic may arrive and what it might look like. The first is: how durable will our immunity be, particularly against severe disease but also against infection? And the second is: how fast will the Sars-CoV-2 virus evolve, in particular with respect to overcoming our immune defences? To answer these questions, we need to look at the lessons the pandemic has taught us so far.  

The year of the Sars-CoV-2 virus was very much 2020, when it caused high levels of mortality and disease, and changed lives around the world. We saw a virus transmit into humans and began to observe some evolution, but thanks to the relatively slow rate of evolution of Sars-CoV-2 compared with other RNA viruses, we did not observe much change beyond the immediate public health impact until the very end of the year, with the emergence initially of the Alpha, Beta and Gamma variants.  

Looking back, 2021 appears to have been the year of the variant. The Alpha variant rapidly displaced the initial strain of the virus: it was more transmissible and more likely to cause severe disease and death, necessitating far more robust public health responses including the reimposition of restrictions in the UK and elsewhere. The degree of adaptation was staggering; the Alpha variant was more than 50% more transmissible in humans compared with the original virus, a leap of adaptation that has never previously been observed in real time.  

The Beta and Gamma variants also displayed a degree of immune escape, a brief glimpse into the possibility that these viruses might be able to, at least in part, evade defences we had built against previous forms of the virus, whether by infection or vaccination. And of course, these variants were succeeded by the Delta variant, which was about 50% more transmissible than the Alpha variant, and also more severe, bringing another wave of disease and devastation.

Towards the end of 2021 we were hit by another variant, Omicron, which brought its own unique challenges and lessons in viral evolution. Omicron is highly evasive of the antibodies that vaccination and prior infection confer, and thereby can breach our immune defences. Fortunately, protection against hospitalisation and disease is not eroded to the same extent, though protection against severe disease has declined. And of course, Omicron is capable of reinfecting individuals who have previously been exposed to other forms of the virus. The idea that viral infection is a “one and done” risk – that you can get it over with by being infected – has well and truly been dispelled by Omicron. Thus, if 2021 was the year of the variant and the vaccine, 2022 so far appears to be the year of reinfection.