H5N1

Multi-country monkeypox outbreak: situation update

WHO has published Multi-country monkeypox outbreak: situation update. Excerpt:

Outbreak at a glance  

Since 13 May 2022, and as of 2 June 2022, 780 laboratory confirmed cases of monkeypox have been reported to or identified by WHO from 27 Member States across four WHO regions that are not endemic for monkeypox virus. Epidemiological investigations are ongoing. Most reported cases so far have been presented through sexual health or other health services in primary or secondary health care facilities and have involved mainly, but not exclusively, men who have sex with men (MSM).  

While the West African clade of the virus has been identified from samples of cases so far, most confirmed cases with travel history reported travel to countries in Europe and North America, rather than West or Central Africa where the monkeypox virus is endemic.  The confirmation of monkeypox in persons who have not travelled to an endemic area is atypical, and even one case of monkeypox in a non-endemic country is considered an outbreak.  

While most cases are not associated with travel from endemic areas, Member States are also reporting small numbers of cases in travelers from Nigeria, as has been observed before.  

The sudden and unexpected appearance of monkeypox simultaneously in several non-endemic countries suggests that there might have been undetected transmission for some unknown duration of time followed by recent amplifier events.  

WHO assesses the risk at the global level as moderate considering this is the first time that many monkeypox cases and clusters are reported concurrently in non-endemic and endemic countries in widely disparate WHO geographical areas.  

WHO continues to receive updates on the situation in endemic countries.  

Description of the outbreak  

As of 2 June 2022, 780 laboratory confirmed cases have been notified to WHO under the International Health Regulations (IHR) or identified by WHO from official public sources in 27 non-endemic countries in four WHO Regions. This represents an increase of 523 laboratory confirmed cases (+203%) since the Disease Outbreak News of 29 May, when a total of 257 cases were reported.  

As of 2 June 2022, there have been no deaths associated within the current monkeypox outbreak in non-endemic countries, however, cases and deaths continue to be reported from endemic countries (see Table 2).  

While investigations are ongoing, preliminary data from polymerase chain reaction (PCR) assays indicate that the monkeypox virus strains detected in Europe and other non-endemic areas belong to the West African clade.  

Figure 1 and Table 1 show the geographical distribution of monkeypox cases reported to or identified by WHO between 13 May to 2 June 2022 in non-endemic countries. The majority of cases (n=688; 88%), were reported from the WHO European Region (20 Countries). Confirmed cases have also been reported from the Region of the Americas (n=80; 10%), Eastern Mediterranean Region (n=9; 1%) and Western Pacific Region (n=3; <1%).  

The case count fluctuates as more information becomes available daily and data is verified by WHO in accordance with the provisions of the IHR.

The prevalence of SARS-CoV-2 infection and uptake of COVID-19 antiviral treatments during the BA.2/BA.2.12.1 surge, New York City, April-May 2022

Via medRxiv: The prevalence of SARS-CoV-2 infection and uptake of COVID-19 antiviral treatments during the BA.2/BA.2.12.1 surge, New York City, April-May 2022. The abstract: 

Importance: Routine case surveillance data for SARS-CoV-2 are incomplete, biased, missing key variables of interest, and may be unreliable for both timely surge detection and understanding the burden of infection.  

Objective: To determine the prevalence of SARS-CoV-2 infection during the Omicron BA.2/BA.2.12.1 surge in relation to official case counts, and to assess the epidemiology of infection and uptake of SARS-CoV-2 antivirals.  

Design: Cross-sectional survey of a representative sample of New York City (NYC) adult residents, conducted May 7-8, 2022. Setting: NYC, April 23-May 8, 2022, during which the official SARS-CoV-2 case count was 49,253 and BA.2.12.2 comprised 20% of reported cases.  

Participants: A representative sample of 1,030 NYC adult residents >18 years.

Exposure(s): Vulnerability to severe COVID-19, including vaccination/booster status, prior COVID, age, and presence of comorbidities.  

Main Outcome(s) and Measure(s): Prevalence of SARS-CoV-2 infection during a 14-day period, weighted to represent the NYC adult population. Respondents self-reported on SARS-CoV-2 testing (including at-home rapid antigen tests), testing outcomes, COVID-like symptoms, and contact with confirmed/probable cases. Individuals with SARS-CoV-2 were asked about awareness/use of antiviral medications.  

Results: An estimated 22.1% (95%CI 17.9%-26.2%) of respondents had SARS-CoV-2 infection during the study period, corresponding to ~1.5 million adults (95%CI 1.3-1.8 million). Prevalence was estimated at 34.9% (95%CI 26.9%- 42.8%) among individuals with co-morbidities, 14.9% (95% CI 11.0%-18.8%) among those 65+ years, and 18.9% (95%CI 10.2%-27.5%) among unvaccinated persons. Hybrid protection against severe disease (i.e., from both vaccination and prior infection) was 66.2% (95%CI 55.7%-76.7%) among those with COVID and 46.3% (95%CI 40.2-52.2) among those without. Among individuals with COVID, 55.9% (95%CI 44.9%- 67.0%) were not aware of the antiviral nirmatrelvir/ritonavir (PaxlovidTM), and 15.1% (95%CI 7.1%-23.1%) reported receiving it.  

Conclusions and Relevance: The true magnitude of NYCs BA.2/BA.2.12.1 surge was vastly underestimated by routine SARS-CoV-2 surveillance. Until there is more certainty that the impact of future pandemic surges on severe population health outcomes will be diminished, representative surveys are needed for timely surge detection, and to estimate the true burden of infection, hybrid protection, and uptake of time-sensitive treatments.

See also this report in The Guardian which discusses the study.

Modeling transmission of SARS-CoV-2 Omicron in China

Via Nature Medicine: Modeling transmission of SARS-CoV-2 Omicron in China. The abstract:

Having adopted a dynamic zero-COVID strategy to respond to SARS-CoV-2 variants with higher transmissibility since August 2021, China is now considering whether and for how long this policy can remain in place. The debate has thus shifted towards the identification of mitigation strategies for minimizing disruption to the healthcare system in the case of a nationwide epidemic. 

To this aim, we developed an age-structured stochastic compartmental susceptible-latent-infectious-removed-susceptible (SLIRS) model of SARS-CoV-2 transmission calibrated on the initial growth phase for the 2022 Omicron outbreak in Shanghai, to project COVID-19 burden (i.e., number of cases, patients requiring hospitalization and intensive care, and deaths) under hypothetical mitigation scenarios. The model also considers age-specific vaccine coverage data, vaccine efficacy against different clinical endpoints, waning of immunity, different antiviral therapies, and non-pharmaceutical interventions. 

We find that the level of immunity induced by the March 2022 vaccination campaign would be insufficient to prevent an Omicron wave that would result in exceeding critical care capacity with a projected intensive care unit peak demand of 15.6-times the existing capacity and causing approximately 1.55 million deaths. 

However, we also estimate that protecting vulnerable individuals by ensuring accessibility to vaccines and antiviral therapies, and maintaining implementation of non-pharmaceutical interventions could be sufficient to prevent overwhelming the healthcare system, suggesting that these factors should be points of emphasis in future mitigation policies.

COVID-19 in South Korea, March 2022

Here's a screenshot of the Johns Hopkins dashboard taken on February 28:

South Korea then ranked 8th in case counts, with 3.273 million cases and 1,303 deaths.  But 2.228 million cases had been recorded in the preceding 28 days. Something was already going wrong in a country that had done a pretty good job through 2020 and 2021.

And here's a screenshot taken this evening, after the March 31 case counts had been posted by the KDCA:

South Korea now ranks first in the world with 13,375,518 cases, of which 16,505 resulted in death. So an advanced, prosperous nation of 52 million has seen 10,102,069 of its citizens fall ill in 31 days. As well, 15,202 of them died in the same 31 days.

And this was the result of deliberate policy, as pointed out in a devastating article in The Korea Herald today. An excerpt: 

The rationale for the omicron plan is that the intensive social distancing of the delta days is “no longer viable nor cost-efficient,” according to the Health Ministry spokesperson on March 2. And as omicron is milder, doing so would pose little threat to the population.

Similarly, Jeong Eun-kyeong, commissioner of the Korea Disease Control and Prevention Agency, said at a March 21 briefing that “as there already has been substantial exposure in the community due to omicron’s high transmissibility, controlling the outbreak with social distancing alone will have significant limits.”

But the focus on social distancing eclipses what health officials should do without having to ask people to stay home and relive the intense isolation of the early pandemic days, according to public health professor Dr. Oh Ju-hwan of Seoul National University.

By using social distancing as a “blanket term” for pandemic control measures, health officials sold people on the idea that we no longer had to sacrifice freedoms to contain the virus, he said. “The narrative that social distancing is the only approach is misleading, and it’s been used as an excuse for authorities to do less of what they ought to be doing.”

With omicron’s rise, first to be abandoned were measures that exact the most administrative burdens, like extensive contact tracing and testing that Korea had prided itself on, he said. While quick to remove the no-cost testing-for-all policy and contact tracing, health officials kept social distancing restrictions, though eased, for the public. The cap on the size of personal gatherings and nighttime curfews for stores are still in effect, though they are anticipated to be removed soon.

Google mobility trends shows movements have been on a decline in Korea after omicron took over as the dominant virus in late January. Visits to retail and recreation facilities especially have fallen considerably compared to when the delta variant was raging across the country in the fall of 2021.

“When cases soar and hospitals fill up, people exercise caution voluntarily,” Oh said. “The mobility trends data demonstrates that the surge we’re seeing now is not in fact attributable to the lack of social distancing, as some officials and experts suggest.”

Although health officials like to emphasize the pains of social distancing, and how they are no longer sustainable, what was glaringly absent were efforts to test and trace cases and grasp the true scale of the outbreak, he said.

Active tracing was also crucial to “monitor variants, as letting the virus run amok in the community gives it more opportunities to evolve,” he said.

This policy seems to be what most governments are adopting now, including the US and Canada. I think we are going to see case counts on a Korean scale well before summer—and like South Korea, the true numbers will be even higher, because we won't be testing or contact tracing either.

Nor will we consider that 10 to 20 percent of these COVID-19 cases will evolve into long COVID, with consequences for millions of people who are now celebrating the end of "restrictions" like mask mandates.

Policy missteps, population density cause worst Omicron wave in Korea

I've been stunned by the COVID numbers coming out of South Korea this week, and now we have an explanation from The Korea Times: Policy missteps, population density cause worst Omicron wave in Korea: experts. The full report with my bolding, and then a comment:

The country's numbers of daily new COVID-19 infections, critical cases and deaths are ballooning to unprecedented levels as Korea enters the peak of the Omicron wave.  

The number of daily new infections for Wednesday hit an all-time high at 621,328, a 55-percent jump from 400,741 the previous day, according to the Korea Disease Control and Prevention Agency (KDCA). The agency added 429 COVID-19-related deaths ― also an all-time high ― while 1,159 patients were in critical condition.  

The health ministry viewed that the spike in infections was attributable to aggressive testing using rapid antigen tests conducted by medical personnel at clinics, which have identified "hidden infections" that have not been detected using only PCR tests.  

Until this Monday, only PCR tests conducted at screening centers had been included in the official daily infection tally, but now rapid antigen tests conducted by doctors and reported to the ministry are also recognized.  

The daily figures have gone far beyond the level the health ministry had anticipated, as it had previously projected that infections would peak at around 370,000 only.  

"We view that the wave is heading toward the peak, and will be reached within this week or early next week," said health ministry spokesman Son Young-rae during a briefing, Thursday.  

While yet to reach its peak, Korea's COVID-19 situation is already far worse than that of other countries during the worst of the Omicron waves there in January, according to figures from Our World in Data.  

In Korea, as of March 15, the number of daily new cases per 1 million people stood at 6,370.47, which is more than double of that of the United States when the Omicron wave there peaked at 2,423.66 on Jan. 16, and that of the United Kingdom (2,607.06 on Jan. 9), as well as higher than that of France at the pinnacle of the Omicron wave (5,356.76 on Jan. 24).

Local medical experts said there are multiple factors that led Korea into the current disaster, but pointed out that the government's quarantine measures in the last few weeks have been heading in the wrong direction.   

"The government began easing quarantine measures substantially as the March 9 presidential election drew nearer. There was no scientific or medical basis for these decisions. Rather, they were driven by political intentions," said Choi Jae-wook, a professor of preventive medicine at Korea University.  

He added, "It seemed like they were trying to appeal to the voters, who were tired of the social distancing measures, by giving them more freedom."  

Choi also criticized the authorities for continuing to downplay the severity of the Omicron variant, comparing it to the seasonal flu.  

"Omicron cannot be considered similar to the flu when the former is five to 10 times more contagious. And let me make something clear: the flu does not take the lives of 2,000 people in just three weeks, nor does it infect over 500,000 people per day," he explained.  

Chon Eun-mi, a respiratory disease specialist at Ewha Woman's University Mokdong Hospital, said there were two main reasons for the explosive number of infections here: the population density and the government's complacency.  

"Omicron has spread like wildfire, especially throughout the Seoul metropolitan area, where about half of population lives. Also, the government made a critical mistake at the beginning of the Omicron wave, relying too much on the high vaccination rate," she said.  

"It should have taken lessons from other countries that vaccines are not a panacea against Omicron. They may prevent patients from falling into critical condition, but the vaccines developed to this date have proven to have little effect in preventing Omicron infections," she said.

Unlike the health authorities who projected that the infections would peak by next week, the experts were more cautious.

"It's becoming more difficult to predict when the infections will peak because the government continues to relax the quarantine measures," Choi said, expressing deep concerns that the sheer numbers of new infections added each day will result in hundreds of daily fatalities in the next couple of weeks.

"To prevent further unnecessary suffering and deaths, the government must immediately admit its failure and provide accurate information about the severity of the current situation," he said.

Chon said, "As a doctor treating COVID-19 patients at the hospital, I don't understand why the government is not actively using oral antiviral treatments to prevent those in vulnerable groups from falling into severe condition. With more supplies to come, Paxlovid should be distributed to as many patients as possible in a timely manner."

The soaring Korean numbers are a prediction of our own in a few weeks. We may not live as densely packed together as they do, but many governments have relaxed "restrictions" when there is little or no evidence that it's wise to do so. 

It's going to be a very bad spring and summer, and it will be worse because of our governments' stupidity.

South Korea reports all-time high of 549,854 daily COVID-19 cases

Via Yonhap, an update to last night's post just below: S. Korea reports all-time high of 549,854 daily COVID-19 cases. Excerpt and then a comment:

SEOUL, March 16 (Yonhap) -- South Korea reported 549,854 new COVID-19 cases on Wednesday, setting a new daily record as the country battles through the worst wave of the virus sparked by the omicron variant.  

The all-time high was reported as of 9 p.m., with three hours left until the daily tally ends. The total will be announced the following morning.  

Seoul reported 128,385 cases, breaching 100,000-mark for the first time.  

Earlier Wednesday, the Korea Disease Control and Prevention Agency (KDCA) said the country added 400,741 daily COVID-19 infections, mostly locally transmitted, raising the total caseload to 7,629,275.  

It was an all-time high since South Korea reported the first COVID-19 case on Jan. 20, 2020, and a big jump from Tuesday's 362,338. The previous record high was 383,659 reported last Saturday.  

The daily count differs from 441,423 reported by South Korean media last night quoting a private data tracker, as the number had not removed overlapping and erroneous data that appears to have been caused after the government began to allow virus tests conducted at local clinics as official results, the KDCA said.  

The death toll from COVID-19 rose 164 to 11,052, with the fatality rate standing at 0.14 percent.  

The number of critically ill patients, seen as a key indicator in the pandemic response, reached another record high of 1,244, up 48 from the previous day.  

South Korea has seen its COVID-19 caseload spike since early this year, with the daily tallies surging from four digits to six digits in about three weeks last month.  

Despite the fast spread of the omicron, the government has been trying to take steps to regain normalcy to the most possible extent while keeping up the fight against the virus.

The omicron wave is heading toward its peak, which will be a critical point in the fight against the virus, Sohn Young-rae, a senior health ministry official, said.  

"If the peak is formed as predicted and the medical system can respond within the prepared range, I think this crisis will be the last major crisis in the overall response to COVID-19," Sohn said.  

"Either this week or next week, at the latest, will be the peak," Sohn added.

On Saturday, South Korea hit a record number of cases with 383,664. On Tuesday, another record, the country saw 441,423. And now over half a million. I expect that in the next few weeks we will see a comparable spike in cases here in North America. 

South Korea reports all-time high of 441,423 daily COVID-19 cases

Via Yonhap: S. Korea reports all-time high of 441,423 daily COVID-19 cases. The authorities seem to be trying to turn COVID into flu, with a tolerably small fatality rate. But many COVID survivors will still experience long COVID, and the South Korean healthcare system is taking punishment it didn't need.

SEOUL, March 15 (Yonhap) -- South Korea reported 441,423 new COVID-19 cases on Tuesday, setting a new daily record as the country battles through the worst wave of the virus sparked by the omicron variant.  

The all-time high was reported as of 9 p.m., with three hours left until the daily tally ends. The total will be announced the following morning.  

Earlier Tuesday, the Korea Disease Control and Prevention Agency (KDCA) said the country added 362,338 new COVID-19 infections the previous day, mostly locally transmitted, putting the total caseload at 7,228,550.  

The previous record was 383,664 cases reported Saturday. The daily counts tend to decline on Mondays due to fewer tests on the weekend before rising sharply toward the end of the week.  

The death toll from COVID-19 hit a record high of 293 on Tuesday, up 93 from Monday, with the total at 10,888. The fatality rate came to 0.15 percent.  

The number of critically ill patients also reached an all-time high of 1,196, up 38 from the previous day.  

South Korea has seen a spike in the COVID-19 caseload since the beginning of this year, with the numbers surging from four digits to six digits in about three weeks last month.  

The focus now in the fight against COVID-19 has been about how to bring back everyday life as much as possible while maintaining steps to rein in the virus surge.  

"Managing the fatality rate is very important," Sohn Young-rae, a senior health ministry official, said in a briefing. "The fatality rate for the past four weeks has been lower than 0.1 percent, so the short-term fatality rate is similar to that of the seasonal flu," Sohn said. The fatality rate of seasonal flu stands at 0.05-0.1 percent.  

Health authorities forecast the current virus wave will enter its peak between later this week and next week. Sohn said the numbers of critically ill cases and deaths are expected to continue to rise until two to three weeks after the peak.  

Health authorities said they would begin to consider readjusting social distancing rules that currently limit business hours till 11 p.m. and private gatherings of up to six people, as those measures are due to end this week.  

The government announced children aged between 5 and 11 will be able to receive vaccine shots starting March 31. It began to allow uninfected students and school staff members to attend school in person even if family members who live with them are virus positive.  

Of the locally transmitted cases reported Tuesday, 66,067 cases came from Seoul and 102,983 from the surrounding Gyeonggi Province. The western port city of Incheon reported 20,444 cases. Fifty-five cases came from overseas, raising the total to 30,358.  

As of Tuesday, 32.15 million people out of the 52 million population, or 62.7 percent, had received booster shots. Fully vaccinated people came to 44.43 million, representing 86.6 percent, the KDCA said.

COVID-19 is in for the long haul

Here's a screenshot of this evening's Johns Hopkins Coronavirus COVID-19 (2019-nCoV) dashboard:

It's notable for several reasons. First, the US is now far back in the 28-day case count—seventh, behind Germany, South Korea, Russia, Vietnam, France, and Brazil.

 

Second, almost all the case and mortality numbers are likely severe undercounts, since so many countries have simply abandoned any pretence of testing and contact tracing. I would not be shocked if the true number of cases were around 1.5 billion, and deaths close to 20 million.

 

The numbers for Russia (3.7 million cases in the last 28 days, 20,000 deaths) and Ukraine (458,000 cases, 3,800 deaths) are especially implausible, given the events of the past 15 days. But we'll surely see an explosive growth in cases as over 2 million Ukrainians move through Europe in search of refuge.

 

The early-success countries have largely succumbed to Omicron. While China pursues its zero-COVID policy, it's still recorded 539,000 cases and 2,600 deaths. Hong Kong has seen 533,000 cases in 28 days, and 2,600 deaths. Vietnam racked up 26 million cases in the last 28 days, and 2,400 deaths. New Zealand had 267,000 cases and 12 deaths; it had only 38,900 cases in the previous 23 months of the official pandemic.

 

The graphs on the right tell us that the Omicron spike has fallen sharply from its peak of 23,333,000 in the week ending January 23; we're now at 10,706,000 as of the week ending March 6. That looks impressive, but it's still about 5 million more than the three previous waves.

 

Omicron also drove a spike in deaths, peaking at 75,000 in the week of February 13 and now fallen to 50,400. Meanwhile, vaccinations have fallen from a recent high of 257,000 in the week of February 6 to 105,600 in the week ending March 6.

 

Yet many countries are effectively declaring the pandemic over, making masks and distancing optional, junking vaccine passports, and dropping regular reports by public health officials. Governments seem to think COVID-19 can now sink back into the background noise with other diseases, while we turn our attention to war and inflation and the next election.

 

On February 1, Johns Hopkins reported 381,232,070 cases, so we have seen almost 72 million cases of COVID-19 in the past six weeks alone. Even if the Omicron spike continue to drop, the next six weeks will see tens of millions more cases, and likely another 40 or 50 thousand people now alive will be dead before May 1. 

 

We are nowhere near the end of the pandemic. In fact, I expect it will in many ways get worse as healthcare systems really do collapse, and as sequelae like Long COVID affect more and more cases. The pandemic that began two years ago really is in the for long haul.

Thoughts on six million deaths

Above is a screenshot from this morning's Johns Hopkins COVID-19 dashboard. We have reached 6 million deaths in two years, and half a billion cases don't seem that far away. But the most alarming development in the pandemic is that we in the West, and many other countries, appear to have normalized COVID-19.

On January 30, the weekly case count reached 23 million; yesterday, March 6, it was down to 10,693,000. That's a dramatic fall, but it's still higher than any previous peak in the pandemic. The highest death count was 100,000 in the week ending January 21, 2021. This past week, it was 50,000.

 

These are of course official numbers; the true case counts and mortality are generally assumed to be two to three times higher.

 

Yet the US, Canada, and many other countries are dispensing with "restrictions." The US has dropped to fourth place in the tally of cases, well behind Germany, Russia, and South Korea. The Americans have endured almost 80 million cases and nearly a million deaths, but seem to think they can now go back to business as usual. 

 

Russia counted 4 million cases in the past 28 days, a quarter of its total 16 million cases, and has lost 350,000 lives to COVID-19. Yet it has launched a war against Ukraine that seems sure to result in far more deaths from disease than from combat. Over a million Ukrainians have sought shelter in neighbouring countries, whose healthcare systems will soon be overwhelmed yet again by rising case counts. 

 

No one seems to care. We appear to have decided that fighting a war is more interesting and important than fighting a pandemic, and it lets us ignore the suffering that continues in countries far from the Black Sea. 

 

It's quite an achievement for a coronavirus no one knew about a couple of years ago: worldwide spread, a Holocaust's worth of deaths, and now acceptance as just another fact of life in the 21st century. I will not be surprised if some preprint soon reports on a new neurological effect of SARS-CoV-2: the stupefaction of all human beings, whether they test positive or not.

COVID-19 in February 2022

Here is a screenshot from the Johns Hopkins Coronavirus COVID-19 (2019-nCoV) dashboard, taken just a few moments ago:

And here is what I posted from that dashboard on February 1, 28 days ago:

We've seen some dramatic changes: a predicted sharp fall in cases, from 23,183,000 in the week ending January 30, to 10,942,000 in the week ending January 27.  

 

Deaths in the week ending January 30 were 66,304. They peaked on February 6 at 75,455, and fell to 60,232 in the week ending February 27.

 

Vaccinations have been erratic, from a low of 166,866,000 in the week of January 30 to a peak of 257,076,000 in the week ending February 6, and ending the month at 162,473,000.

 

Meanwhile the US with 4,487,000 cases in February has been overtaken in case counts by Germany with almost 5 million cases, and Russia with 4,508,000. Around the world, 60,265,061 persons contracted COVID-19 in February, and 285,999 died of it.

 

All these numbers are of course probably serious undercounts, and the pandemic seems likely to continue indefinitely. It will receive media attention when it afflicts rich or strategically important countries; otherwise the media will go back to stories about sports and entertainment, politics and scandal. We have probably already passed the billionth case, but the official billionth case will trigger lots of headlines. Then COVID-19 will fade out of our awareness until a new strain emerges, or someone in our family falls ill and dies of an old one.

 

I hope I'm still here to post the Johns Hopkins numbers for February 28, 2023.