H5N1

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.

New Zealand Covid-19 update: Nearly 20,000 community cases, 373 in hospital, 9 in ICU

Via Radio New Zealand: Covid-19 update: Nearly 20,000 community cases, 373 in hospital, 9 in ICU. Excerpt: 

There are nearly 20,000 new cases of Covid-19 in the community today, the Ministry of Health reports.  

Director-General of Health Dr Ashley Bloomfield said there were just under 100,000 active cases across the motu.  

"I know that such a high daily case number can be concerning for people to hear, and many of us will now have whānau members who now have Covid-19, but it's important to remember that Covid-19 now is a very different foe to what it was at the beginning of the pandemic."  

He said the high vaccination rate meant for most people it would be a more mild illness and could be managed safely at home.  

He said PCR testing had served NZ incredibly well, but with thousands of cases each day NZ did reach the point last week where rapid antigen testing became both useful and appropriate.  

He said samples were typically pooled earlier on in the outbreak, but a positive test in a batch means each will need to be retested. Higher test positivity rates now however meant it becomes less feasible. 

He said prior to 7 February, none of the labs had ever exceeded 5 percent test positivity, but the swift increase in positive cases has affected that. Labs had also had other difficulties including vacancies in roles and sickness because some lab workers have contracted the virus.

Canada's abandoning of COVID-19 testing leaves us vulnerable to future variants, experts say

As the saying goes, "If you don't count it, it doesn't count." Via CBC News: Canada's abandoning of COVID-19 testing leaves us vulnerable to future variants, experts say. Excerpt:

Canada is entering a period of relative calm as the Omicron-driven fifth wave subsides across much of the country. But our ability to track new and existing variants is in jeopardy with testing access still heavily restricted — leaving us vulnerable to pandemic whiplash.  

Dr. Theresa Tam, Canada's chief public health officer, said Friday that COVID-19 levels have continued to decline in most of Canada, with weekly case counts down 26 per cent and hospitalizations and ICU admissions down 20 per cent compared to the previous week.   

"Nevertheless, as the virus is still circulating widely, some jurisdictions are reporting weekly increases in case counts and others could see additional bumps in the weeks ahead," she said.   

"At the same time, there is a continued high volume of PCR testing being performed and ongoing genetic sequencing of circulating virus variants."   

But the level of COVID-19 testing in Canada has actually dropped off dramatically since the start of the Omicron wave — with more than 100,000 daily tests being performed in early December, about 150,000 in early January, down to just over 50,000 as of Friday.   

That makes it nearly impossible to get a clear sense of what the true number of COVID-19 cases are in Canada, and severely limits the number of testing samples that can undergo genomic sequencing to detect for the presence of variants.

World 'cannot abandon' testing amid threat of variants  

The World Health Organization's leading coronavirus expert Maria Van Kerkhove said this week that while there has been a 20 per cent drop in COVID-19 levels globally in the past week compared to the previous week, the decline "may not be real" due to a lack of testing. 

"We are very concerned about a reduction in testing around the world," she said Tuesday.

A turning point in coverage of COVID data

Via the Columbia Journalism Review, a column by Jon Allsop: A turning point in coverage of COVID data. Click through for the full article and many links. Excerpt:

There's important information down the toilet—and no, I’m not talking about sensitive documents from the Trump White House. Early this month, the Centers for Disease Control and Prevention updated its online COVID data tracker to include wastewater analyses from hundreds of communities across the US, information that can serve as an early indicator of increased viral spread, or the circulation of a new variant, given that people shed the virus via their feces without having to take and report a test result. (Wastewater data is also collective, obviating privacy issues inherent to other forms of medical-data reporting.) 

Wastewater experts who spoke with Apoorva Mandavilli, a reporter at the New York Times, were “understanding” of the fact that it took the CDC so long to publicly share data that it was, in some cases, already collecting. Not everyone shared that assessment, though. Robinson Meyer, a journalist at The Atlantic who co-founded the COVID Tracking Project to fill the gap left by official data shortages early in the pandemic, called the delayed publication “a scandal.”  

It’s not just wastewater—as Mandavilli reported over the weekend, it turns out that the CDC “has published only a tiny fraction of the data it has collected” during the pandemic. The agency has tracked data breaking down hospitalization stats by age, race, and vaccination status for more than a year now but has mostly not published it; when officials shared data on the effectiveness of vaccine boosters recently, they left out the figures for a huge tranche of younger recipients until the Times inquired.  

CDC representatives told Mandavilli that the agency withholds data for a variety of reasons, from the numbers being “not yet ready for prime time” to the agency’s slow and cumbersome bureaucracy as well as a fear that the public might misinterpret certain trends, particularly where the hospitalization of vaccinated people is concerned.  

Jessica Malaty Rivera, who has also worked with the Tracking Project, slammed the latter rationale, in particular, noting that rather than reduce the risk of misinterpretation, “data vacuums” only heighten it. So, too, did Meyer, who called such attitudes not only “counterproductive” but “profoundly undemocratic.” The “approach has now persisted in the CDC across two presidents,” he noted. “It’s an issue with that agency—and with the overweeningly scholastic culture of public health in the US.” 

The availability of good, timely data has been a persistent challenge for the press throughout the pandemic, as I’ve explored many times in this newsletter. So, too, has knowing how best to relay the data that we do have to our audiences. The recent Omicron wave sharpened the challenge again by posing a different type of threat than prior variants: low for most individuals, especially the vaccinated, but sharp for many immunocompromised and unvaccinated people as well as at the collective level of US healthcare infrastructure, given the variant’s high transmissibility.

Even before Omicron, some health officials and experts had urged news outlets to emphasize hospitalization and death rates more than case counts in their coverage, as mass vaccination frayed the previously close link between those numbers; as Omicron further frayed the link, those calls intensified. If Omicron cast fresh doubt on the usefulness of case counts, it also cast fresh doubt on their accuracy, as testing—which was not adequate to make US case counts fully reliable to begin with—became harder to access and many people neglected to report at-home results. The Associated Press, among other outlets, told staffers to be more cautious around case counts, and not to hype supposed new records by writing whole stories about them.

Clinical severity of Omicron sub-lineage BA.2 compared to BA.1 in South Africa

Via medRxiv: Clinical severity of Omicron sub-lineage BA.2 compared to BA.1 in South Africa. The abstract:

Early data indicated that infection with Omicron BA.1 sub-lineage was associated with a lower risk of hospitalisation and severe illness, compared to Delta infection. Recently, the BA.2 sub-lineage has increased in many areas globally. We aimed to assess the severity of BA.2 infections compared to BA.1 in South Africa. 

We performed data linkages for (i) national COVID-19 case data, (ii) SARS-CoV-2 laboratory test data, and (iii) COVID-19 hospitalisations data, nationally. For cases identified using TaqPath COVID-19 PCR, infections were designated as S-gene target failure (SGTF, proxy for BA.1) or S-gene positive (proxy for BA.2). Disease severity was assessed using multivariable logistic regression models comparing individuals with S-gene positive infection to SGTF-infected individuals diagnosed between 1 December 2021 to 20 January 2022. 

From week 49 (starting 5 December 2021) through week 4 (ending 29 January 2022), the proportion of S-gene positive infections increased from 3% (931/31,271) to 80% (2,425/3,031). The odds of being admitted to hospital did not differ between individuals with S-gene positive (BA.2 proxy) infection compared to SGTF (BA.1 proxy) infection (adjusted odds ratio (aOR) 0.96, 95% confidence interval (CI) 0.85-1.09). 

Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ for individuals with S-gene positive infection compared to SGTF infection (aOR 0.91, 95%CI 0.68-1.22). 

These data suggest that while BA.2 may have a competitive advantage over BA.1 in some settings, the clinical profile of illness remains similar.

California adopts nation's 1st 'endemic' virus policy

Via The Associated Press:California adopts nation's 1st 'endemic' virus policy | AP News. Excerpt:

SACRAMENTO, Calif. (AP) — California became the first state to formally shift to an “endemic” approach to the coronavirus with Gov. Gavin Newsom’s announcement Thursday of a plan that emphasizes prevention and quick reaction to outbreaks over mandated masking and business shutdowns.  

The milestone, nearly two years in the making, envisions a return to a more normal existence with the help of a variety of initiatives and billions in new spending to more quickly spot surges or variants, add health care workers, stockpile tests and push back against false claims and other misinformation.  

“We are moving past the crisis phase into a phase where we will work to live with this virus,” he said during a news conference from a state warehouse brimming with pandemic supplies in Fontana, east of Los Angeles.  

The first-term Democrat, who last year survived a recall election driven by critics of his governance during the pandemic, promised the state’s nearly 40 million residents that as the omicron surge fades, “we’re going to keep them safe and we’re going to stay on top of this.”  

A disease reaches the endemic stage when the virus still exists in a community but becomes manageable as immunity builds. But there will be no definitive turn of the switch, the Democratic governor said, unlike the case with Wednesday’s lifting of the state’s indoor masking requirements or an announcement coming Feb. 28 of when precisely schoolchildren can stop wearing face coverings. 

And there will be no immediate lifting of the dozens of remaining executive emergency orders that have helped run the state since Newsom imposed the nation’s first statewide stay-home order in March 2020.  

“This pandemic won’t have a defined end. There’s no finish line,” Newsom said.  

The World Health Organization declared the COVID-19 outbreak a pandemic on March 11, 2020, and with omicron fading in many parts of the world some countries have begun planning for the endemic stage. But no state has taken the step Newsom did and offered a detailed forward-looking plan.

SARS-CoV-2 infection in Africa: A systematic review and meta-analysis of standardised seroprevalence studies, from January 2020 to December 2021

Via medRxiv: SARS-CoV-2 infection in Africa: A systematic review and meta-analysis of standardised seroprevalence studies, from January 2020 to December 2021. The abstract:

Introduction  

Estimating COVID-19 cumulative incidence in Africa remains problematic due to challenges in contact tracing, routine surveillance systems and laboratory testing capacities and strategies. We undertook a meta-analysis of population-based seroprevalence studies to estimate SARS-CoV-2 seroprevalence in Africa to inform evidence-based decision making on Public Health and Social Measures (PHSM) and vaccine strategy.  

Methods  

We searched for seroprevalence studies conducted in Africa published 01-01-2020 to 30-12-2021 in Medline, Embase, Web of Science, and Europe PMC (preprints), grey literature, media releases and early results from WHO Unity studies. All studies were screened, extracted, assessed for risk of bias and evaluated for alignment with the WHO Unity protocol for seroepidemiological investigations. We conducted descriptive analyses of seroprevalence and meta-analysed seroprevalence differences by demographic groups, place and time. We estimated the extent of undetected infections by comparing seroprevalence and cumulative incidence of confirmed cases reported to WHO. PROSPERO: CRD42020183634.  

Results  

We identified 54 full texts or early results, reporting 151 distinct seroprevalence studies in Africa Of these, 95 (63%) were low/moderate risk of bias studies. SARS-CoV-2 seroprevalence rose from 3.0% [95% CI: 1.0-9.2%] in Q2 2020 to 65.1% [95% CI: 56.3-73.0%] in Q3 2021. The ratios of seroprevalence from infection to cumulative incidence of confirmed cases was large (overall: 97:1, ranging from 10:1 to 958:1) and steady over time. Seroprevalence was highly heterogeneous both within countries - urban vs. rural (lower seroprevalence for rural geographic areas), children vs. adults (children aged 0-9 years had the lowest seroprevalence) - and between countries and African sub-regions (Middle, Western and Eastern Africa associated with higher seroprevalence).  

Conclusion  

We report high seroprevalence in Africa suggesting greater population exposure to SARS-CoV-2 and protection against COVID-19 disease than indicated by surveillance data. As seroprevalence was heterogeneous, targeted PHSM and vaccination strategies need to be tailored to local epidemiological situations.

See this Washington Post report for details of this and other studies indicating Africa has been hit far harder by COVID-19 than we imagined.

Pandemics disable people — the history lesson that policymakers ignore

Via Nature, an excellent article by Laura Spinney: Pandemics disable people — the history lesson that policymakers ignore. Excerpt:

When Ashley Shew turned up for an appointment at a medical centre in spring 2020, a member of staff told her she could remove her mask because only people with pre-existing conditions were vulnerable to COVID-19. Shew was surprised. “A hard-of-hearing amputee battered by chemotherapy and more”, as she describes herself, she is a regular at the centre — the appointment that day concerned her prosthetic leg. Who, she wondered, did the staff member think counted as a person with pre-existing conditions?  

The invisibility of disability is not new, says Shew, a 38-year-old philosopher who explores the intersection of technology and disability at Virginia Polytechnic Institute and State University in Blacksburg. “But it is particularly deadly that we don’t frame COVID-19 as a disability issue,” she says. “Even linguistically we’re pointed away from it. ‘Pre-existing conditions’ is a way of not saying ‘disability’.”  

From the beginning of this pandemic, people with disabilities understood that the disease would target them and would swell their ranks. Disability historians knew that there was a penumbra of ill health to previous mass-death events. Health economists warned that, as with tuberculosis, HIV and other diseases, morbidity would stalk mortality. Too many others have clung stubbornly to a belief that COVID-19 is something from which a minority of people die, and that most bounce back quickly and intact, with only their immune system updated. The longer the pandemic drags on, the harder it is to maintain that fiction.  

Two years in, the debilitating tail of the pandemic has revealed itself in the form of tens of millions of people living with long COVID1. It is high time to ask whether attitudes to disability will change as a result. Will society grasp that the body can be altered for a long period — even permanently — by infectious disease, just as it seems to have accepted that the body politic will never be the same again? And will it make the necessary accommodations?  

These questions have been asked before.  

Long influenza  

Consider the ‘mother of all pandemics’ — the 1918 Spanish influenza outbreak. Even in the 1920s, scientists understood that this flu had neurological and other effects. The most notorious and debated of those — still — is the overlapping pandemic of encephalitis lethargica (EL) or ‘sleepy sickness’. Eighty per cent of EL survivors went on to develop a Parkinson’s-like disease. According to cell biologist Richard Smeyne at the Jefferson Hospital for Neuroscience in Philadelphia, Pennsylvania, it has never been proved biologically that flu caused both EL and this post-encephalitic parkinsonism — at least not in the sense of catching the virus in flagrante in the brain tissue of people who had died. Yet the statistical case for it seems strong. 

The neurological tails of two subsequent flu pandemics, in 1957 and 1968, were less pronounced, but both were followed by rises in cases of encephalitis (brain inflammation), among other conditions. Once again, researchers failed to demonstrate a clear causal link with an earlier flu infection, but it has since been established that the flu virus can infect the brain and trigger inflammation there and elsewhere in the body. Clinicians see this after every flu season, in a wave of strokes and heart attacks predominantly among older people. And flu can cause encephalitis in children. It’s rare, but it can kill, and those who survive can be left with long-term brain damage.

US ‘excess deaths’ during pandemic surpassed 1 million, with covid killing most but other diseases adding to the toll, CDC says

Via The Washington Post: U.S. ‘excess deaths’ during pandemic surpassed 1 million, with covid killing most but other diseases adding to the toll, CDC says. Excerpt:

The United States has recorded more than 1 million “excess deaths” since the start of the pandemic, government mortality statistics show, a toll that exceeds the officially documented lethality of the coronavirus and captures the broad consequences of the health crisis that has entered its third year.

The excess-deaths figure surpassed the milestone last week, reaching 1,023,916, according to Robert Anderson, chief of the mortality statistics branch of the Centers for Disease Control and Prevention’s National Center for Health Statistics. The center updates its estimate weekly.  

Although the vast majority of the excess deaths are due to the virus, the CDC mortality records also expose swollen numbers of deaths from heart disease, hypertension, dementia and other ailments across two years of pandemic misery.  

“We’ve never seen anything like it,” Anderson said.  

In 2019, before the pandemic, the CDC recorded 2.8 million deaths. But in 2020 and 2021, as the virus spread through the population, the country recorded roughly a half-million deaths each year in excess of the norm.  

The virus emerged in China in late 2019 and began killing people there in January 2020. It did not spread significantly in the United States until that February, and it wasn’t until the final week of March 2020 that it began to send the excess-deaths metric soaring.  

The CDC’s excess deaths tracker shows in detail the speed and intensity of that initial wave: Deaths soared more than 40 percent above normal in the United States in the second week of April 2020.  

The lethality in early April was concentrated in a few hot spots; for example, deaths in New York City were seven times the norm, but some regions had minimal change in mortality for many months.  

The CDC mortality branch’s official count of deaths from covid-19 stood at 911,145 as of Tuesday. (The mortality researchers rely on death certificates, and that tally can be slightly lower than other CDC or academic trackers that rely on data from other sources.)  

Anderson said 91 percent of the deaths from covid-19 tracked by his unit were attributed directly to the disease. In the other 9 percent of deaths, covid-19 was listed as a contributing factor but not the primary cause.  

The CDC documented 13 other types of non-covid causes of death that were inflated during the pandemic compared with historical trends starting in 2013. For example, since the start of the pandemic, the category of ischemic heart disease has recorded an additional 30,000 deaths beyond what would be expected. Deaths from hypertensive disease were nearly 62,000 higher than expected.  

Anderson said the numbers carry a degree of ambiguity: Some heart attacks and hypertensive disease could have been associated with undiagnosed cases of coronavirus infections.  

The CDC’s analysis estimates 208,431 excess deaths from all the non-covid causes since the start of the pandemic. At first glance, that number plus the 911,000 covid-19 deaths would suggest the excess deaths were greater than 1.1 million.  

But Anderson notes that many of the people who died of covid-19 were elderly, sick or very frail, and, even without a pandemic, some might not have survived across the two-year span of the pandemic.  

“Some of those covid deaths are not, strictly speaking, excess deaths,” he said. The million-deaths figure highlights the broad reach of the pandemic beyond the direct lethality of the virus itself.

Modelling shows BC likely undercounting death toll from COVID-19

Via CBC News: Modelling shows B.C. likely undercounting death toll from COVID-19. Excerpt:

British Columbia could be significantly undercounting its COVID-19 death toll, according to modelling data from a national project.  

The project, led by University of Toronto professor Dr. Tara Moriarty, looks at the risk of future severe outcomes from COVID-19 for every province and region in Canada.  

It has been tracking various metrics, including excess mortality resulting from COVID-19 and the effect of vaccines in reducing deaths and cases.  

One of the metrics tracked is the difference between expected deaths and reported deaths — the former an estimate by epidemiologists based on infection rates, vaccination rates and fatality rates.  Reported deaths reflect the official government count.  

According to that estimate, B.C. should have seen more than 980 deaths from Dec. 18 to Feb. 11 compared to just over 340 cases that were reported officially.  

"Outside of Quebec, which captures almost all of its COVID deaths, the rest of Canada in general historically under-reports, under-detects, about 50 per cent of its COVID deaths," Moriarty told CBC News.  

B.C. is currently experiencing a sustained spike in deaths, with the seven-day rolling average of COVID deaths up to 10.29 per day as of Friday.  

Moriarty says recent testing changes in B.C., which reserves COVID-19 tests for higher-risk populations, further complicate pandemic analysis.   

She says predicting the number of deaths beyond February is not possible given that modellers do not know how the virus is circulating in the community.  

"We really do have to resume or have surveillance testing in a way that's meaningful," she said.   

"We can't wait till we see [numbers of] hospitalizations and deaths, because Omicron moves so fast that we can't wait to see those lagging indicators to be able to respond."