H5N1

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.

Defining immunization: Types, statistics, and resources

Thanks to Regis College Online for sending the link to this resource just before World Immunization Week: Defining Immunization: Types, Statistics, and Resources. Click through to see the very good infographic on immunization. The introduction:

Immunization prevents an estimated 2 to 3 million deaths per year, according to the World Health Organization (WHO). The administration of vaccines has increased significantly over the last century, and developments in the field continue to improve and strengthen them. It’s important for every individual to understand the different types of vaccines and stay aware of recommendations for immunizations put forth by public health organizations.

WHO: Democratic Republic of Congo declares new Ebola outbreak in northwest province

A news release from WHO AFRO: Democratic Republic of Congo declares new Ebola outbreak in North West Province.

Brazzaville/Kinshasa, April 23, 2022 – Health authorities in the Democratic Republic of the Congo declared an Ebola outbreak today after the confirmation of a case in Mbandaka, capital of Equateur province (north -west). This is the third outbreak in this province since 2018.  

So far, only one case has been confirmed. The patient, a 31-year-old man, began experiencing symptoms on April 5 and after more than a week of home care, he sought treatment at a local health facility. On April 21, the patient was admitted to an Ebola treatment center for intensive care but died later that night. After recognizing the symptoms, health workers immediately took samples for laboratory testing for Ebola virus disease. Investigations to determine the source of the outbreak are ongoing.  

“Time is not on our side,” said Dr Matshidiso Moeti, World Health Organization (WHO) Regional Director for Africa. “The disease has taken a two-week head start and we are now playing catch-up. The good news is that health authorities in the Democratic Republic of the Congo have more experience than anyone else in the world in rapidly controlling Ebola outbreaks."  

The Democratic Republic of Congo is experiencing its fourteenth Ebola outbreak since 1976. The current outbreak is the sixth since 2018 alone, the most frequent event in the country's Ebola history. In Equateur province, previous outbreaks date back to 2020 and 2018, with 130 and 54 cases recorded respectively.  

Efforts to stem the current outbreak are already underway. The deceased patient received a dignified and safe burial, which involves modifying traditional funeral ceremonies in ways that minimize the risk of contagious fluids infecting attendees.   

Anyone who has been in contact with the patient is also identified and their state of health will be monitored. The health facility where the patient received care has been decontaminated.  

WHO experts based in the Democratic Republic of the Congo are supporting national authorities to strengthen key areas of outbreak response, including testing, contact tracing, infection prevention and control, treatment, as well as risk communication and engagement with communities to support public health measures to prevent infections.  

Vaccination should start in the next few days. The country already has stocks of rVSV-ZEBOV Ebola vaccine available in the cities of Goma and Kinshasa. The vaccines will be sent to Mbandaka and administered using the "ring vaccination" strategy - where contacts and contacts of contacts will be vaccinated to curb the spread of the virus and protect lives.  

"Many people in Mbandaka are already vaccinated against Ebola, which should help reduce the impact of the disease," said Dr Moeti. "All those who were vaccinated during the 2020 epidemic will be revaccinated."  

Ebola is a potentially deadly disease, affecting humans and other primates. Case fatality rates have ranged from 25% to 90% in past epidemics. Effective treatment now exists and if patients receive early treatment, as well as supportive care, their chances of survival improve dramatically.

China’s zero-Covid policy is a pandemic waiting to happen

An op-ed in The New York Times: China’s Zero-Covid Policy Is a Pandemic Waiting to Happen. Much as I respect Drs. Emanuel and Osterholm, I'm nervous about their use of terms like "have to live with it" and "endemic." They sound at this point like acceptance of high mortality and morbidity rates, which will be endured much more by working-class people and people of colour. Excerpt:

As the Winter Olympics approach and some 3,000 athletes, their retinues and the media converge in and around Beijing, the Chinese government has gone to extraordinary lengths to prevent the 24th version of the games from becoming a Covid super spreading event. 

Though athletes and coaches will be required to be vaccinated, they will face severe restrictions. Those who receive a medical exemption from vaccination are being required to quarantine for 21 days after entering the country. Even the vaccinated will have to present two negative tests. Olympic participants must submit to daily Covid tests and will be restricted to an Olympic bubble where they will be confined to prevent spread to the local population.  

These extreme measures are in line with China’s zero-Covid policy. President Xi Jinping and his government seem to believe that the country can be sealed off until the virus is eradicated around the world.  

But that goal is unattainable with the highly transmissible Omicron variant and has set the nation up for disaster. The coronavirus is not going to disappear — the world will have to live with it. Making matters worse, China’s vaccines are much less effective against Omicron. And the Chinese health care system simply is not equipped to care for millions of people sickened by the virus.  

Yes, China has weathered the pandemic well so far. Even with about four times the population of the United States, China has had fewer than 140,000 confirmed Covid cases and fewer than 6,000 deaths since January 2020, according to the World Health Organization. A vast majority of factories continued to operate. Early in the pandemic, China added thousands of hospital beds to its health care system in days.  

All of this seems like an enormous success when compared with the messy and often chaotic response to the virus in the United States, where more than 860,000 people have died and some 2,000 more die each day. Many hospitals are under siege. The economy has been disrupted.  

But this may very well be the future China is facing. Its pursuit of zero Covid will prove to be a huge mistake. The policy has left it wholly unprepared for what will become endemic Covid.

Static socio-ecological COVID-19 vulnerability index and vaccine hesitancy index for England

Via The Lancet Regional Health: Static Socio-Ecological COVID-19 Vulnerability Index and Vaccine Hesitancy Index for England. The summary:

Background  

Population characteristics can be used to infer vulnerability of communities to COVID-19, or to the likelihood of high levels of vaccine hesitancy. Communities harder hit by the virus, or at risk of being so, stand to benefit from greater resource allocation than their population size alone would suggest. This study reports a simple but efficacious method of ranking small areas of England by relative characteristics that are linked with COVID-19 vulnerability and vaccine hesitancy.  

Methods  

Publicly available data on a range of characteristics previously linked with either poor COVID-19 outcomes or vaccine hesitancy were collated for all Middle Super Output Areas of England (MSOA, n=6790, excluding Isles of Scilly), scaled and combined into two numeric indices. Multivariable linear regression was used to build a parsimonious model of vulnerability (static socio-ecological vulnerability index, SEVI) in 60% of MSOAs, and retained variables were used to construct two simple indices. Assuming a monotonic relationship between indices and outcomes, Spearman correlation coefficients were calculated between the SEVI and cumulative COVID-19 case rates at MSOA level in the remaining 40% of MSOAs over periods both during and out with national lockdowns. Similarly, a novel vaccine hesitancy index (VHI) was constructed using population characteristics aligned with factors identified by an Office for National Statistics (ONS) survey analysis. The relationship between the VHI and vaccine coverage in people aged 12+years (as of 2021-06-24) was determined using Spearman correlation. The indices were split into quintiles, and MSOAs within the highest vulnerability and vaccine hesitancy quintiles were mapped.  

Findings  

The SEVI showed a moderate to strong relationship with case rates in the validation dataset across the whole study period, and for every intervening period studied except early in the pandemic when testing was highly selective. The SEVI was more strongly correlated with case rates than any of its domains (rs 0·59 95% CI 0.57-0.62) and outperformed an existing MSOA-level vulnerability index. The VHI was significantly negatively correlated with COVID-19 vaccine coverage in the validation data at the time of writing (rs -0·43 95% CI -0·46 to -0·41). London had the largest number and proportion of MSOAs in quintile 5 (most vulnerable/hesitant) of SEVI and VHI concurrently.  

Interpretation  

The indices presented offer an efficacious way of identifying geographical disparities in COVID-19 risk, thus helping focus resources according to need.

Omicron accounts for nearly three-quarters of new US cases

Via The New York Times: Omicron accounts for nearly three-quarters of new U.S. cases. Excerpt:

The extremely contagious Omicron variant is now the dominant version of new coronavirus cases in the United States, according to the Centers for Disease Control and Prevention, and has prompted the resumption of mask mandates in some cities and states in the Northeast, where the growth in new cases has been particularly steep.  

Omicron, first discovered overseas around Thanksgiving and identified in this country on Dec. 1, now accounts for more than 70 percent of new cases in the United States, according to federal estimates released Monday.  

The estimates underscored the rapid spread of the new variant. Two weeks ago, the C.D.C. said Omicron accounted for just 1 percent of U.S. cases; a week ago, it was about 13 percent. Delta, which for months had been the dominant form of the virus, accounted for about 26 percent of new cases over the last week, the C.D.C. estimated.  

Omicron, discovered thanks to its distinctive combination of more than 50 mutations, has turned out to be highly transmissible — two to three times as likely to spread as Delta — and less susceptible to vaccines than other variants. Early cases raised hopes that it may cause milder disease than other variants, but scientists say more research is needed.  

In New York, new cases have shot up more than 80 percent over two weeks. In Washington, D.C., where the mayor reinstated an indoor mask mandate on Monday, more than three times as many cases are being identified each day as at the start of December. In Boston, where cases are also surging, Mayor Michelle Wu on Monday announced proof-of-vaccination requirements for certain indoor spaces like gyms and restaurants.  

In a news conference on Monday, Mayor Bill de Blasio of New York City said that the city must “move faster” in its response to the latest wave of new cases, but insisted that another lockdown “would have horrible impacts on the people of this city.”  

New York’s governor, Kathy Hochul, on Monday called the surge in new cases “a vertical increase” because “it is going straight up,” but she did not announce new restrictions. Ms. Hochul, a Democrat, appeared at her daily coronavirus briefing without the state’s health commissioner, Dr. Mary T. Bassett, who tested positive for coronavirus via a rapid test earlier in the day. 

The tens of thousands of new cases in recent days have included prominent politicians and lawmakers, such as Larry Hogan, the governor of Maryland, and Senators Cory Booker of New Jersey and Elizabeth Warren of Massachusetts.  

The surge is coming as many hospitals have reached capacity and governors in several states have mobilized the National Guard to help with hospital staffing shortages. As Covid-19 cases crowd into hospitals, leaders of health care facilities in multiple states have taken out newspaper ads begging local residents to get vaccinated.

Growth, population distribution and immune escape of Omicron in England

Via the MRC Centre for Global Infectious Diseases: Report 49 - Growth, population distribution and immune escape of Omicron in England. If I'm reading this correctly, Omicron is no "milder" than Delta. That is very worrying news. The summary, with my bolding:

To estimate the growth of the Omicron variant of concern (1) and its immune escape (2–9) characteristics, we analysed data from all PCR-confirmed SARS-CoV-2 cases in England excluding those with a history of recent international travel. We undertook separate analyses according to two case definitions. For the first definition, we included all cases with a definitive negative S-gene Target Failure (SGTF) result and specimen dates between 29/11/2021 and 11/12/2021 inclusive. For the second definition, we included cases with a positive genotype result and specimen date between 23/11/2021 and 11/12/2021 inclusive. We chose a later start date for the SGTF definition to ensure greater specificity of SGTF for Omicron.  

We used logistic and Poisson regression to identify factors associated with testing positive for Omicron compared to non-Omicron (mostly Delta) cases. We explored the following predictors: day, region, symptomatic status, sex, ethnicity, age band and vaccination status. Our results suggest rapid growth of the frequency of the Omicron variant relative to Delta, with the exponential growth rate of its frequency estimated to be 0.34/day (95% CI: 0.33-0.35) [2.0 day doubling time] over the study period from both SGTF and genotype data. The distribution of Omicron by age, region and ethnicity currently differs markedly from Delta, with 18–29-year-olds, residents in the London region, and those of African ethnicity having significantly higher rates of infection with Omicron relative to Delta.  

Hospitalisation and asymptomatic infection indicators were not significantly associated with Omicron infection, suggesting at most limited changes in severity compared with Delta.  

To estimate the impact of Omicron on vaccine effectiveness (VE) for symptomatic infection we used conditional Poisson regression to estimate the hazard ratio of being an Omicron case (using SGTF definition) compared with Delta, restricting our analysis to symptomatic cases and matching by day, region, 10-year age band, sex and ethnicity. We found a significant increased risk of an Omicron case compared to Delta for those with vaccine status AZ 2+weeks post-dose 2 (PD2) , Pfizer 2+w PD2, AZ 2+w post-dose 3 (PD3) and PF 2+w PD3 vaccine states with hazard ratios of 1.86 (95%CI: 1.67-2.08), 2.68 (95%CI: 2.54-2.83), 4.32 (95%CI: 3.84-4.85) and 4.07 (95%CI: 3.66-4.51), respectively, where PD3 states are categorised by the dose 1/2 vaccine used. Depending on the Delta VE estimates used (10), these estimates translate into Omicron VE estimates of between 0% and 20% PD2 and between 55% and 80% PD3 against Omicron, consistent with other estimates (11). Similar estimates were obtained using genotype data, albeit with greater uncertainty. 

To assess the impact of Omicron on reinfection rates we relied on genotype data, since SGTF is associated with a higher observed rate of reinfection, likely due to reinfections typically having higher Ct values than primary infections and therefore being subject to a higher rate of random PCR target failure.  

Controlling for vaccine status, age, sex, ethnicity, asymptomatic status, region and specimen date and using conditional Poisson regression to predict reinfection status, Omicron was associated with a 5.41 (95% CI: 4.87-6.00) fold higher risk of reinfection compared with Delta. This suggests relatively low remaining levels of immunity from prior infection.

In New Mexico, the pandemic rages on

Via The New Yorker: In New Mexico, the Pandemic Rages On.

 Excerpt:.

At one of the hospitals where I work, in rural New Mexico, the covid-19 patients are often young. Many are extremely sick, and most are unvaccinated. Not long ago, I walked into a room to find a woman in her mid-thirties. (Patient details have been changed to protect privacy.) She was unvaccinated, and had tested positive the week before. Her oxygen saturation was just fifty per cent, and her chest X-ray looked terrible. She seemed resigned and scared. When I asked her why she hadn’t got the vaccine, she shrugged. 

Down the hall, I visited a man in his early twenties who was breathing forty times a minute. We were still waiting for his test results, but his chest X-ray also looked terrible. When I asked him why he hadn’t got immunized, he said, “I don’t know,” and shrugged, too. Outside, in the hall, I checked our status board. A ten-year-old had been checked in with worsening covid symptoms. Fifteen more patients were waiting to get tested. 

In New Mexico, it doesn’t feel like we’re experiencing a new “wave” of the pandemic—it’s more like we’re in the middle of an endless voyage, in twenty-foot seas, miles from land. 

I’ve been working as an emergency-room physician all through the pandemic, first in Boston and now here. Taking care of unvaccinated patients stirs up complicated emotions in me. Severe covid-19 is now a largely preventable illness, and I often feel anger and frustration: I think, You couldn’t be bothered to do something as simple as schedule two shots, and now you might die—what is wrong with you? I contemplate the risk that each unvaccinated person poses to everyone around, including to me, and my family, and our nurses, and their families, and the hospital staff who will clean the virus-slick rooms, and their families—the risks branch out with dizzying complexity, like ice crystals forming in a cloud. I try to keep these thoughts to myself, for obvious reasons. Who wants to hear, after they’ve totalled their car and broken their legs, that they shouldn’t have been speeding? 

Sometimes, when I stand at the bedsides of young, critically ill patients who shake their heads when I ask if they’ve got the vaccine, I murmur, almost to myself, “I really wish you had.” But their past choices are no longer the most important thing. They are sick and afraid, and need our help as much as anyone else. I tell them that we’ll do everything we can to keep them safe. I never tell them that, for some patients, everything won’t be enough.

By asking people why they have avoided these incredibly safe and effective shots, I’ve learned a lot about how confusing the information ecosystem has become. Patients used to tell me that they worried about adverse effects, such as myocarditis or blood clots. (These effects are vanishingly rare.) 

Then, in September, I started hearing about a new concern: “the VAERS report.” I heard more about it by listening to a conservative talk radio show; listeners kept dialing in to talk about it. They said that tens of thousands of Americans had died after receiving the coronavirus vaccine, and that this report proved it. My patients in the E.R. began saying this, too.

Vietnam: Ho Chi Minh City starts vaccinating school children against COVID-19

Via VietnamPlus: HCM City starts vaccinating school children against COVID-19. Excerpt:

HCM City (VNA) – Ho Chi Minh City on October 27 morning started giving COVID-19 vaccines to school children in the district of Cu Chi.  

According to Chairwoman of the People’s Committee of Cu Chi Pham Thi Thanh Hien, the vaccination is being piloted at one site initially, with about 1,500 students aging from 16-17 to receive the shots.  

Doctor Nguyen Thanh Danh, head of the Health Care Division of Cu Chi said that the vaccination will only be carried out with agreement from their parents. The students are receiving Pfizer COVID-19 vaccine, he added. 

Duong Anh Duc, Vice Chairman of the HCM City People’s Committee said that Cu Chi district, together with District 1, are the first localities in the city chosen for the vaccination of children.  

Duc noted that so far, the city has administered nearly 13 million doses of COVID-19 vaccines to locals with utmost safety. The city has also made careful preparations to give the vaccines to children, he said, adding that the city will be the first locality in the country to conduct a massive vaccination campaign on children starting from November. 

Russia's Covid deaths hit new record high ahead of nationwide restrictions

Via The Moscow Times: Russia's Covid Deaths Hit New Record High Ahead of Nationwide Restrictions.

Russia reported a record high number of coronavirus deaths Tuesday as Europe’s hardest-hit country braces for nationwide restrictions this week.   

Russia has repeatedly set new all-time highs for Covid-19 deaths over the past month and is currently reporting the second-highest number of daily fatalities in the world after the U.S.  

According to government figures, 1,106 people have died from Covid-19 over the last 24 hours.  

Tuesday's increase brings the official death toll to 232,775 — Europe’s highest — though authorities are accused of dramatically downplaying that figure. A Moscow Times analysis of excess deaths published by the federal statistics agency Rosstat puts Russia's total excess fatality count since the start of the pandemic at 660,000.  

All of Russia's 85 regions across 11 time zones have now mandated vaccines for certain categories of workers, Anna Popova, who heads the federal health watchdog that is leading the country’s response to the virus, said Tuesday.

The latest figures come days before Russia’s mandated paid vacation for non-essential workers in hopes of putting the brakes on spiraling Covid-19 deaths and cases from this Sunday, Oct. 30, to Nov. 7.  

Moscow, the epicenter of Russia’s coronavirus outbreak, will go into the so-called “non-working” period this Thursday, with all businesses and services except grocery stores and pharmacies suspended.  

Russia’s coronavirus task force also reported 36,446 coronavirus cases Tuesday.  

Russia has the world’s fifth-highest total caseload of more than 8.3 million infections since the start of the pandemic, with the more-infectious Delta variant and stubbornly low vaccination rates fueling the virus’ spread since the summer.  

Only around 36% of Russians have been fully vaccinated despite the availability of four homegrown vaccines and several regions mandating shots for certain categories of workers.