Sunday, October 24, 2021

Denmark SSI: Expert Group Forecasts Increased COVID Cases & Hospital Admissions

Credit Our World In Data 


While some parts of the world - including the United States - are currently enjoying a drop in COVID cases, across the UK and most of Europe, COVID rates are headed in the wrong direction (see chart above), with the biggest increases being reported in the Baltic region of Europe (Latvia, Lithuania, Estonia, etc.)

Even highly vaccinated countries - like the UK and Denmark - are seeing significant increases in COVID transmission, and last week we saw calls by some professional organizations to reinstate some COVID restrictions (see UK: NHS Confederation - Enact ‘Plan B plus’ to avoid ‘stumbling into winter crisis’).

While vaccination still provides moderate-to-good protection against severe illness, hospitalization, and death we are seeing growing evidence that `breakthrough' infections are becoming more common, suggesting that vaccination alone may not be enough to curb COVID transmission this winter. 

From Denmark's SSI (Statens Serum Institut) we get the following forecast for COVID activity through mid-November, which predicts increasing infections and hospitalizations.  One hope, not included in the models, is that the COVID Booster shots - given primarily to those > 60 - will blunt the impact of this expected surge. 

Expert group expects increases in both infection and new admissions

The expert group for mathematical modeling has projected the development in covid-19 infection and new admissions until mid-November. In a new note, the group expects significant increases in both the daily infection rates and new admissions. How large they actually become is, in turn, more uncertain.
Last edited October 21, 2021

On September 20, 2021, the expert group for mathematical modeling announced that it would issue notes at shorter intervals that follow the development of the covid-19 epidemic. The first note in the series comes today. Here, two different models have been used to estimate the expected development in the daily infection rates and new admissions in the coming weeks.

Read the new note here.

“The models show how it will go in a scenario where the activity in the community and the vaccination connection both correspond to the level we have now. Based on that, we still expect to see an increase in the daily infection rates and new admissions in the next six weeks. But it is also still uncertain how big the increase will be, ”says doctor Camilla Holten Møller, who heads the expert group for mathematical modeling.
It shows the new note

According to the new note, it is estimated that in mid-November we will see between 600-3,200 daily infections and between 25-110 daily new admissions.
Although the population's behavior may change, and it is unknown what significance the autumn holidays have for the spread of infection, the model group assesses that both infection rates and new admissions are more likely to end up in the lower part of the range.

It is estimated that most infected people will be found in the younger and unvaccinated age groups. However, a significant number of breakthrough infections are also expected among vaccinated 12-59-year-olds. That is, people who are diagnosed with covid-19 infection, even though they are fully vaccinated and the full effect of the vaccines should have entered into force.

If you look at the number of new admissions in the age groups 0-59 years, they consist primarily of people who have not been vaccinated. On the other hand, if you look at people aged 60 and up, the majority of newly admitted people have been vaccinated.
3rd connector can limit increase

However, the effect of the 3rd vaccination is not included in the models. It is therefore expected that the number of admissions among the elderly will be reduced as a result of revaccination.

The expert group expects that in future they will be able to present updated estimates for the development in the daily infection rates and new admissions every two to three weeks.
Read more

Read the new note here. 

Figure 1. Daily infection rates in two different models for unvaccinated (left column), vaccinated (middle column) and the total number of infected (right column). The development in popIBM is illustrated in the orange curve, while the development in pop9 is illustrated in the green curve. The black curve shows for each week the observed average infection rates per day until 3 October 2021. The purple dots are the observed infection until 11 October on a daily basis. Days with <5 are excluded. Vaccine efficacy against infection ranges between 60-80%, while the reduction in transmission risk ranges between 50-80% for vaccinated.

We've seen recent models suggesting that COVID may have peaked in the United States, and the number of COVID cases, hospitalizations, and deaths are likely to decline over the next six months. While I hope that proves correct, we were told pretty much the same thing last May, only to be hit by a summer wave of infections. 

We also don't know how COVID and Influenza will interact this winter, or what impact (if any) the AY.4.2 variant will have on the future course of this pandemic. 
All reasons why, if you haven't been vaccinated against COVID and Influenza, you should definitely make getting both a priority.  If you are eligible for COVID booster, it should offer additional protection as well, particularly if you are in a high-risk group.

I'm also continuing to wear face masks in public, and recommend it to others, even if they are fully vaccinated. This winter, it can help protect against both COVID and influenza, and potential COVID/Flu coinfections

As tired as we all are of dealing with this pandemic, SARS-CoV-2 shows little signs of fading away anytime soon. 

Upcoming COCA Call: Recent Updates to CDC’s Recommendations for COVID-19 Boosters



On tuesday of this week (Oct 26th) the CDC will hold a 1-hour COCA Call for clinicians on recent changes to their recommendations on COVID vaccine boosters, which now includes Moderna and J&J vaccines.  On Friday, in CDC Expands Eligibility For Booster Shots (Moderna & J&J) Following ACIP Vote, we looked at last week's approval process. 

This latest ruling also allows individuals to decide which booster shot they want (mix & match). 

COCA Calls are often technical, and are of greatest interest to clinicians and healthcare providers, but also may be of interest to the general public. As always, If you are unable to attend the live presentation, these (and past) webinars are archived and available for later viewing at this LINK.

Details on Tuesday's webinar follow:
What Clinicians Need to Know about the Recent Updates to CDC’s Recommendations for COVID-19 Boosters


This COCA call will provide an overview of the most recent recommendations for administering COVID-19 booster vaccines. The Centers for Disease Control and Prevention will provide updates about the latest recommendations and clinical considerations for administering COVID-19 boosters, including an update on early safety monitoring for additional COVID-19 vaccine doses.


Anne Hause, PhD
Vaccine Task Force
COVID-19 Response
Centers for Disease Control and Prevention

Kathleen Dooling, MD, MPH
Vaccine Task Force
COVID-19 Response
Centers for Disease Control and Prevention

Sujan Reddy, MD, MSc
Vaccine Task Force
COVID-19 Response
Centers for Disease Control and Prevention

Call Materials

None at this time

Call Details

Tuesday, October 26, 2021,
2:00 PM – 3:00 PM ET

Webinar Link: icon

Passcode: 581643

Dial In:
US: +1 669 254 5252
or +1 646 828 7666
or +1 669 216 1590
or +1 551 285 1373

International numbersexternal icon

One-tap mobile:
US: +16692545252,,1603968267#,,,,*581643# or +16468287666,,1603968267#,,,,*581643#

Webinar ID: 160 396 8267

Saturday, October 23, 2021

UKHSA Technical Briefing On Delta Sub-Lineage AY.4.2



Yesterday we saw the UK Health Security Agency (UKHSA) elevate the AY.4.2 variant from being simply monitored to a VUI (Variant Under Investigation). Several hours later, the same agency released a Technical Briefing (#26) dedicated primarily to this emerging COVID variant.

While it is far from clear whether AY.4.2 will become the next COVID threat, it does appear to be making inroads against the dominant Delta B.1.617.2 parental strain in the UK, and their early analysis suggests it may have a transmission advantage. 

That said, UK researchers are quick to add this is very preliminary information and it carried a high degree of uncertainty.   So far, we've not seen AY.4.2 making the same strides against Delta here in the United States. 

I've only included a few excerpts from a much longer, and highly detailed, 31-page PDF report.  Follow the link to download and read it in its entirety.

22 October 2021
Summary This extra report has been produced to provide information on the new Variant Under Investigation VUI-21OCT-01, AY.4.2. The specialist technical briefings contain early data and analysis on emerging variants and findings have a high level of uncertainty. 
In summary: 
1. AY.4.2. accounts for a slowly increasing proportion of cases in the UK. It is also present in multiple other countries on GISAID and is seen in travellers to the UK from a large number of countries. It is not clear where it originated or when. 
2. This lineage has the mutations of Delta and AY.4, and in addition S: A222V and Y145H. These mutations are in the N terminal domain. They could plausibly be biologically significant but there is minimal laboratory evidence. 
3. AY.4.2. appears to have a modestly increased growth rate compared to Delta. Growth rates are included here and similar findings were reported by another Variant Technical Group contributor using a different method. A high observed growth rate may be due to a biological change in the virus (transmissibility or immune escape) or to epidemiological context, such as being introduced into an area or population subgroup with high existing levels of transmission. It is still uncertain whether AY.4.2 is growing due to a biological difference. 
4. The secondary attack rate for household contacts of cases with VUI-21OCT-01 was 12.4% (95% CI: 11.9% to 13.0%), higher than that observed for other Delta cases where it was 11.1% (95% CI: 11.0% to 11.2%). In non-household settings, the secondary attack rate was higher for VUI-21OCT-01 than other Delta cases, but this difference was not significant. No significant variation between regions was observed. 
5. Based on these considerations and the high level of uncertainty, AY.4.2 was designated a new Variant Under Investigation, VUI-21OCT-01. 
6. Preliminary epidemiology and some of the supporting data used in the VUI assessment are included in this report. In addition, comparative analyses of deaths, hospitalisation, and vaccine effectiveness have commenced and will be reported once available. Crude data on deaths and hospitalisations are included in this report for information but are not definitive analyses. Further severity and transmissibility modelling will be undertaken. Pseudovirus work has been initiated and residual biological materials are being cultured for live virus. 
7. Lambda (C.37) and C36.3 have been de-escalated as of the 20 October 2021 to variants in monitoring. SARS-CoV-2 variants of concern and variants under investigation 4 

All risk assessments are published separately, except for Gamma, which was published within Technical Briefing 7 and Alpha within Technical Briefing 9. As Delta is the dominant variant in the UK, epidemiological data in the weekly surveillance report is also relevant.


2.2 Epidemiology of VUI-21OCT-21 in England
As of 21 October 2021, there are 22,017 VOC-21OCT-01 genomes in the UK dataset, linked to 15,120 cases in England. VUI-21OCT-01 accounts for 3.8%, 5.2%, and 5.9% of Delta cases in England in the weeks beginning 19 September, 26 September, and 3 October 2021 respectively (Figure 4). Data are incomplete for more recent weeks.
Variant prevalence for all cases in England as of 21 October 2021 is shown in Figure 4, by region in Figure 5 and travel status in Figure 6. Figure 7 shows AY.4.2 as a proportion of all Delta cases in England using Pangolin lineage call.
Cases have been detected across all regions in England (Table 5 and Figure 8). Of the 15,120, 420 had a recent travel history, with the most frequent country of travel being or Spain (96) or Greece (75). At least 32 countries of travel have been reported. Age data are shown in Figure 9.
Severity outcomes
To assess severe outcomes from VUI-21OCT-01 outcomes of cases between 15 May 2021 and 23 September 2021 were assessed and compared against Delta cases from the same time period. This time period was selected to cover the emergence of VUI-21OCT-01 and allow 28 days since first specimen to elapse to assess outcomes.
Information on attendance to emergency care is derived from the Emergency Care Data Set (ECDS) and Secondary Uses Service (SUS), provided by NHS Digital. These data only show whether a case has attended emergency care at an NHS hospital and was subsequently admitted as an inpatient. The data does not include cases who were directly admitted without first presenting to emergency care.
ECDS and SUS reporting is lagged, where NHS trusts routinely provide monthly data by the 21st of the following month. However, some trusts report daily data, and the linkage between coronavirus (COVID-19) cases and ECDS data is updated twice-weekly.
These initial crude analyses do not show strong evidence of a difference in risk of hospitalisation or death between VUI-21OCT-01 and Delta. However, these analyses do not adjust for crucial factors that can influence outcomes such as age and vaccination status and should be interpreted with caution.

          (Continue . . .)


CDC Update On Multi-State Outbreak Of Melioidosis

Credit CDC PHIL  


Three times over the summer (see here, here, and here) we've looked at an unusual multi-state outbreak of Melioidosis - a bacterial infection caused by Burkholderia pseudomallei - a gram negative saprophytic (feeds on dead or decaying organic matter) bacterium that is often found in soil and water in endemic regions.

It has never, as far I'm aware, been isolated in the wild in the United States. 

While naturally occuring in the tropics, and Southeast Asia, Burkholderia pseudomallei is considered a Tier-1 Select agent, because - and I quote the CDC `. . .  these biological agents and toxins present the greatest risk of deliberate misuse with significant potential for mass casualties or devastating effect to the economy, critical infrastructure, or public confidence, and pose a severe threat to public health and safety"

While rare, about a dozen (usually imported) human infections have been reported in the United States each year.  As we saw last year in an EID Journal dispatch (see Melioidosis in a Resident of Texas with No Recent Travel History, United States), sometimes the source of infection is never determined. 

Yesterday the CDC announced a promising break in the current investigation, when Burkholderia pseudomallei was detected in a bottle of aromatherapy spray found in the home of the 4th victim (from Georgia). 

CDC labs are now attempting to determine if the genetic fingerprint of this bacteria matches that found in the 4 victims, and if any of the other 3 known cases used similar products. The Consumer Product Safety Commission has issued a recall notice (below).

Walmart Recalls Better Homes and Gardens Essential Oil Infused Aromatherapy Room Spray with Gemstones Due to Rare and Dangerous Bacteria; Two Deaths Investigated

The CDC update follows: 

CDC Identifies Rare Bacteria in Aromatherapy Product
Aromatherapy spray tests positive for deadly bacteria
Press Release
For Immediate Release: Friday, October 22, 2021
Contact: Media Relations
(404) 639-3286

Laboratory testing at the U.S. Centers for Disease Control and Prevention (CDC) has identified the bacteria Burkholderia pseudomallei in an aromatherapy spray — the same type of bacteria that sickened four people in the United States earlier this year. The spray, “Better Homes & Gardens Lavender & Chamomile Essential Oil Infused Aromatherapy Room Spray with Gemstones,” was found Oct. 6 in the home of a Georgia resident who became ill with melioidosis in late July. CDC is continuing testing to see if the genetic fingerprint of the bacteria in the bottle matches those of the bacteria identified in the four patients – one each in Georgia, Kansas, Texas, and Minnesota. Two of the four patients died.

The contaminated spray was sold at about 55 Walmart stores and on Walmart’s website between February and October 21, 2021, when Walmart pulled remaining bottles of this spray and related products from store shelves and its website. The Consumer Product Safety Commission and Walmart are issuing a recall for the lavender and chamomile room spray and five other scents in the same product line. Investigation continues into whether other related scents and brands may pose a risk.

CDC recommends that anyone who has this aromatherapy spray in their home:
  1. Stop using this product immediately. Do not open the bottle. Do not throw away or dispose of the bottle in the regular trash.
  2. Double bag the bottle in clean, clear zip-top bags and place in a small cardboard box. Return the bagged and boxed product to a Walmart store.
  3. Wash sheets or linens that the product may have been sprayed on using normal laundry detergent and dry completely in a hot dryer; bleach can be used if desired.
  4. Wipe down counters and surfaces that might have the spray on them with undiluted Pine-Sol or similar disinfectant.
  5. Limit how much you handle the spray bottle and wash hands thoroughly after touching the bottle or linens. If you used gloves, wash hands afterward.
  6. If you have used the product within the past 21 days and have fever or other melioidosis symptoms, seek medical care and tell your doctor you were exposed to the spray. If you do not have symptoms but were exposed to the product in the last 7 days, your doctor may recommend that you get antibiotics (post-exposure prophylaxis) to prevent infection.
CDC has been testing blood samples from the patients, as well as soil, water, and consumer products from in and around the four patients’ homes since the agency began receiving samples in May. A sample of the Better Homes & Gardens spray tested positive this week. The genetic fingerprint of the bacteria that sickened the four patients is similar to that of strains usually found in South Asia; the aromatherapy spray was made in India. CDC is coordinating with state health departments in Kansas, Minnesota, and Texas to try to determine whether the other three patients may have also used this or similar products.

“Our hearts go out to the families that have been impacted by this situation,” said Inger Damon, MD, MPH, director of CDC’s Division of High-Consequence Pathogens and Pathology, which manages melioidosis. “We at CDC have been very concerned to see these serious related illness spread across time and geography. That is why our scientists have continued to work tirelessly to try to find the potential source for the melioidosis infections in these patients. We hope this work can help protect other people who may have used this spray.”

Melioidosis is a rare but serious disease in the United States, with about 12 cases reported annually. Worldwide, most cases are in people who live in or have traveled to areas where the bacteria naturally occurs, such as parts of South and Southeast Asia and northern Australia. It is also occasionally found in the Americas (e.g., Brazil, Mexico, Puerto Rico). Melioidosis causes a wide range of symptoms that can be confused with other common illnesses, like flu or a cold. Person-to-person spread is extremely rare.

For more information about the investigation, please visit the webpage on this cluster of illnesses and the Health Alert Network notice. For information about melioidosis, please go to:

Friday, October 22, 2021

CDC FluView Week 41: Two Novel Influenza Infections (H1N1v & H3N2v) Reported



Today's CDC's weekly FluView Report contains details on two novel flu infections - one from the 2020-2021 flu season (which ended with week 39), and one from the current (2021-2022) flu season. Both are swine variant viruses. 

While most swine variant infections can be traced to contract with pigs - either on farms or at agricultural exhibits - one of today's announced case does not appear to have had contact with swine, raising the possibility that it may have been transmitted from human-to-human.

While rare, we've seen other cases of limited H-2-H transmission with swine variants, and of course, the 2009 H1N1 swine flu was highly transmissible between humans. The CDC's risk assessment for Swine Variant viruses reads:

Sporadic infections and even localized outbreaks among people with variant influenza viruses may occur. All influenza viruses have the capacity to change and it’s possible that variant viruses may change such that they infect people easily and spread easily from person-to-person. The Centers for Disease Control and Prevention (CDC) continues to monitor closely for variant influenza virus infections and will report cases of H3N2v and other variant influenza viruses weekly in FluView and on the case count tables on this website 

The risk of one of these swine variant viruses sparking a pandemic is relatively low, but it isn't zero. The CDC's IRAT (Influenza Risk Assessment Tool) lists 3 North American swine viruses as having at least some pandemic potential (2 added in 2019). 

H1N2 variant [A/California/62/2018]      Jul   2019    5.8   5.7 Moderate
H3N2 variant [A/Ohio/13/2017]          Jul   2019   6.6  5.8 Moderate
H3N2 variant [A/Indiana/08/2011]      Dec 2012   6.0  4.5 Moderate 
And the CDC currently ranks a Chinese Swine-variant EA H1N1 `G4' as having the highest pandemic potential of any flu virus on their list.

Today's cases represent the 11th detected in the United States during the 2020-2021 flu season and the first case of the 2021-2022 flu season, although it is very likely that other cases have gone undetected. Most infections are mild, and most people will never be tested.

Novel Influenza A Virus

Two human infections with novel influenza A viruses were reported. One infection with an influenza A(H1N1) variant (A(H1N1)v) virus was reported by North Dakota that occurred during the 2020-21 influenza season and one infection with an influenza (A(H3N2)v) virus was reported by Ohio that occurred during the 2021-22 influenza season.
Both patients are <18 years of age, were not hospitalized, and have recovered or are recovering from their illness. One of the patients had close contact with swine prior to illness onset. The other patient had no known swine contact or attendance at agricultural exhibits where swine were present; it is possible that limited human-to-human transmission occurred. No ongoing human-to-human transmission has been identified associated with either patient.

When an influenza virus that normally circulates in swine (but not people) is detected in a person, it is called a “variant influenza virus”. Most human infections with variant influenza viruses occur following close proximity to swine, but human-to-human transmission can occur. It is important to note that in most cases, variant influenza viruses have not shown the ability to spread easily and sustainably from person to person.

During the 2021-22 influenza season, one human infection with novel influenza A virus has been reported in the United States: H3N2v (OH). During the 2020-21 influenza season, 11 human infections with a novel influenza A virus were reported in the United States, including two H3N2v (IA, WI), three H1N2v (IA, OH (2)), and six H1N1v (IA, NC, ND, WI (3)) virus infections.

Early identification and investigation of human infections with novel influenza A viruses are critical so that the risk of infection can be more fully understood and appropriate public health measures can be taken. Additional information on influenza in swine, variant influenza virus infection in humans, and strategies to interact safely with swine can be found at
Additional information regarding human infections with novel influenza A viruses can be found at

For now, sporadic jumps of swine variant influenza from pigs to humans pose only a minor public health risk. But with every reassortment, and every species jump, these viruses are afforded new opportunities to overcome the barriers that have prevented them from becoming a pandemic strain.  

And so we monitor there progress with considerable interest. 

UKHSA: Delta Sub-lineage AY.4.2 Designated as a Variant Under Investigation



Yesterday, in Russia COVID Updates: Delta AY.4.2 Detected - Extended School Holidays & 10-Day Business Closures, we looked at announcements by both Russia and the United States on their recent detection of the Delta sub-lineage AY.4.2 variant.  

While a descendent of - and similar to - the currently dominant Delta B.1.617.2, this variant has a couple of notable mutations in its spike protein (A222V and Y145H) that have raised concerns, and its incidence in the UK (Est. at 6%) has been increasing. 

It is unknown whether this sub-variant can successfully compete against Delta, or if these mutations offer any substantial advantage to the virus.  Until now, it has been deemed a variant worthy of monitoring, but today the UK Health Security Agency (UKHSA) elevated its status to a VUI (Variant Under Investigation). 

We've seen VUIs declared, and downgraded after a period of time, once their threat is better understood.  So this change isn't necessarily a harbinger of the next COVID threat.  But AY.4.2 is worth paying attention to, particularly since it seems to be making headway in the UK, and has been increasingly detected around the globe. 

Delta sub-lineage AY.4.2 designated as a Variant Under Investigation by UK Health Security Agency

The Delta variant sub-lineage known as Delta AY.4.2 was designated a Variant Under Investigation (VUI) by the UK Health Security Agency (UKHSA) on 20 October 2021 and has been given the official name VUI-21OCT-01.

The designation was made on the basis that this sub-lineage has become increasingly common in the UK in recent months, and there is some early evidence that it may have an increased growth rate in the UK compared to Delta. More evidence is needed to know whether this is due to changes in the virus’ behaviour or to epidemiological conditions.

The genome of VUI-21OCT-01 does not have many mutations compared to Delta. However, a small change may be enough to cause a difference in the virus properties in some circumstances. UKHSA is monitoring this closely.

The original Delta variant remains overwhelmingly dominant in the UK, making up approximately 99.8% of all cases. As of 20 October, there were 15,120 cases of VUI-21OCT-01 confirmed by whole genome sequences in England since it was first detected in July. In the last week, VUI-21OCT-01 accounted for approximately 6% of all Delta cases. Cases have been confirmed through whole genome sequencing in all 9 regions of England.

While evidence is still emerging, so far it does not appear this variant causes more severe disease or renders the vaccines currently deployed any less effective. As is routine for any new variants under investigation, UKHSA is carrying out laboratory and epidemiological investigations to better understand the properties of this variant.

Dr Jenny Harries, Chief Executive of the UK Health Security Agency, said:

  • Viruses mutate often and at random, and it is not unexpected that new variants will continue to arise as the pandemic goes on, particularly while the case rate remains high. It is testament to the diligence and scientific expertise of my colleagues at UKHSA, and the genomic sequencing capacity developed through the pandemic, that this new variant has been identified and analysed so quickly. However, it should serve as objective evidence that this pandemic is not over.
  • The public health advice is the same for all current variants. Get vaccinated and, for those eligible, come forward for your third or booster dose as appropriate as soon as you are called. Continue to exercise caution. Wear a mask in crowded spaces and, when meeting people indoors, open windows and doors to ventilate the room. If you have symptoms take a PCR test and isolate at home until you receive a negative result.

UKHSA continues to examine all available data relating to SARS-CoV-2 variants in the UK and abroad. We constantly assess the genetic diversity within the known Variants of Concern (VOCs) to inform our ongoing public health response to the pandemic. New sub-lineages within Delta continue to be identified. This is to be expected and UKHSA is monitoring the situation closely.