Wednesday, December 01, 2021

South Korean CDC Confirms Omicron Cluster (Imported & Local Cases) - Additional Tests Pending



Earlier today, in South Korea Sets New Record (n=5,123) For Daily COVID Cases - Preparing For Omicronwe looked at an initial report of a suspected cluster of Omicron variant infections in a family living in Incheon, where two members has recently returned from Nigeria. 

In the past hour, South Korea's CDC has confirmed three of those cases (2 family members & acquaintance) , while testing on 4 others is pending. Additionally, two more imported cases - also returning from Nigeria - have tested positive. 

While we still don't have any evidence to suggest that Omicron is more dangerous than Delta, it continues to demonstrate impressive transmissibility. 

The following (machine translated) excerpt from today's announcement suffers a bit from kludgy syntax, but is certainly readable. 

A total of 5 confirmed cases of the Omicron mutant virus in Korea were implemented urgently for additional measures to block the inflow into Korea and prevent its spread

Posted on 2021-12-01
Last modified date of 2021-12-01
Department in charge Central Quarantine Countermeasures Headquarters General Coordination Team

A total of 5 confirmed cases of the Omicron mutant virus in Korea were implemented urgently for additional measures to block the inflow into Korea and prevent its spread
Omicron mutation confirmed in a total of 5 people including couples in their 40s who entered Nigeria after visiting Nigeria
Prepare a countermeasure plan by holding an emergency meeting of the inter-ministerial task force to respond to new mutations and the relevant ministries to evaluate the situation of overseas inflows
Additional designation of Nigeria as a quarantine-strengthened country, a dangerous country, and a country exempted from quarantine in the existing 8 countries including South Africa
◇ All countriesē™¼entrants 10 days isolation and PCR tests three embodiments times
[A total of 5 confirmed cases of Omicron mutated virus]

□ The Central Quarantine Countermeasures Headquarters (Director Jeong Eun-kyung) announced on November 30 (Tuesday) that omicron mutations were suspected and 3 cases of whole-genome testing* were confirmed as omicron mutations.

○ The index couple, who traveled to Nigeria* after completing vaccinations in Korea and entered the country on November 24, were subject to exemption from quarantine.

* Completed the second dose of Moderna on October 28th. November 14-23 travel to Nigeria. Arrival at Incheon International Airport on November 24th at 15:30 via Ethiopia from Nigeria on November 23rd

○ Through contact tracing of cases in which Omicron mutation was confirmed, family members (2 people) and acquaintances (1 person) of Case #4 were additionally confirmed, and additional cases (#5~#7) were confirmed. Full-length genome analysis is ongoing.

* The previous day (November 30. Thursday), the case (#4) that was reported as confirmed on November 30 and in their 40s in the press release was additionally confirmed by age group (40s → 30s) and confirmation date (11.30. → 11.29.) change.

○ Meanwhile, contact tracing management of confirmed Omicron (#1, 2, 4) and epidemiologic related cases (#5~#7) is in progress.
- So far, one additional confirmed case of passengers* on the same aircraft used by the index couple (#1~#2) was confirmed as a delta as a result of mutation analysis.
* A total of 45 people, including married couples, entered the country, *** 8 residents

- The contact investigation for cases #3 to #7 is being conducted quickly with priority on family, work, and acquaintances.

□ Meanwhile, as a result of analyzing Omicron mutations in overseas confirmed cases other than the above cases, two additional cases of Omicron mutation were confirmed on December 1, and contact tracing is under way.
* #8~#9 female in her 50s (acquaintance relationship), visited Nigeria (11.13~22), entered on November 23rd, confirmed on November 24th
[Held a TF to respond to new mutations]

□ The government organized the “New Mutation Response Pan-Ministry Task Force” and held the first meeting today for a quick response to block the inflow of Omicron mutations and prevent domestic transmission.

○ The pan-ministerial task force to respond to new mutations is headed by the head of the Korea Centers for Disease Control and Prevention and is composed of high-ranking public officials at the relevant department* level.

* Korea Centers for Disease Control and Prevention, Ministry of Health and Welfare, Office of National Affairs, Ministry of Strategy and Finance, Ministry of Public Administration and Security, Ministry of Foreign Affairs, Ministry of Justice, Ministry of Land, Infrastructure and Transport, Ministry of Food and Drug Safety, etc.

○ Regular and occasional meetings will be held once a week to discuss cross-ministerial countermeasures to identify overseas trends, block foreign inflows, monitor and analyze mutations, and block domestic radio waves. It will be implemented as soon as possible after reporting to the task force headquarters.
(Continue . . . )


In light of these recent cases, South Korea has formed a new Task Force, and is ramping up their defenses against the spread of this new variant, and has directed:

① Reinforcement of overseas inflow management

② Enhanced Genomic Surveillance
③ Strengthening of quarantine measures related to Omicron
In the future, the Central Quarantine Countermeasure Headquarters plans to expand or adjust the designation of countries with enhanced quarantine measures through continuous monitoring of the degree of risk and spread of Omicron mutated virus abroad.

Stay tuned. 

U.S. Government Classifies COVID Omicron a VOC (Variant of Concern)

Photo Credit NIAID  


Although it was pretty much a foregone conclusion, yesterday the United States officially classified the Omicron variant as a VOC (Variant of Concern), with the following announcement on the CDC's Coronavirus website. 

What You Need to Know about Variants

Updated Nov. 30, 2021

Omicron Variant

On Tuesday, November 30, 2021, the U.S. government SARS-CoV-2 Interagency Group made the decision to classify the Omicron variant as a Variant of Concern (VOC). This decision is based on multiple factors, including the detection of Omicron cases in multiple countries, transmission and displacement of Delta in South Africa, and mutations in the virus that could indicate a reduction in the effectiveness of COVID-19 vaccines and certain monoclonal antibody treatments. No cases of this variant have been identified in the U.S. to date. CDC is following the details of this new variant.

While the WHO declared Omicron a VOC on Friday, each country has its own evaluation system, and indeed, their own classification system, for variants.  In the United States there are currently 4 categories of COVID variants (VBMs, VOIs, VOCs, and VOHC), with VOHC representing the highest threat level. 

There are currently no variants anywhere in the world classified as VOHC, and in the United States only Delta and Omicron are listed as VOCs.

The following description of variant classifications comes from the CDC:
How Variants Are Classified

The US Department of Health and Human Services (HHS) established a SARS-CoV-2 Interagency Group (SIG) to improve coordination among the Centers for Disease Control and Prevention (CDC), National Institutes of Health (NIH), Food and Drug Administration (FDA), Biomedical Advanced Research and Development Authority (BARDA), and Department of Defense (DoD). This interagency group is focused on the rapid characterization of emerging variants and actively monitors their potential impact on critical SARS-CoV-2 countermeasures, including vaccines, therapeutics, and diagnostics.

The SIG meets regularly to evaluate the risk posed by SARS-CoV-2 variants circulating in the United States and to make recommendations about the classification of variants. This evaluation is undertaken by a group of subject matter experts who assess available data, including variant proportions at the national and regional levels and the potential or known impact of the constellation of mutations on the effectiveness of medical countermeasures, severity of disease, and ability to spread from person to person. Given the continuous evolution of SARS-CoV-2 and our understanding of the impact of variants on public health, variants may be reclassified based on their attributes and prevalence in the United States.

The status of variants often change, and some VOIs and VOCs we were watching over the summer have been purged from the list as Delta totally dominated them this fall.   

VOCs are defined by the CDC as:

Variant of Concern (VOC)

A variant for which there is evidence of an increase in transmissibility, more severe disease (e.g., increased hospitalizations or deaths), significant reduction in neutralization by antibodies generated during previous infection or vaccination, reduced effectiveness of treatments or vaccines, or diagnostic detection failures.

Possible attributes of a variant of concern:

In addition to the possible attributes of a variant of interest
  • Evidence of impact on diagnostics, treatments, or vaccines
  • Widespread interference with diagnostic test targets
  • Evidence of substantially decreased susceptibility to one or more class of therapies
  • Evidence of significant decreased neutralization by antibodies generated during previous infection or vaccination
  • Evidence of reduced vaccine-induced protection from severe disease
  • Evidence of increased transmissibility
  • Evidence of increased disease severity
Variants of concern might require one or more appropriate public health actions, such as notification to WHO under the International Health Regulations, reporting to CDC, local or regional efforts to control spread, increased testing, or research to determine the effectiveness of vaccines and treatments against the variant. Based on the characteristics of the variant, additional considerations may include the development of new diagnostics or the modification of vaccines or treatments.

While we've yet to see a VOHC (Variant of High Consequence) - and hopefully never will - the CDC's  criteria for inclusion in this category are:

Variant of High Consequence (VOHC)

A variant of high consequence has clear evidence that prevention measures or medical countermeasures (MCMs) have significantly reduced effectiveness relative to previously circulating variants.

Possible attributes of a variant of high consequence:

In addition to the possible attributes of a variant of concern
  • Impact on Medical Countermeasures (MCM)
  • Demonstrated failure of diagnostic test targets
  • Evidence to suggest a significant reduction in vaccine effectiveness, a disproportionately high number of infections in vaccinated persons, or very low vaccine-induced protection against severe disease
  • Significantly reduced susceptibility to multiple Emergency Use Authorization (EUA) or approved therapeutics
  • More severe clinical disease and increased hospitalizations
A variant of high consequence would require notification to WHO under the International Health Regulations, reporting to CDC, an announcement of strategies to prevent or contain transmission, and recommendations to update treatments and vaccines.

South Korea Sets New Record (n=5,123) For Daily COVID Cases - Preparing For Omicron



While all eyes are on the emerging Omicron variant, Delta continues to be the overwhelmingly dominant strain, and has recently been rising in many regions (see here, here, and here), making its biggest gains in Africa, the Western Pacific and Europe over the past week (see WHO chart below). 

Even without the added burden of Omicron, the threat from the COVID pandemic is far from over, and could be further compounded this winter with the return of Influenza. 

Overnight South Korea reported their highest 1-day total of cases since the pandemic began (n=5,123), a jump of 60% over the previous day's tally (n=3,032).  

We'll have to wait to see if this is a short-lived anomaly, or a trend - but combined with the threat posed by Omicron - the South Korean Government has reportedly shelved plans to relax COVID-19 curbs (see CNBC Report). 

Yesterday South Korea also addressed plans to deal with the Omicron variant in the following (translated)  document, which also discusses a suspected family cluster recently returned from Nigeria:

Date Created :2021-11-30 20:19

□ The Ministry of Health and Welfare and the Korea Centers for Disease Control and Prevention held an emergency meeting related to Omicron mutation on November 30 (Tuesday) to check the current status and response directions.

○ This is to urgently designate Omicron as a major mutation by WHO, and to analyze the current situation and discuss necessary measures in the future as the number of imported countries continues to increase.

□ Starting with today's meeting, the government will form a cross-ministerial task force* to preemptively discuss countermeasures against domestic inflows, and will continue to monitor the relevant situation and take a preemptive response.

* Korea Centers for Disease Control and Prevention, Ministry of Health and Welfare, Office of National Affairs, Ministry of Strategy and Finance, Ministry of Public Administration and Security, Ministry of Foreign Affairs, Ministry of Justice, etc.

○ The new mutation response TF will focus on ① measures to strengthen management of foreign inflows such as quarantine, ② measures to strengthen monitoring of domestic outbreaks and spreads, ③ measures to strengthen quarantine response such as epidemiological investigations upon inflow into the country, and ④ measures to strengthen patient management.

□ Meanwhile, a couple living in Incheon, who visited Nigeria (11.14.~11.23.), were suspected of having an Omicron mutation and are conducting a whole genome test to confirm the mutation.

○ The couple completed the Moderna vaccination on October 28 and returned to Korea after visiting Nigeria.

○ As a result of contact tracing after confirmation, one acquaintance* and one family living together** who supported the transfer from the airport to their home were additionally confirmed.

* Male in his 40s, confirmed on November 30, ** 1 out of 2 family members living together (in their teens) confirmed on November 30

○ As a result of the mutation PCR test on an acquaintance who was an additional confirmed patient this morning, Omicron was suspected.

Increasingly Nigeria is being mentioned as a focal point for Omicron, and this morning there are reports that the Nigerian CDC has retrospectively identified cases from last October.  While this predates the South African announcement by a month, this doesn't tell us when, or from where, this new variant first  emerged. 

But it does speak to the head start this variant has had in its world tour, and helps explain why this new virus has shown up in so many countries over the past week. 

A list that is certain to expand over the coming days. 

Tuesday, November 30, 2021

UKHSA: England identifies 8 Additional Omicron Cases (n=13) & Scotland Adds 3 More (n=9)



The total number of Omicron cases detected in the UK has more than doubled over the past 24 hours (see yesterday's UK: Scotland Announces 6 Omicron Cases (Some Locally Acquired) & UKHSA Update On 3rd Case), and it seems likely that number will rise substantially over the next few days. 

With growing evidence that this variant has been in Europe for at least 2 weeks - and probably longer - it is likely well into its world tour.  Travel restrictions may slow its spread somewhat, but this virus is out of the bag. 

Earlier today Israeli media reported on two doctors - both fully vaccinated - who have tested positive for Omicron, with one of them recently returning from a medical conference in London.  

While I've not been able to find any official statement out of Israel, those with long memories will recall that some of the early spread of COVID into Europe was traced back to a business conference in Singapore. 

The statement from the UKHSA follows:

Further 8 cases of Omicron variant confirmed

The UK Health Security Agency (UKHSA) has identified 8 further cases of COVID-19 with mutations consistent with B.1.1.529 in England, in addition to the previous 5 confirmed cases of the SARS-CoV-2 variant known as B.1.1.529. The total number of confirmed cases in England is now 13.

The individuals that have tested positive and their contacts are all isolating. Work is underway to identify any links to travel to Southern Africa. We have now identified cases in the East Midlands, East of England, London and North West. UKHSA is carrying out targeted testing at locations where the positive cases were likely to be infectious.

Nine cases have also been identified in Scotland, with 5 cases in the Lanarkshire area and 4 in the Greater Glasgow and Clyde area.

Dr Jenny Harries, Chief Executive of UKHSA, said:

We are continuing our efforts to understand the effect of this variant on transmissibility, severe disease, mortality, antibody response and vaccine efficacy.
Vaccination is critical to help us bolster our defences against this new variant – please get your first, second, third or booster jab without delay.
Following the change in Joint Committee on Vaccination and Immunisation (JCVI) advice yesterday, a booster dose for everyone over 18 years is now recommended at a minimum of 3 months from your last primary course jab. Please take up this offer as soon as you are invited to protect yourself, your families and your communities.
Please make sure to wear a mask in line with government guidance, including on public transport and in shops, to help break the chains of transmission and slow the spread of this new variant.
It’s very likely that we will find more cases over the coming days as we are seeing in other countries globally and as we increase case detection through focused contact tracing. That’s why it’s critical that anyone with COVID-19 symptoms isolates and gets a PCR test immediately.
UKHSA is acting to get scientific information available as quickly as possible in order to inform the right balance of interventions to prevent transmission and protect lives. This will include analysing live samples of the new variant in our laboratories to investigate properties such as response to current vaccines.

As viruses mutate often and at random, it is not unusual for small numbers of cases to arise featuring new sets of mutations. Any variants showing evidence of spread are rapidly assessed.

Netherlands RIVM: Omicron Detected In Sample Collected On Nov. 19th




Although its discovery was only announced 5 days ago, exactly how long Omicron has been spreading in Africa - or internationally - still isn't known.  A report from the Netherlands RIVM (National Institute for Public Health) today confirms that two samples collected on Nov 19th and on Nov 23rd have tested positive for the Omicron variant. 

It is likely that we'll continue to learn about earlier transmissions of this variant, now that public health officials know what they should be looking for. 

All of this matters because the longer Omicron has been in the wind, the further it will have spread.  

Omikron variant found in two previously collected test samples

Publication date 11/30/2021 | 11:15

the RIVM National Institute for Health and Environment has found the corona variant omikron in two test samples that had already been taken in the Netherlands in November. These are samples taken from the GGDMunicipal health service on 19 and 23 November 2021. Saltro, the lab that performed the tests, sent the samples to RIVM.

The samples gave in a special PCR polymerase chain reaction-tests for an abnormality in the so-called spike protein. This gave rise to the suspicion that it was the omikron variant. The samples have been sent to RIVM National Institute for Health and Environment sent to confirm. On November 29, it turned out that two samples were indeed the omikron variant. It is not yet clear whether the people concerned have also been to southern Africa. The RIVM has the GGD Municipal health service'and where the samples were taken. The GGDs inform the people concerned and start source and contact investigations.

On November 26, 624 people returning from South Africa were tested for the corona virus at Schiphol. Of these, 61 passengers received a positive test result. In total, the omikron variant was diagnosed in 14 of them. During the laboratory investigation, different types of virus strains of the omikron variant were found. This means that the people most likely got infected separately from each other, from a different source and in a different place.
Follow the spread in the Netherlands

In the coming period, various studies will be conducted into the distribution of the omikron variant in the Netherlands. For example, the samples of positively tested people returning from southern Africa are further examined at various laboratories in the Netherlands. RIVM will also retroactively examine more samples from laboratories that routinely perform the special PCR test and that showed the abnormality in the protein. Finally, RIVM, together with 31 Dutch laboratories, monitors the occurrence of variants of the coronavirus via the National Germ Surveillance .
Exchange information internationally

Internationally, the distribution of the omikron variant is closely monitored. Experts would like to know more as soon as possible. How contagious and sickening is the variant? And how well do the existing vaccines work against this variant? There are daily contacts with experts from all over the world about this. For example, experts from RIVM are represented in weekly meetings of the World Health Organization (WHO) and ECDCEuropean Center for Disease Prevention and Control (the European RIVM) and there is a special European network where signals about the coronavirus and variants are exchanged daily.

The reference laboratories at RIVM and Erasmus MCErasmus University Medical Centerwork closely with various laboratories and the GGDs to collect more information about the omikron variant. On Tuesday 7 December, RIVM will provide an update on the situation on the website.

PLoS NTD: Clinical & Virological Impact of Single and Dual Infections with influenza A (H1N1) and SARS-CoV-2


One of the topics we've been following for more than a year is the potential for - and the impact of - dual infection with COVID-19 and Influenza A (or B).  Data has been limited, but what we have seen has suggested that a co-infection increases the severity of illness, and the risk of death. 

A little over a year ago, in PHE Study: Co-Infection With COVID-19 & Seasonal Influenzawe looked at a Public Health England study that warned that being co-infected with influenza and COVID more than doubled the risk of death over having COVID alone.

 Interactions between SARS-CoV-2 and Influenza and the impact of coinfection on disease severity: A test negative design


While being infected with Influenza lowered the risk of contracting SARS-CoV-2 (likely due to `viral interference'), among those who did contract both, they determined:

 `. . . the risk of death was nearly six times greater among individuals with a SARS-CoV-2 and influenza coinfection than those with neither influenza nor SARS-CoV-2 and that this effect is significantly higher than the risk associated with SARS-CoV-2 infection alone.'

Since then, we've seen animal studies (see here and here) that further support these concerns, but the lack of an influenza season last year has limited the amount of real world data on human co-infections. 

With influenza (A/H3N2) recently on the ascendent (see CDC HAN # 00458 : Increasing Seasonal Influenza A (H3N2) Activity), COVID Delta still circulating globally, and a new Omicron variant on its way, getting more data on COVID-Flu coinfections takes on new importance this fall. 

With the caveat that this study is based on a limited number of cases in Guangdong Province, China between January 2020 and November 2020 - a time before the emergence of any of the COVID variants (Alpha, Delta, Omicron) of concern and when a milder H1N1 flu virus was circulating - this study also finds:
  • Co-infection had an increased odds of acute kidney injury, acute heart failure, secondary bacterial infections, multilobar infiltrates and admittance to ICU than monoinfection.
  • Co-infection by SARS-CoV-2 and H1N1 caused more severe disease than monoinfection by either virus in adult inpatients. 
The full (open access) paper is available on the PloS NTD website. I've only posted the link and some excerpts below.  I'll have a brief postscript after the break.
Clinical and virological impact of single and dual infections with influenza A (H1N1) and SARS-CoV-2 in adult inpatients

Jiazhen Zheng, Fengjuan Chen, Keyi Wu, Jiancheng Wang, Furong Li, Shan Huang, Jianyun Lu, Jinghan Huang, Huamin Liu, Rui Zhou, Zhiwei Huang, Bingyao Meng, Zelin Yuan, Xianbo Wu

Published: November 29, 2021


Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mimics the influenza A (H1N1) virus in terms of clinical presentation, transmission mechanism, and seasonal coincidence. Comprehensive data for the clinical severity of adult patients co-infected by both H1N1 and SARS-CoV-2, and, particularly, the relationship with PCR cycle threshold (Ct) values are not yet available.
All participants in this study were tested for H1N1 and SARS-CoV-2 simultaneously at admission. Demographic, clinical, treatment, and laboratory data were extracted from electronic medical records and compared among adults hospitalized for H1N1 infection, SARS-CoV-2 infection and co-infection with both viruses. Ct values for viral RNA detection were further compared within SARS-CoV-2 and co-infection groups. Score on seven-category ordinal scale of clinical status at day 7 and day 14 were assessed.
Among patients with monoinfection, H1N1 infection had higher frequency of onset symptoms but lower incidence of adverse events during hospitalization than SAR-CoV-2 infection (P < 0.05).
Co-infection had an increased odds of acute kidney injury, acute heart failure, secondary bacterial infections, multilobar infiltrates and admittance to ICU than monoinfection.
Score on seven-category scale at day 7 and day 14 was higher in patients with coinfection than patients with SAR-CoV-2 monoinfection (P<0.05). Co-infected patients had lower initial Ct values (referring to higher viral load) (median 32) than patients with SAR-CoV-2 monoinfection (median 36). Among co-infected patients, low Ct values were significantly and positively correlated with acute kidney injury and ARDS (P = 0.03 and 0.02, respectively).
 Co-infection by SARS-CoV-2 and H1N1 caused more severe disease than monoinfection by either virus in adult inpatients. Early Ct value could provide clues for the later trajectory of the co-infection. Multiplex molecular diagnostics for both viruses and early assessment of SAR-CoV-2 Ct values are recommended to achieve optimal treatment for improved clinical outcome.

Author summary

The baseline enrolled 505 patients admitted to Guangzhou Eighth People’s Hospital (Guangzhou, Guangdong) with a diagnosis of COVID-19 or H1N1. All the patients were tested by both viruses at admission. Demographic, clinical, treatment, and laboratory data were extracted from electronic medical records and compared among adults (≥18 years) hospitalized for H1N1 infection (n = 220), SARS-CoV-2 infection (n = 249) and co-infection with both viruses (n = 36).
The prevalence rate of H1N1 co-infection was 12.6% (36/285) among patients hospitalized with COVID-19. Co-infection affected a predominantly older age group and was associated with poorer clinical outcome.
We also described the viral load trajectory in patients with diverse types of infection. Lower initial Ct values (higher viral loads in nasopharyngeal swabs) of co-infected patients was found to be associated with a higher number of adverse events and clinical symptoms.
Considering the COVID-19 pandemic and a simultaneous epidemic of seasonal influenza, the data in China may critically inform future therapeutic or prophylactic strategies, especially for other developing countries.


Our findings are relevant in the context of the COVID-19 pandemic. Co-infection affected a predominantly older age group and was associated with poorer clinical outcomes. The prevalence rate of co-infections in COVID-19 cases shows the importance of flu vaccination and warrants its increased coverage. Additionally, molecular diagnostic testing for H1N1 virus is recommended for COVID-19 inpatients to provide timely and appropriate treatments for improved outcomes. The Ct value collected with nasopharyngeal swabs in the early stage of co-infection could provide clues for the later trajectory of the disease.

          (Continue . . . )

Since this study deals with a milder H1N1 Influenza A virus (in adults) and the `wild type' COVID virus that dominated in during most of 2020 - and was conducted before COVID vaccinations became widely available - it makes direct comparisons to today more difficult. 

But it is probably safe to assume that you really, really don't want to endure a dual infection, regardless of the influenza strain or the COVID variant. 

Last winter we got lucky, and influenza was a no-show, but this year that appears less likely.  All reasons why, even if they aren't 100% effective, it makes sense to get both the COVID and Flu vaccines and to resume wearing face masks in  public. 

Hospitals are likely to be stretched to their limits this winter due to the expected arrival of Omicron, and in several states Crisis Standards of Care are already invoked (see The Realities Of Crisis Standards Of Care).

Making anything you can do to reduce your odds of being infected with either virus (or both), or hospitalized for any reason, well worth your effort.