Preprint: SARS-CoV-2 Omicron VOC Transmission in Danish Households

 

Omicron's Record Surge - Credit Our World In Data

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Six weeks ago, nobody had ever heard of the Omicron variant, but in a little over a month it has become the dominant COVID strain in the United States, much of Europe, and threatens to conquer the world in early 2022.  

According to the New York Times, more than 580,000 cases were reported in the United States over the past 24 hours - more than doubling the heights reached during last winter's epidemic wave - and even this is likely an undercount. 

While there is some evidence to suggest that Omicron may be milder - at least in vaccinated individuals - the sheer volume of cases over the next few weeks threatens healthcare delivery systems (see Maryland: Multiple Hospitals Activate Crisis Standards of Care, and society in general.  

No matter how difficult things may get in the weeks ahead, we have to count ourselves lucky that the first wave of COVID in early 2020 - before anyone had any immunity - wasn't as aggressive as Omicron appears to be now.  

But immunity, either through previous infection or vaccination, against Omicron isn't as robust as we saw against Delta.  Transmission of Omicron is remarkably high, even among those who are fully vaccinated, but there is evidence to suggest that vaccination still reduces your odds of infection. 

We've a new preprint, from researchers in Denmark, that attempts to quantify the effects of vaccination (including booster shots) on the household transmission of Omicron.  First the SSI Summary, followed by a link and the abstract to the preprint. 

I'll have a brief postscript after the break. 

Vaccination protects against infection in households shows new study

Researchers from the University of Copenhagen, Statistics Denmark, DTU and the Statens Serum Institut have investigated how much the omicron variant is contagious in relation to the delta variant in Danish households. The new study takes into account a number of factors including vaccination.

Last edited December 31, 2021

Ever since the omicron variant appeared in November, researchers have been working to find out how contagious it is compared to other covid-19 variants.

Now comes a new Danish study with part of the answer. Researchers from the University of Copenhagen, Statistics Denmark, DTU and the Statens Serum Institut (SSI) have investigated how much the omicron variant is contagious in relation to the delta variant in Danish households.

The results indicate that the rapid spread of the omicron variant is largely due to its ability to evade immunity built up by vaccination.

Read the pre-print version of the new studio here.

Higher infection among unvaccinated

The study also looked at the effect of vaccination in relation to household infection. In general, there was a higher transmission for unvaccinated individuals and a lower transmission for booster-vaccinated individuals compared to fully vaccinated individuals. This applied regardless of the variant with which the household was infected.

Transmission is here an overall estimate of transmission from an infected vaccinated and a vaccinated "recipient" of the infection.

And higher infection in "omikron households"

When comparing households infected with the omicron variant and households infected with the delta variant, there was a significantly higher transmission depending on vaccination status.

11,937 households surveyed

The study included 11,937 households (of which 2,225 with omicron infection) and 27,874 household members.

A total of 6,397 household members were tested positive within 1-7 days after the first person in the household was tested positive. The calculated attack rate was 31% and 21% in omicron- and delta-variant-infected households, respectively.

Read more

The study has just been published as a working paper (not yet peer-reviewed) and is available on a pre-print server:

SARS-CoV-2 Omicron VOC Transmission in Danish Households

Frederik Plesner Lyngse, Laust Hvas Mortensen, Matthew J. Denwood, Lasse Engbo Christiansen, Camilla Holten Møller, VRobert Leo Skov,Katja Spiess, Anders Fomsgaard, Ria Lassauniere, Morten Rasmussen, ProfileMarc Stegger, Claus Nielsen, Raphael Niklaus Sieber, Arieh Sierra Cohen, Frederik Trier Møller, Maria Overvad, Kåre Mølbak, Tyra Grove Krause, Carsten Thure Kirkeby

doi: https://doi.org/10.1101/2021.12.27.21268278

Preview PDF

Abstract

The Omicron variant of concern (VOC) is a rapidly spreading variant of SARS-CoV-2 that is likely to overtake the previously dominant Delta VOC in many countries by the end of 2021. We estimated the transmission dynamics following the spread of Omicron VOC within Danish households during December 2021.

We used data from Danish registers to estimate the household secondary attack rate (SAR). Among 11,937 households (2,225 with the Omicron VOC), we identified 6,397 secondary infections during a 1-7 day follow-up period. The SAR was 31\% and 21\% in households with the Omicron and Delta VOC, respectively.

We found an increased transmission for unvaccinated individuals, and a reduced transmission for booster-vaccinated individuals, compared to fully vaccinated individuals.

Comparing households infected with the Omicron to Delta VOC, we found an 1.17 (95\%-CI: 0.99-1.38) times higher SAR for unvaccinated, 2.61 times (95\%-CI: 2.34-2.90) higher for fully vaccinated and 3.66 (95\%-CI: 2.65-5.05) times higher for booster-vaccinated individuals, demonstrating strong evidence of immune evasiveness of the Omicron VOC. Our findings confirm that the rapid spread of the Omicron VOC primarily can be ascribed to the immune evasiveness rather than an inherent increase in the basic transmissibility.

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Due to the finding that transmission of Omicron was only marginally higher among the unvaccinated than it was Delta, these researchers suggest the rapid spread of Omicron is due mostly to reduced protection from prior immunity (via vaccines and/or previous infection) compared to the Delta variant. 

This does not say (as some on the internet will undoubtedly misconstrue), that the vaccinated are more likely to be infected, or to spread Omicron, than the unvaccinated. 

Instead the authors conclude:

Our results show that the Omicron VOC is generally 2.7-3.7 times more infectious than the Delta VOC among vaccinated individuals (Table 3). This observation is in line with data from (18), which estimated that 19% of Omicron VOC primary cases in households in the UK resulted in at least one other infection within the household, compared to only 8.3% of those associated with the Delta VOC.

Furthermore, we show that fully vaccinated and booster-vaccinated individuals are generally less susceptible to infection compared to unvaccinated individuals (Table 2). We also show that booster-vaccinated individuals generally had a reduced transmissibility (OR: 0.72, CI: 0.56-0.92), and that unvaccinated individuals had a higher transmissibility (OR: 1.41, CI: 1.27-1.57), compared to fully vaccinated individuals.

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While vaccination against COVID is no guarantee you won't catch, or pass on, Omicron - it does lower your odds of infection - and likely reduces your risk of experiencing severe illness, or death. 

Perhaps not as much as we had initially hoped from a COVID vaccine, but it is still far better than it might have been. 

UK Daily COVID Numbers & Omicron Overview (Dec 30th)

 

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The UK's Health Security Agency updated today's COVID numbers more than 3 hours later than usual, citing data collection problems.  Once again, the UK has set a new record with 189,213 new cases - which likely under represents the true burden of the virus - along with a jump in COVID-related deaths (n=332). 

This jump in deaths appears to be the result of a data backlog. Given the reporting interruptions over the Christmas (and soon to be New Year's) Holidays, we'll have to wait a week or so to see if deaths are truly rising, or if this is just an aberration. 

Although COVID patients admitted to the hospital has increased by 32% over 7 days, this data is only current through Dec. 24th, making it difficult to draw any conclusions about Omicron's impact. 

The next-to-last Omicron Daily Overview, which will reportedly be discontinued after tomorrow's report, shows a modest increase in Omicron-related Hospitalizations, and one additional Omicron-related death. 




Once again, reporting is `iffy' at best, and unlikely to improve until later next week.

CDC Raises Cruise Ship Travel Health Notice To Level 4

 

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Early in the pandemic the CDC issued a No-Sail order on cruise ships - effective March 14, 2020 - due to the risk of introducing, transmitting, or spreading COVID-19, which was extended several times during 2020. 

In late 2020, the CDC released a Framework for Conditional Sailing Order, which led to the resumption of cruise activity from U.S. ports under specific conditions. 

Earlier this month, in Louisiana Dept of Health: COVID Outbreak On Cruise Ship Returning To New Orleans, we looked into the COVID status of Cruise ships (see CDC Cruise Ship Color Status), and at that time the CDC was monitoring 9 minor cruise ship outbreaks and actively investigating 24. outbreaks.

As to today, CDC is investigating roughly 90 Cruise Ship outbreaks (yellow), and monitoring an additional 3 (orange). 

Today the CDC raised their travel advisory for Cruise Ships to its highest level - Red Level 4 

Level 4: Very High Level of COVID-19

Summary of Recent Changes

December 30, 2021

The COVID-19 Travel Health Notice level has been updated from Level 3 to Level 4, the highest level. This reflects increases in cases onboard cruise ships since identification of the Omicron variant.

 

Avoid cruise travel, regardless of vaccination status.

 

If you travel on a cruise ship, make sure you are fully vaccinated before travel and get a COVID-19 vaccine booster dose if you are eligible. Getting vaccinated is still the best way to protect yourself from severe disease, slow the spread of COVID-19, and reduce the number of new variants. People who are not fully vaccinated should follow additional recommendations before, during, and after travel.

 

Vaccination provides some (perhaps substantial) protection against serious illness and death from the Omicron (and Delta) variants, but does a far less effective job preventing infection, making this steep rise in shipboard outbreaks all but inevitable. 

Three Blind Spots Going Into 2022

 My Original Wuhan Post  12/31/19

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Two years ago tonight the dedicated newshounds at FluTrackers began posting numerous reports out of China on an outbreak of an unidentified viral pneumonia in Wuhan; the capital and largest city (pop. 11 million) in Hubei Province.

FluTrackers - which has volunteers monitoring international news feeds practically 24/7 - first post on the matter went live at 11:35 pm on the night of the 30th (see below). 

By the time I had the story, and enough coffee to allow myself to write semi-coherently, FT had already published 7 reports.  Before that first day had ended, they had posted more than a dozen more. 

My first post went live at 3:54 am and would be the 1st of three I would publish that day (see here, here, and here). 

While none of us knew the world was about to change, it `felt' important. Reminiscent, in some ways, of the early reports of H7N9 emerging in China on March 31st, 2013 (see China: Two Deaths From H7N9 Avian Flu). 

Within hours Crof (who is 3 hours behind on the west coast) had his first blog (Hong Kong: CHP closely monitors cluster of pneumonia cases on Mainland), but it would literally be days before the mainstream news took notice. 

On January 6th, the CDC Issued a Level 1 (Watch) Travel Notice For Unidentified Pneumonia - Wuhan, China, but it would take another 10 days before the WHO would report `Evidence of Limited Human-to-Human Transmission' - WHO WPRO.

By that time, COVID was already well established in China, and rapidly wending its way across Europe and around the world.  

While the world may have felt blindsided by COVID, this very scenario is one that had been discussed, analyzed, and had been the subject of numerous `tabletop' simulations over the years (see JHCHS Pandemic Table Top Exercise (EVENT 201) Videos Now Available Online). 

Dire pre-COVID pandemic predictions by global health agencies include:

WHO/World Bank GPMB Pandemic Report : `A World At Risk'

WHO: On The Inevitability Of The Next Pandemic

World Bank: The World Ill-Prepared For A Pandemic

Six weeks before the Wuhan outbreak, in African Swine Fever's (ASF) Other Impacts; Pharmaceuticals, Bushmeat, and Food Insecurity, I even speculated that China's ASF outbreak could lead to increased `bushmeat' consumption, which in turn might spark another SARS-like outbreak.  

A lucky guess, proving that if you write 15,000+ blog posts, you're bound to get something right eventually. 

The point being, the only people who were truly surprised that the world was facing a pandemic threat in January of 2020 were those who hadn't been paying attention.  

And sadly, despite the brutal lessons of the past two years, there are many plausible viral candidates for sparking the next pandemic that are given far less attention than they deserve. 

While the list is long, three of the main contenders (and a bonus) include:

HPAI H5N6 Avian Influenza 

China's H5N6 Problem - 31 Cases in 2021

It's been more than two weeks since the last report from China (see Hong Kong CHP Monitoring 4 More H5N6 Human Infections On the Mainland), but its a pretty safe bet that human infections with H5N6 haven't stopped now that winter has arrived.  

China doles out infectious disease reports according to their own needs, and we often only hear about them weeks or months after the fact. 

While H5N6 hasn't acquired the ability to transmit efficiently between humans, it continues to evolve, which has spurred a number of recent risk analyses from public health agencies around the globe (see here, here, and here), leading up to the CDC Adding A New H5N6 Avian Flu Virus To IRAT List three weeks ago. 

Unlike COVID, which has a CFR (Case Fatality Rate) of 1%-2%, H5N1 has killed nearly half of those known to have been infected.

While H5N6 is currently our biggest HPAI H5 concern, it isn't the only one we are watching (see Science: Emerging H5N8 Avian Influenza Viruses). 

 

MERS-COV 

Before COVID, the Coronavirus of greatest concern was MERS-CoV - first identified in 2012 on the Arabian Peninsula - which is endemic in camels, and carries a hefty 35% CFR when it jumps to humans. 

In the 8 years prior to 2020, MERS had infected well over 2,000 people, and had sparked several large nosocomial outbreaks in hospitals in the Middle East and South Korea. 

All of these numbers are expected to be massive undercounts, as we've seen estimates  (see EID Journal: Estimation of Severe MERS Cases in the Middle East, 2012–2016) that only a fraction of cases are captured by surveillance.

Since COVID emerged, reporting on MERS has slipped even further, with Saudi Arabia only reporting 17 cases in 2021 (a drop of > 90% over 2019). 

We have seen analyses (see Study: A Pandemic Risk Assessment Of MERS-CoV In Saudi Arabia), suggesting the virus doesn't have all that far to evolve before it could also pose a genuine global threat.

While nobody really knows how big of a threat it might pose, the possibility of SARS-CoV-2 and MERS-CoV simultaneously infecting the same host is regarded as a theoretical breeding ground - via recombination - of new, potentially more dangerous, coronaviruses (see Co-infection of MERS-CoV and SARS-CoV-2 in the same host: A silent threat).

Swine Variant Influenza (Including EA H1N1 `G4' )

The risk of one of these swine variant viruses sparking a pandemic is relatively low, but it isn't zero. A swine-origin H1N1v virus jumped to humans and sparked a mild-to-moderate flu pandemic in 2009, 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.

The CDC's IRAT (Influenza Risk Assessment Tool) also 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 

While Swine variant influenza viruses tend to be less severe than avian influenza viruses in humans, all of the human influenza pandemics we know of going back 130 years have been caused by H1, H2, or H3 viruses (see Are Influenza Pandemic Viruses Members Of An Exclusive Club?). 

Bonus : Virus X 

While this short list could easily include Monkeypox, Lassa Fever,  and even Nipah the possibility exists that we could be hit by something entirely new, or at least not on our radar. 

A little over 4 months ago, in PNAS Research: Intensity and Frequency of Extreme Novel Epidemics, we looked at a paper that suggested that the probability of novel disease outbreaks will likely grow three-fold in the next few decades.

Like it or not, COVID-19 won't be the last - and perhaps not the worst -  pandemic we'll face in the years ahead. The time to begin preparing is now, not after the next threat emerges. 

Maryland: Multiple Hospitals Activate Crisis Standards of Care

https://emergency.cdc.gov/coca/calls/2020/callinfo_121720.asp

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Although there is some apparent good news regarding the relative severity of the Omicron variant (see More Reports Suggest Omicron May Be Less Severe Than Delta), its greatly enhanced transmissibility and ability to evade previously acquired immunity are generating the biggest pandemic waves of COVID we've seen to date. 

When you add in rising seasonal influenza to the mix (see PAHO: Epidemiological Update - Influenza in the context of the COVID-19 pandemic), high rates of absenteeism due to illness in the healthcare sector - and a growing number of people needing hospital beds - there are genuine reasons to worry over the ability of hospitals to function properly. 

Three weeks ago, in More U.S. Hospitals Inch Towards Invoking Crisis Standards of Care, we looked at the rising number of hospitals adopting emergency protocols to deal with overwhelmed ERs, increasing admissions, and growing staff shortages.

We've explored the impact of these protocols often in the past few months (see The Realities Of Crisis Standards Of Care), but in short it can mean hospitals are allowed - under certain dire circumstances - to ration care (including access to ventilators, ICU beds, etc.), invoke DNR (Do Not Resuscitate) protocols (see Standards Of Care During A Pandemic: CPR & Cardiac Arrest), and even turn some patients away.

Ten days ago, in Ohio Governor Mobilizes National Guard To Assist Hospitals Struggling With COVID, we looked at an increasingly common tactic; using military or National Guard troops to keep overburdened hospitals operational.  

This week, as new COVID cases have averaged 250,000 a day, and as influenza picks up around the nation (see CDC Urges Flu Vaccination as Flu Activity Picks Up), more hospitals have announced plans to activate crisis standards of care.

A couple of high profile examples from Maryland include:

Johns Hopkins Bayview Medical Center Activates Crisis Standards of Care

12/29/2021

Baltimore, Md. (December 29, 2021) – While communities across the country grapple with the recent surge in COVID-19 cases, the pandemic continues to critically stress staffing and resources at hospitals and health care facilities, including the six hospitals within the Johns Hopkins Health System (JHHS). As a result, today, JHHS and Johns Hopkins Bayview Medical Center (JHBMC) leaders announced that JHBMC will implement Crisis Standards of Care (CSC) protocols.

“This decision was not taken lightly,” said Kevin Sowers, president of the Johns Hopkins Health System and executive vice president of Johns Hopkins Medicine. “Unfortunately, we’ve seen Johns Hopkins Bayview’s census of patients with COVID-19 and non-COVID-19 clinical needs spike dramatically in recent days. Working closely with the Johns Hopkins Medicine Unified Command Center staff, we have agreed that moving to CSC is the right decision.”

(Continue . . . )

UNIVERSITY OF MARYLAND HARFORD MEMORIAL HOSPITAL DECLARES CRISIS STANDARDS OF CARE

BY WMAR BALTIMORE | DECEMBER 29, 2021

 

The substantial increase of COVID-19 positive patients over the past month at UM Upper Chesapeake Medical Center (UM UCMC) in Bel Air has forced the hospital to declare Crisis Standards of Care (CSC) protocols as part of its pandemic plan. Effective today, the UM Harford Memorial Hospital (UM HMH) in Havre de Grace will adopt CSC as well.

          (Continue . . . )

Even when it isn't making headlines, hospitals, clinics, and EMS services around the country are making daily - sometimes hourly - adjustments to the level of care they can deliver.  Increasingly I'm seeing local hospitals go on Volume Bypass here in Central Florida, and EMS response times are rising. 

The challenge going into 2022 is keeping emergency services intact amid a blizzard of COVID (and increasingly, flu) cases, and a steep increase in HCW absenteeism. 

Although rising COVID and flu cases may be the primary cause of these disruptions, anyone who needs any kind of emergency (or sometimes, elective) medical care will be affected. This is simply a bad time to have a heart attack, a stroke, get in an accident, need elective surgery, dialysis, or even routine medical care from your primary physician. 

While you and I can't do much to alleviate the crisis, we can make reasonable choices that can help avoid being part of the problem. 

Get vaccinated (against COVID and Flu), stay home when you can, avoid crowds, wear a face mask in public, and avoid any needlessly risky behavior that might put you in need of emergency services in the weeks ahead.    

And hope you get lucky.

UK Daily COVID Number & Omicron Overview (Dec 29th)

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The UK, like many other countries, is having difficulty collecting, collating, and publishing COVID data in the face of rapidly rising Omicron cases.  Today, their daily update - published 2 hours late - sets a new record (n=183,037), but it includes 5 days worth of previously missing data from Northern Ireland. 

29 December 2021
Log category: DATA ISSUE Reported figures for Northern Ireland cover 5-day period

Newly reported figures from Northern Ireland for testing, cases and deaths reflect the difference in totals reported on 29 December and those last published by Northern Ireland on 24 December 2021.

Figures for cases and deaths are available by specimen date and date of death respectively. Retrospective report date figures for each day from 25 to 28 December are not available.

The UK's Health Security Agency also announced that on Friday, publication of their detailed Omicron Overview report - which began less than 2 weeks ago - will be ended.

While the UK Dashboard provides a decent overview of COVID in the UK, having less data is never preferable to having more, particularly during a crisis. And some data on the Dashboard lags a week or more behind, such as today's update on Hospitalizations (up 13.2% in a week), which is only current through Dec 21st. 

Today's (soon to be discontinued) 7-page Omicron Overview adds nearly 33K confirmed Omicron cases, increases Omicron related hospitalizations to 766 (+98) and deaths to 53 (+4). 

 

Reporting on COVID, particularly over the holidays, has become increasingly chaotic and unreliable.  And not just in the UK.  A lot is due to logistical constraints - including a lack of testing capacity - both of which ought to be in much better shape two years into this pandemic. 

But too many people and governments assumed that vaccines would defeat SARS-CoV-2 by the end of the year, and declared victory prematurely (see last September's NPR Is The Worst Over? Modelers Predict A Steady Decline In COVID Cases Through March).  

While there were reasons to question these projections, and warnings that new variants might emerge that could evade vaccines (see UK SAGE: Can We Predict the Limits of SARS-CoV-2 Variants and their Phenotypic Consequences?), most were ignored in favor of a more optimistic scenario. 

So we find ourselves going into a 3rd year of the pandemic faced with a massive new wave of infection, too little testing capacity, increasing pressure on hospitals, and very few options to deal with Omicron's impact other than to reduce isolation and quarantine times, and hope this wave burns out quickly and ends the pandemic.  

While that could happen, it is based more on hope than on science.  And it ignores the possibility that the next global health crisis won't emerge while we are still dealing with COVID. 

As bad as COVID has been, we got very lucky in that its fatality rate wasn't higher - and that the really transmissible strain waited nearly two years to emerge - giving us time to develop a vaccine and get it into the arms of billions of people.  

The next emerging virus may not be nearly as accommodating. 

And if we approach the next crisis as fragmented, flat-footed, and oblivious to the threat as we've approached this one, we could end up looking back at 2020-2021 and calling it the `good old days'. 

PAHO: Epidemiological Update - Influenza in the context of the COVID-19 pandemic

 

Influenza Increasing Across Americas - Credit PAHO

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While COVID Delta & Omicron continue their global tug-of-war, seasonal influenza has been making a return after more than 20 months of little to no activity, and leading this flu charge is a `drifted' A/H3N2 virus that may reduce the VE (Vaccine Effectiveness) of this year's flu shot. 

Last week, WHO Europe announced Influenza Season Has Begun, a month ago we saw CDC HAN # 00458 : Increasing Seasonal Influenza A (H3N2) Activity, and we've seen recent ports from Brazil on their escalating spread of H3N2. 

Yesterday (Dec. 28th) PAHO (Pan American Health Organization) released a new Epidemiological Report on the recent rise in influenza amid an ongoing COVID pandemic.  A brief summary and a link to the 9-page document follow:

Epidemiological Update: Influenza - 28 December 2021

Considering the increase of cases of influenza A(H3N2) in some countries in the region, mainly in the Northern Hemisphere, the Pan American Health Organization/World Health Organization (PAHO/WHO) recommends that Member States adopt the necessary measures to prepare for the concomitant circulation of influenza and SARS-CoV-2 to ensure appropriate clinical management, including the procurement of antivirals supplies and their early administration to persons at risk of severe disease, ensure strict compliance with infection prevention control measures in health care services, and continue vaccination to prevent severe cases and deaths.

A summary of the influenza situation in the Region of the Americas by subregions, and of the cases reported in the last four epidemiological weeks can be found in this document.

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Concerns that we could see a `twindemic' of Influenza and COVID have risen in recent weeks, and that could not only impact our ability to differentiate between viral infections, it could seriously increase the load on already overburdened healthcare delivery services in the weeks and months ahead. 

Complicating matters further, there are genuine concerns over the impact of coinfections with COVID and Influenza, which - while only rarely reported thus far - are feared could increase mortality rates over monoinfection by either virus.  

PHE Study: Co-Infection With COVID-19 & Seasonal Influenza,

Clinical and virological impact of single and dual infections with influenza A (H1N1) and SARS-CoV-2 in adult inpatients

ASM Journal: SARS-CoV-2 and Influenza A Virus Co-infections in Ferrets 

While the concomitant circulation of seasonal influenza and SARS-CoV-2 was all but assured to happen at some point, it comes a particularly bad time, with the global spread of a new, highly transmissible Omicron variant. 

Although it may feel like `piling on' at this point, viruses simply don't care. 

CDC MMWR: Investigation of a SARS-CoV-2 Omicron Variant Cluster — Nebraska, Nov–Dec 2021

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Although we only got our first look at a new, emerging COVID variant (now dubbed Omicron) from South Africa 5 weeks ago (see Nov 25th South African NICD Statement On B.1.1.529 Variant), we now know this highly transmissible virus had already embarked on its world tour.

While there are reports suggesting Omicron may produce milder illness than Delta, its increased  transmissibility and heightened ability to evade prior immunity - either from vaccination or previous infection - more than makes up for any reduced pathogenicity. 

Yesterday the CDC's MMWR published an Early Release report on the earliest known importation of Omicron into the United States by a traveler from Nigeria who arrived on Nov 23th, and its subsequent spread to the index cases' 5 close contacts.  

While this report covers just one small cluster (n=6) of Omicron cases, it suggests that incubation times for Omicron may be lower than we've seen previously with COVID, and that the clinical course of their illness was `similar to or milder than' what has previously been reported among vaccinated and/or previously infected individuals infected with Delta. 

They did note that:

The unvaccinated patient without a previous COVID-19 diagnosis experienced cough, joint pain, congestion, fever, and chills.

None of the five, however, became ill enough to be hospitalized. 

Whether this cluster is representative of Omicron's impact on a wider scale remains to be seen, but it does generally correspond to some of the anecdotal reports we are hearing; rapid onset of symptoms, vaccine breakthroughs and reinfections being common, and milder symptoms among the vaccinated. 

First a link, and excerpts from this MMWR Early Release, after which I'll return with a postscript. 

Investigation of a SARS-CoV-2 B.1.1.529 (Omicron) Variant Cluster — Nebraska, November–December 2021

Early Release / December 28, 2021 / 70

Lauren Jansen, MD1,2; Bryan Tegomoh, MD1,3; Kate Lange4; Kimberly Showalter4; Jon Figliomeni, MHA1; Baha Abdalhamid, MD, PhD5; Peter C. Iwen, PhD5; Joseph Fauver, PhD6; Bryan Buss, DVM1,7; Matthew Donahue, MD1

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The B.1.1.529 (Omicron) variant of SARS-CoV-2 (the virus that causes COVID-19) was first detected in specimens collected on November 11, 2021, in Botswana and on November 14 in South Africa;* the first confirmed case of Omicron in the United States was identified in California on December 1, 2021 (1). On November 29, the Nebraska Department of Health and Human Services was notified of six probable cases† of COVID-19 in one household, including one case in a man aged 48 years (the index patient) who had recently returned from Nigeria.

Given the patient’s travel history, Omicron infection was suspected. Specimens from all six persons in the household tested positive for SARS-CoV-2 by reverse transcription–polymerase chain reaction (RT-PCR) testing on December 1, and the following day genomic sequencing by the Nebraska Public Health Laboratory identified an identical Omicron genotype from each specimen (Figure). Phylogenetic analysis was conducted to determine if this cluster represented an independent introduction of Omicron into the United States, and a detailed epidemiologic investigation was conducted. This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy.§

The index patient, who was unvaccinated, had a history of domestically acquired symptomatic SARS-CoV-2 infection confirmed by RT-PCR a year prior in November 2020. He reported unmasked close contact¶ with a masked, coughing person on November 20, 2021, during an international conference in Nigeria, which included attendees from multiple African countries. Before his return trip to the United States, he completed required pretravel testing with receipt of a negative antigen test result on November 21.

Upon his return on November 23, while still asymptomatic, he had unmasked close contact with five household contacts. One household contact was fully vaccinated** (second Pfizer-BioNTech vaccine dose received in August 2021) and had previous symptomatic COVID-19 (RT-PCR confirmed in November 2020), three were unvaccinated and had previous symptomatic COVID-19 (RT-PCR confirmed in November 2020), and one was unvaccinated and had mild upper respiratory symptoms in November 2020, just before illness onset in the other household members, but received a negative SARS-CoV-2 RT-PCR test result at that time. No household members reported underlying medical conditions or immunocompromising conditions known to increase the risk for severe COVID-19 or diminish response to vaccination.††

On November 24, 2021, the index patient experienced symptoms consistent with COVID-19§§ and initially received a positive SARS-CoV-2 antigen test result from a local medical center on November 26. All six household members (median age = 18.5 years; range = 11–48 years) experienced symptom onset during November 24–26; median interval between earliest possible exposure to the index patient and symptom onset was 73 hours (range = 33–75 hours). The index patient and the four household contacts with previous confirmed infections described the symptoms and severity of their recent COVID-19 infection as being similar to or milder than those during their first infection.

The five reinfected patients experienced fewer current symptoms, including loss of taste (none), loss of smell (none), and subjective fever (two), compared with symptoms reported during their first infections (four, four, and four, respectively). The unvaccinated patient without a previous COVID-19 diagnosis experienced cough, joint pain, congestion, fever, and chills. None required hospitalization for either their first or second infections. Twelve close community contacts of the family were identified. Four consented to testing for SARS-CoV-2 (median of 10.5 days postexposure; range = 10–11 days); specimens from these four close contacts tested negative.

Epidemiologic and clinical features of Omicron infection are still being described. Observations from this investigation, which included one patient who experienced reinfection¶¶ after having been fully vaccinated, four patients who experienced reinfection, and one who experienced their first infection, suggest a shorter incubation period and a clinical syndrome similar to or milder than that associated with previously described variants in persons who have been vaccinated or previously infected, and add to existing evidence suggesting an increased potential for reinfection.*** Whereas the median SARS-CoV-2 incubation period has been described as ≥5 days (2,3), and closer to 4 days for the SARS-CoV-2 B.1.617.2 (Delta) variant,††† the median incubation period§§§ observed in this cluster was approximately 3 days.

Although few clinical descriptions of Omicron infections are available, mild illness among vaccinated patients has been reported (4). It is unknown whether the mild clinical syndromes or differing symptom descriptions are a result of existing immunity or altered clinical features associated with Omicron infection. The five reinfections, including one after full vaccination, might be explained by waning immunity, the potential for partial immune evasion by Omicron, or both. Conclusions drawn from these observations are limited by small sample size. More data will be needed to fully understand the epidemiology of the Omicron variant.

Travel history of the index patient and phylogenetic analysis of the secondary cases indicate an international introduction of the Omicron variant, consistent with other early cases identified in the United States (1). The recent emergence of Omicron, which is now projected to be the dominant variant in the United States,¶¶¶ reinforces the importance of vaccination, in coordination with other prevention strategies (e.g., masking and physical distancing), to protect people from COVID-19, slow transmission, and reduce the likelihood of new variants emerging. In addition, the rapid identification and epidemiologic characterization of this cluster underscore the importance of robust and timely genomic surveillance to detect and respond to emerging SARS-CoV-2 variants of concern.

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Although this report adds weight to the notion that Omicron may produce a milder course of illness (on average) than Delta - there remain large gaps in our knowledge - and there are enough `bad' things about Omicron (enhanced vaccine and immune escape, greatly increased transmissibility, etc.) to make it a formidable foe. 

But since it is such short supply, we'll take whatever `good' news we can get. 

UK Daily COVID Numbers & Omicron Overview (Dec. 28th)

 Credit HKHSA 

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Warning once again of incomplete data (see below) the UKHSA reported another record number of COVID cases (n=129,461) over the past 24 hours, and have updated their daily Omicron Overview Report. 

28 December 2021
Log category : DATA ISSUE Incomplete data for cases due to the holidays

During the holidays, consistency of cases data for different areas vary for both publish and specimen date metrics:

• Figures for Wales represent the sum of figures that would have been reported on 25 and 26 December 2021.

• Provisional figures for Scotland are not included in the data. They will be added to the time series once confirmed.

• No figures have been reported for Northern Ireland.

See the breakdown of cases by publish date for 28 December 2021 in the details section.

The crucial hospitalization numbers, as mentioned in yesterday's blog, still have not been updated since Dec 20th. 

The Omicron Daily Update for the 28th, however, shows another big jump in Omicron cases (+17K), hospitalizations (+261), and Omicron-related deaths (+10).  These figures are also incomplete, however. 

While it is difficult, without better patient information, to speculate on the relative severity of Omicron based on these 668 hospitalizations and 50 deaths, these numbers to suggest that some Omicron cases are seeing severe - and sometimes fatal - illness. 

Some of these data reporting issues will be resolved by late next week, after the New Year's Holiday, but the number of cases, the difficulty in identifying Omicron cases, and overwhelmed and short-staffed hospitals will likely still take their toll on data collection. 

CDC Rolls Back Nowcast Omicron Projections

 

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One of the realities of life in this pandemic is that our disease surveillance and reporting capabilities aren't as good as we'd like; they vary considerably from state to state, and they are further degraded by interruptions due to 3 major holidays (Thanksgiving, Christmas, and New Year's) all within 5 weeks time. 

Case in point, just two weeks ago the CDC added the Omicron variant to their Nowcast projections (see CDC Nowcast: Omicron Begins To Show Up Around The Country), which they initially pegged at 2.9% of all cases.

Six days later (Dec 20th) the CDC revised the previous week's projection up to 13%, and announced a stunning 73% of New Cases Were Likely Omicron.

Today, we get another shifting of numbers, with Omicron rolled back to a still hefty 58% share of all cases, and last week's numbers being adjusted down by more than 2/3rds, to just 22.5%.   The previous week's number was cut to just 6.6%

I'm sure they have good reasons to believe this weeks numbers to be more accurate, but given the wide swings in the numbers we've seen over the past 14 days - and the ongoing gaps in reporting over the Holidays - it is probably best to take all of these numbers with a large grain of salt.

I don't really expect to see the daily numbers sort themselves out until late next week. But what we can be pretty sure of is that Omicron is making inroads across the country over a very short period of time, and shows no signs of abating. 

The national map below, however, shows that Delta is still very much with us in many parts of the country. 

Stay tuned, and fasten your seat belts.  January is still going to be a bumpy ride. 

ASM Journal: SARS-CoV-2 and Influenza A Virus Co-infections in Ferrets

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One of the big unknowns going into 2022 is just how much of impact coinfection with COVID and Influenza will have on individual outcomes, and on hospital resources.  Some early studies suggest that coinfection brings a higher risk of severe illness and death. 

• A little over a year ago, in PHE Study: Co-Infection With COVID-19 & Seasonal Influenza, we 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.

• More recently, in Clinical and virological impact of single and dual infections with influenza A (H1N1) and SARS-CoV-2 in adult inpatients, coinfection was linked to increased odds of acute kidney injury, acute heart failure, secondary bacterial infections, multilobar infiltrates and admittance to ICU than monoinfection.

Since influenza essentially disappeared right after COVID appeared, there aren't a lot of examples to study, but with influenza on the rise once more (see CDC FluView) - and Omicron surging - that is likely to change. 

For now, we mostly have animal studies, and one of the most recent is a ferret study that finds that coinfection with influenza and COVID increases the severity of illness in these lab animals, and that receipt of the flu vaccine prior to infection - even when it doesn't prevent infection - can help ameliorate the severity of illness.

First the abstract (and link) to the study, then I'll return with a postscript.

SARS-CoV-2 and Influenza A virus Co-infections in Ferrets

Authors: Ying Huang, Amanda L. Skarlupka, Hyesun Jang, Uriel Blas-Machado, Nathan Holladay, R. Jeffrey Hogan, Ted M. Ross https://orcid.org/0000-0003-1947-7469 tedross@uga.eduAUTHORS INFO & AFFILIATIONS

DOI:https://doi.org/10.1128/JVI.01791-21

PDF/EPUB

22 December 2021

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and seasonal influenza viruses are co-circulating in the human population. However, only a few cases of viral co-infection with these two viruses have been documented in humans with some people having severe disease and others mild disease. In order to examine this phenomenon, ferrets were co-infected with SARS-CoV-2 and human seasonal influenza A viruses (IAVs) (H1N1 or H3N2) and were compared to animals that received each virus alone.

Ferrets were either immunologically naïve to both viruses or vaccinated with the 2019-2020 split-inactivated influenza virus vaccine. Co-infected naive ferrets lost significantly more body weight than ferrets infected with each virus alone and induced more severe inflammation in both the nose and lungs than ferrets single-infected with each virus.

Co-infected naïve animals had predominantly higher IAV titers than SARS-CoV-2 titers, and IAVs efficiently transmitted to the co-housed ferrets by direct contact. Comparatively, SARS-CoV-2 failed to transmit to the ferrets that co-housed with co-infected ferrets by direct contact.

Moreover, vaccination significantly reduced IAVs virus titers and shortened the viral shedding, but did not completely block influenza virus direct contact transmission. Notably, vaccination significantly ameliorated the influenza associated disease by protecting vaccinated animals from severe morbidity after IAV single infection or IAV and SARS-CoV-2 co-infection, suggesting that seasonal influenza virus vaccination is pivotal to prevent severe disease induced by IAVs and SARS-CoV-2 co-infection during the COVID-19 pandemic.

Just over a week ago, in Preprint: Antigenic & Virological properties of an H3N2 Variant That Will Likely Dominate the 2021-2022 Influenza season, we looked at a report that suggested this year's flu vaccine will likely be less effective in preventing infection than originally hoped.

While a `mismatch' between the vaccine component and the H3N2 virus currently circulating is less than ideal, the vaccine is still expected to reduce the severity of one's illness if they are infected. 

Given the challenges that lie ahead, I'm glad I got the flu vaccine last September, and will gladly take whatever level of protection it offers. 

That, combined with getting the COVID vaccine and booster, wearing face masks in public, and practicing good hygiene, should increase my odds of coming through the next few months relatively unscathed. 

But if it doesn't, at least I'll know I did everything I reasonably could to prevent a bad outcome.  

China: Xi'an Reports Another Jump In COVID Cases

Credit Wikipedia

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Yesterday, in China: Xi'an COVID Lockdown, we looked at the lockdown, and mass testing measures being used to try to contain the worst outbreak of COVID reported by China in more than 21 months. Although Omicron has been detected in travelers arriving in China, early reports suggest this outbreak is due to Delta.

While still small compared to outbreaks in other countries, China has placed a lot of faith in their Zero-COVID strategy - particularly with the Beijing Winter Olympics just 5 weeks away - and any breach risks seeing COVID cases spread rapidly across the nation. 

Today's update from China's National Health Commission finds 175 cases reported over the past 24 hours in Xi'an, bringing their total to over 800 cases in December. 

The latest situation of the novel coronavirus pneumonia epidemic as of 24:00 on December 27

Release time: 2021-12-28 Source: Health Emergency Office

From 0-24 o'clock on December 27, 31 provinces (autonomous regions and municipalities) and the Xinjiang Production and Construction Corps reported 209 new confirmed cases. Among them, 27 were imported cases from abroad (8 in Shanghai, 6 in Guangxi, 2 in Fujian, 2 in Shandong, 2 in Guangdong, 2 in Yunnan, 2 in Shaanxi, 1 in Tianjin, 1 in Zhejiang, 1 in Chongqing); local cases 182 cases (180 in Shaanxi, including 175 in Xi'an, 3 in Xianyang, and 2 in Yan'an; 1 in Zhejiang, in Shaoxing, and 1 in Yunnan, in Kunming). There were no new deaths. There are no new suspected cases.

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Some (translated) excerpts from a press conference held Dec 27th by Ma Guanghui, deputy director of the Provincial Health Commission, and others follow:

1. The epidemic situation in our province

From 0-24 o'clock on December 26, Shaanxi newly reported 152 local confirmed cases. From December 9th to December 26th at 24:00, a total of 651 confirmed cases were reported across the province. Among the 651 cases, in terms of gender and age distribution, there are 340 males and 311 females. The oldest age is 90 years, the youngest age is 6 months, and the median age is 36 years. In terms of occupational distribution, it covers household chores and unemployed, business services, farmers, students, workers and other groups.

In the past week, there have been 598 newly confirmed local cases in the province, including 152 on December 26 and 157 on December 25. At present, the local epidemic situation in our province is still in a stalemate, and the number of cases is expected to continue in a short period of time. It is not ruled out that some spot-like outbreaks will occur. Regarding the spot-like outbreaks that have already occurred, we have taken quick measures. With the escalation and implementation of various closure measures, and with the support and cooperation of the general public, we strive to reduce potential social risks in the shortest possible time.

2. Progress in handling the epidemic

Epidemic prevention and control is the most important political task of our province at present. The whole province deeply understands the importance, urgency and complexity of epidemic prevention and control, strengthens confidence, grit your teeth, fights every second and works day and night, and resolutely fights against the epidemic. Control this tough battle.

One is to take strict measures to prevent spillage and control spread. Focusing on Xi'an, we will strengthen the management and control of risk areas, and adopt classified management and control measures in medium and high risk areas, closed areas, controlled areas and prevention areas to reduce the flow and gathering of people. Xi'an has adopted the measures of "not leaving the city if it is not necessary" to strictly control the outflow of people from high-speed exits and two stations. Starting at 0:00 on December 27, Xi’an’s epidemic prevention and control measures have been further strengthened. All residents will not leave their homes or gather except to participate in nucleic acid sampling as required.

The second is to take multiple rounds of nucleic acid testing to screen out infected persons as quickly as possible. Xi'an City has completed 4 rounds of acid testing, and the fourth round of testing has collected a total of 11.8236 million people. The testing has been completed. A new round of nucleic acid testing was launched at 12:00 on December 27 to maximize the detection of concealed infections in the society. Yan'an City has carried out regional nucleic acid testing for 1.136 million person-times, and Xianyang City has already tested 1.514 million person-times.

The third is to intensify the traceability of circulation and make every effort to control the risk population. In terms of traceability, the Provincial Center for Disease Control and Prevention has completed the complete genetic sequencing of 137 local cases, which are all highly homologous to the imported cases reported on Pakistan's inbound flight on December 4. In terms of circulation, all cities, especially Xi'an, have stepped up efforts to "integrate the three publics". Once a positive case is reported, the public security department will immediately take the lead, the public health agency will cooperate, and the industry and information department will support the backstage, using big data to study and judge the trajectory of actions, and cooperate with the traditional Face-to-face flow adjustment, quickly and accurately target the target population, strengthen work connection, speed up the flow adjustment speed of cases, and continuously improve the flow adjustment efficiency. At present, the province controls 16,798 people in close contact, and 34,291 people in close contact.

The fourth is to concentrate the power of experts in the province and go all out to treat patients. Leaving the Xi'an Chest Hospital and Xi'an People's Hospital as designated hospitals for the treatment of new crown patients. Emergency transfer of medical personnel from medical institutions such as the First Affiliated Hospital of Xi’an Jiaotong University, the Second Affiliated Hospital of Xi’an Jiaotong University, Tangdu Hospital, the First Affiliated Hospital of Xi’an Medical College, Xi’an International Medical Center Hospital, Xi’an Daxing Hospital, etc., to form a number of medical teams to work with Xi’an Medical staff from the Science Hospital and Xi’an People’s Hospital actively carried out medical treatment.

Three, the next step

At present, the province's epidemic prevention and control is in a tough period. The vast number of cadres and the masses of the province must strengthen their confidence, work together, and gather a strong joint force to fight the epidemic.

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