Sunday, January 23, 2022

Omicron's Trajectory In 6 Countries: Three Up, Three Down

 Our World In Data - Confirmed Cases In 3 Countries (UK,US, Canada)


Barely 60 days after it was first announced (see South African NICD Statement On B.1.1.529 Variant), and after causing a record number of infections over a very short period of time, there are some hopeful signs that the first Omicron wave may be slowing in the UK, the United States, and Canada (see chart above).

All three countries appeared to have reached their peaks in the first 10 days of January, although changes in data collection and reporting, and milder illnesses, may be skewing the picture somewhat.  

While case levels remain high, they are no longer climbing like a homesick angel; they have leveled off and have even declined in some regions. Anecdotally, I'm seeing fewer hospitals where I live (central Florida) on Divert or Bypass the past few days, suggesting a drop in patient levels. 

As hopeful as these signs are, there are three European nations which reported the arrival of Omicron at roughly the same time as the UK, US and Canada, that are still reporting increasing cases; Denmark, Sweden, and Norway (see chart below).

Our World In Data - Confirmed Cases In 3 Countries (Norway, Sweden Denmark)

While it is possible that differences in testing and reporting by these countries may be affecting these trends, there is another possibility worth noting.   In the United States, Canada, and the UK the primary Omicron variant being reported is BA.1., which is currently the most commonly reported (>99%) Omicron variant being reported worldwide.

But earlier this week, in Omicron Subvariant BA.2 Now Accounts For Nearly Half Of All Danish Cases, we learned that a different Omicron variant was surging in Denmark.  To a lesser extent, we saw similar reports from Norway and Sweden (see Norwegian Institute of Public Health Also Reports A Rapid Increase In Omicron BA.2 Subvariant).

On Friday, just two days after the UK announced their plans to roll back Plan B COVID restrictions, the UKHSA announced that due to rising detections, the Omicron Sublineage BA.2 was Designated as A VUI (Variant Under Investigation).

For now, data is very limited on BA.2.  Currently there is no evidence that BA.2 produces more severe illness, or poses any greater threat than BA.1.  But it does appear to be able to compete successfully with BA.1 in parts of Scandinavia, and may even be more transmissible. 

The $64 question - one that remains unanswered right now - is whether infection with Omicron BA.1 conveys reasonably long-lasting immunity against BA.2.  If it does, the BA.2 may be a problem reserved for next fall or winter.  If it doesn't, then our current plateauing of cases here in the United States may not last very long.  

For what its worth, there are reports in the Danish media of an interview with SSI Chief researcher Anders Fomsgaard, where he suggests that infection with BA.1 may provide only limited protection against reinfection with BA.2.  But this appears to be preliminary information. 

Which is why we'll be watching Denmark, Norway, and Sweden - and potentially the UK -  to see if they experience a second Omicron wave, propelled by BA.2.  

Even if BA.2 turns out to be a flash in the pan, SARS-CoV-2 continues to evolve, and additional variants are almost certain to emerge to challenge herd immunity. 

Which is why, while I'm somewhat encouraged by the recent trends here in the US, UK, and Canada, I'm not putting my N95s back into storage anytime soon. 

Saturday, January 22, 2022

Denmark SSI: COVID Vaccine Breakthrough Infections Report



Because of Demark's relatively small population (5.8 million), a well-monitored universal healthcare system, and a high degree of testing, Denmark's ability to track the spread of COVID is among the best in the world.

As a result, Denmark's SSI (Statens Serum Institut) continues to provide us with some of the earliest, and most accurate, assessments on emerging variants, reinfection rates, and vaccine effectiveness, including these recent reports:

The SARS-CoV-2 virus continues to evolve, and what we could say about the pandemic's trajectory - even as few as three months ago - has changed due to the emergence of Omicron.  

COVID vaccines - which were designed nearly two years ago, and for an antigenically different virus (see Preprint: Mapping the Antigenic Diversification of SARS-CoV-2) - became less effective in preventing `breakthrough' infection with the arrival of Delta, and that trend has continued and accelerated with Omicron. 

Luckily, while it isn't as effective as it once was in preventing infection, fully vaccinated (and boosted) individuals continue to be far less likely to fall severely ill with COVID, end up hospitalized, or dying.  

But of course, the further out into this pandemic we go, and the more mutations that accrue in the virus, the more tenuous the benefits from the original vaccine are likely to become.  Monitoring breakthrough infections, hospitalizations, and deaths among the vaccinated (and unvaccinated) become increasingly important. 

Denmark's SSI has released a new vaccine breakthrough report, which indicates that while breakthrough infections have continued to rise, hospitalizations appear to have stabilized over the past 3 weeks. 

The rapid replacement of Delta by Omicron (BA.1) since late November, and the recent surge in BA.2, have made comparisons with the `Delta phase' of the pandemic increasingly difficult, and so no Vaccine Effectiveness (VE) estimates are provided in this report. 

First, the key points from the report, followed by a (translated) summary from the SSI.

Key points 

- An increasing number of SARS-CoV-2 infections are observed after completed primary vaccination and after full effect of revaccination. Since the last report the number of breakthrough infections have increased with 139,818 cases after primary vaccinations schedule and 70,811 cases after revaccination.

- The number of COVID-19 related hospital admissions after breakthrough infections has been gradually increasing from week 41 with a steep increase from week 51 to week 52. The number of hospital admissions after breakthrough infections is at the highest level since the beginning of the vaccination rollout, however, it seems the number has stabilized in the last three weeks (week 52 2021 to week 2 2022).

- The total number of COVID-19 related deaths among individuals with completed primary vaccination and revaccination has increased since week 44 and has been stable at a higher level in week 47 to week 52. For the first two weeks of 2022 the number of deaths has increased further. 

- The estimates of vaccine effectiveness (VE) against COVID-19 infections and COVID-19 related admissions are not included in this report because the latest four week time period cannot be compared to previous time periods where Delta was the dominating variant. Furthermore, the unvaccinated group is now very small and differ from the vaccinated groups, thus, it can no longer be used as reference group in the estimates of vaccine effectiveness.

The SSI Summary follows:

The number of inpatients after breakthrough infection has been stable over the last three weeks

434,803 cases of covid-19 have now been registered in persons with full effect of the primary vaccination course. In addition, 105,271 cases after full effect of revaccination. This is shown by the latest report for breakthrough infections from the Statens Serum Institut.

Last edited January 21, 2022

The number of people who become infected with covid-19 even though they have been vaccinated - the so-called breakthrough infections - is steadily rising. But the number of inpatients after a breakthrough infection has been stable over the past three weeks.

This is shown by the latest breakthrough report from the Statens Serum Institut (SSI).

According to the report - which runs until 18 January 2022 - 434,803 cases of covid-19 have now been registered in people with full effect of the primary vaccination course. In addition, 105,271 cases after full effect of revaccination. That is an increase of 139,818 and 70,811, respectively, since the last report two weeks ago.

At the end of 2021, the increase in infection among vaccinated people was primarily driven by the younger age groups. In week 52, an increase was seen in several age groups, including people aged 65 and over. But the infection has been stable in this age group for the past two weeks at a slightly higher level than before Christmas. (see Figure 1).

In addition, there is a decrease in the number of infections after breakthrough infection in people aged 20-29 years.

Number of inpatients after breakthrough infection has stabilized

Despite the continued high number of infections after vaccination, the number of people hospitalized with a breakthrough infection has been stable over the past three weeks.

The fact that the number of inpatients is stable indicates that vaccination and revaccination also provide good protection against serious illness, even though the omicron variant is now dominant. However, the fact that the infection is increasing among the older age groups may mean that the number of inpatients will also increase.

The revaccinated now make up the largest proportion of deaths

The number of deaths after a breakthrough infection has been steadily increased in the weeks 47-52 2021, but at the beginning of 2022 there has been an increase to a slightly higher level.

During the same period, revaccinated people accounted for an increasing proportion of deaths following breakthrough infections. This is a consequence of the fact that an increasing proportion of the older age groups in the same period have been revaccinated.

The revaccinated now make up the largest proportion of deaths after a breakthrough infection.

Vaccine efficacy

In this week's report, the statements on vaccine efficacy are deleted. This is because the introduction and spread of the infection with the omicron variant has taken place over a very short period of time.

Thus, the period of the last four weeks is not comparable with the previous calculation periods, where the delta variant was the dominant variant.

In addition, the unvaccinated now form such a small group that they are not comparable to the vaccinated. Therefore, they can no longer be used as a reference group in the calculation of the RE estimates.


With the majority of Denmark's population fully vaccinated, and the highest risk populations (elderly, immunocompromised, etc.) likely to have received the booster shot as well, it is not surprising that the number of deaths among the vaccinated continues to rise.   

The elderly, and those with comorbidities, are at a higher risk of hospitalization and/or death than younger healthier people, regardless of their vaccination status. 

With Denmark likely transitioning from BA.1 to BA.2, it will take a few more weeks before we can see where these trends are headed.  The vaccine obviously isn't perfect, and it grows less so over time, but it still appears to provide significant protection against severe illness and death. 

And right now, that is still a benefit very much worth having. 

Friday, January 21, 2022

UKHSA: Omicron Sublineage BA.2 Designated as A VUI (Variant Under Investigation)


Although we first looked at it's growing diversity in mid-December (see The Omicron Uncertainty Principle), the now dominant Omicron variant is actually comprised of four closely-related viral lineages; B.1.1.529, BA.1, BA.2 and BA.3.

While B.1.1.529 was the progenitor of the Omicron lineage, BA.1 has been, by far, the most commonly reported version (> 99%).

BA.3 remains the rarest of the four, but the BA.2 sublineage has in recent weeks begun to make a move in several scandinavian countries (Denmark, Norway, Sweden). 

Yesterday, in Denmark SSI: Omicron Subvariant BA.2 Now Accounts For Nearly Half Of All Danish Cases  and in Norwegian Institute of Public Health Also Reports A Rapid Increase In Omicron BA.2 Subvariant) we looked at these reports. 

At this time, we have zero information on how BA.2 infection might differ from BA.1, assuming it does at all.  But there are concerns that BA.2 may prove even more transmissible. 

Today the UK's Health Security Agency (UKHSA) has taken notice of a low, but rising number, of BA.2 cases in the UK, and has designated BA.2 as a VUI.  

Unlike BA.1 - which has the SGTF (Spike Gene Target Failure) which helps identify it with certain PCR tests - BA.2 simply tests positive as COVID, and requires additional genomic sequencing to identify its lineage. 

This from the UKHSA.

Omicron sub-lineage BA.2 designated as a variant under investigation (VUI)

The Omicron variant sub-lineage known as BA.2 has been designated a variant under investigation ( VUI-22JAN-01) by the UK Health Security Agency (UKHSA).

Overall, the original Omicron lineage, BA.1, is dominant in the UK and the proportion of BA.2 cases is currently low. The designation was made on the basis of increasing numbers of BA.2 sequences identified both domestically and internationally. There is still uncertainty around the significance of the changes to the viral genome, and further analyses will now be undertaken.

To date, there have been 426 cases of Omicron BA.2 confirmed by Whole Genome Sequencing (WGS), with the earliest dated 6 December 2021.

The areas with the largest number of confirmed cases are London (146) and the South East (97). Data for the devolved administrations will follow in due course.

Early analyses suggest an increased growth rate compared to BA.1, however, growth rates have a low level of certainty early in the emergence of a variant and further analysis is needed.

In total, 40 countries have uploaded 8,040 BA.2 sequences to GISAID since 17 November 2021. At this point it is not possible to determine where the sublineage may have originated. The first sequences were submitted from the Philippines, and most samples have been uploaded from Denmark (6,411). Other countries that have uploaded more than 100 samples are India (530), Sweden (181), and Singapore (127).

Omicron BA.2 lacks the genetic deletion on the spike protein which produces S-gene target failure (SGTF) in some polymerase chain reaction (PCR) tests, which has been used as a proxy for Omicron cases previously.

Dr Meera Chand, COVID-19 Incident Director at UKHSA, said:

It is the nature of viruses to evolve and mutate, so it’s to be expected that we will continue to see new variants emerge as the pandemic goes on. Our continued genomic surveillance allows us to detect them and assess whether they are significant.

So far, there is insufficient evidence to determine whether BA.2 causes more severe illness than Omicron BA.1, but data is limited and UKHSA continues to investigate.

Case rates remain high throughout the UK and we must remain vigilant and take up vaccinations. We should all continue to test regularly with LFDs and take a PCR test if symptoms develop.

Health and Social Care Secretary, Sajid Javid, said:

We are learning to live with this virus – and thanks to our world-leading surveillance system we can rapidly detect and carefully monitor any genetic changes to COVID-19.

Our exceptional vaccine rollout means the number of people severely affected by COVID-19 is low, and the UK’s innovation and research has discovered life-saving treatments for those most at risk from COVID-19.

As we cautiously return to Plan A, I encourage you to give yourself and your loved ones the best protection possible and Get Boosted Now.

As is routine for any new variants under investigation, UKHSA is carrying out laboratory and epidemiological investigations to better understand the characteristics of this variant. We will continue to monitor this situation closely and recommend appropriate public health measures if needed.

More detail will be available in UKHSA’s regular variant technical briefings.

While there is considerable consternation in the media, and on some social media sites, over this BA.2 lineage, it is still too early to know how much of an impact it will have on the pandemic.  It does remind us, however, that SARS-CoV-2 continues to evolve, and that more surprises may lay ahead.

Stay tuned. 

MMWR: COVID-19 Cases & Hospitalizations by COVID-19 Vaccination Status and Previous COVID-19 Diagnosis


Two days ago the CDC's MMWR published a new report that found - over a specific period of time, before the emergence of Omicron - that people who had recovered from a previous bout of COVID were better protected against reinfection with the Delta strain, than those who were only vaccinated. 

Many who oppose the vaccine, or who believe a prior infection should exempt one from getting the vaccine, took to social media to declare victory. But as usual, there is more to unpack here than  can be posted in a twitter taunt. 

The highest rate of hospitalization were among persons who were unvaccinated (without previous infection hx) Prior to the arrival of Delta, vaccinated individuals were better protected (against hospitalization) than those unvaccinated but with previous infection

The change came after Delta become dominant. Suddenly prior infection provided better protection than the vaccine alone.

By the week beginning October 3, compared with COVID-19 cases rates among unvaccinated persons without a previous COVID-19 diagnosis, case rates among vaccinated persons without a previous COVID-19 diagnosis were 6.2-fold (California) and 4.5-fold (New York) lower; rates were substantially lower among both groups with previous COVID-19 diagnoses, including 29.0-fold (California) and 14.7-fold lower (New York) among unvaccinated persons with a previous diagnosis, and 32.5-fold (California) and 19.8-fold lower (New York) among vaccinated persons with a previous diagnosis of COVID-19.

The combination of prior infection AND vaccination provided the best level of protection, but - as we've discussed many times - the COVID vaccine alone was struggling against Delta.  

And of course, since this study, Delta has been supplanted by Omicron, which appears to have a much higher reinfection and breakthrough rate than Delta. 

First stop, a link and some excerpts from the MMWR report (which you'll want to read in its entirety), followed by a statement by the CDC. 

COVID-19 Cases and Hospitalizations by COVID-19 Vaccination Status and Previous COVID-19 Diagnosis — California and New York, May–November 2021

Early Release / January 19, 2022 / 71

Tomás M. León, PhD1; Vajeera Dorabawila, PhD2; Lauren Nelson, MPH1; Emily Lutterloh, MD2,3; Ursula E. Bauer, PhD2; Bryon Backenson, MPH2,3; Mary T. Bassett, MD2; Hannah Henry, MPH1; Brooke Bregman, MPH1; Claire M. Midgley, PhD4; Jennifer F. Myers, MPH1; Ian D. Plumb, MBBS4; Heather E. Reese, PhD4; Rui Zhao, MPH1; Melissa Briggs-Hagen, MD4; Dina Hoefer, PhD2; James P. Watt, MD1; Benjamin J. Silk, PhD4; Seema Jain, MD1; Eli S. Rosenberg, PhD2,3 (View author affiliations)View suggested citation


What is already known about this topic?

Data are limited regarding the risks for SARS-CoV-2 infection and hospitalization after COVID-19 vaccination and previous infection.

What is added by this report?

During May–November 2021, case and hospitalization rates were highest among persons who were unvaccinated without a previous diagnosis. Before Delta became the predominant variant in June, case rates were higher among persons who survived a previous infection than persons who were vaccinated alone. By early October, persons who survived a previous infection had lower case rates than persons who were vaccinated alone.

What are the implications for public health practice?

Although the epidemiology of COVID-19 might change as new variants emerge, vaccination remains the safest strategy for averting future SARS-CoV-2 infections, hospitalizations, long-term sequelae, and death. Primary vaccination, additional doses, and booster doses are recommended for all eligible persons. Additional future recommendations for vaccine doses might be warranted as the virus and immunity levels change.

        (Continue . . . )

Anticipating that this MMWR report might be misconstrued, the CDC published the following statement on Wednesday. 

CDC Statement on MMWR: COVID-19 Cases and Hospitalizations by COVID-19 Vaccination Status and Previous COVID-19 Diagnosis — California and New York, May–November 2021
Media Statement

Embargoed Until: Wednesday, January 19, 2022, 1:00 p.m. ET
Contact: Media Relations
(404) 639-3286

Today’s MMWR study finds that during the Delta wave, both COVID-19 vaccination and surviving a prior infection provided protection against infection and hospitalization from COVID-19. Scientists reviewed data from New York and California to determine the level of protection offered by COVID-19 vaccines, previous infection, and both. Between May and November 2021, people who were unvaccinated and did not have a prior COVID-19 infection remained at the highest risk of infection and hospitalization, while those who were previously infected, both with or without prior vaccination, had the greatest protection.

Viruses are constantly changing, including the virus that causes COVID-19. These changes occur over time and can lead to the emergence of new variants that have new characteristics, including ones that impact the level of immunity vaccination and/or prior infection can provide. The level of protection offered by vaccination and surviving a previous infection changed during the study period. Vaccination remains the safest strategy for protecting against COVID-19.

There are important caveats to the data presented in this study:
  • The analysis was conducted before the emergence of the Omicron variant and the findings cannot be applied to the current Omicron wave.
  • The study ended prior to the widespread implementation of booster doses and does not reflect the immunologic benefit of additional vaccine doses.
  • The analysis did not include information on the severity of initial infection and does not reflect the risk of morbidity and mortality from COVID-19 infection.
Additionally, a recent study shows with increasing time since prior infection, vaccination provides greater protection against COVID-19 compared to prior infection alone, emphasizing the importance of being up to date on COVID-19 vaccination. Later this week, CDC will publish additional data on COVID-19 vaccines and boosters while Omicron has been circulating.

          (Continue . . . )

We've known for quite some time that coronavirus infections tend to leave behind immunity of limited duration (see Nature Medicine: Seasonal Coronavirus Protective Immunity Is Short-Lastingmaking herd immunity - from natural infection or a vaccine - more difficult to achieve. 

As someone who had COVID before he was eligible for the vaccine, and who has subsequently been vaccinated and boosted, I take this report as encouraging news.  I presumably have the best of both worlds, although their value in preventing Omicron infection is certainly less than against Delta. 

But there is data showing that being vaccinated substantially lowers the risk of severe disease, even when it doesn't prevent infection. So I'll gladly take whatever I can get. 

SARS-CoV-2 is a constantly evolving virus.  And anything that we might say about the impact of vaccination (and boosters), prior infection - or both -  against this virus will undoubtedly change over time.  

Netherlands DWHC Reports another Mammal (Polecat) Infected With H5N1


Just over a week ago, in Netherlands: WBVR Diagnoses Avian H5N1 In Another Fox, we looked at the latest in a series of mammalian infections reported in Western Europe by the avian H5N1 virus, which is currently sparking a record avian epizootic across all of Europe (see DEFRA: Highly pathogenic avian influenza (HPAI) in the UK, and Europe (Update #8)

While  Asian H5Nx viruses (H5N1, H5N6) have a long history of infecting terrestrial mammals (see HPAI H5: Catch As Cats Can) this appears to be a relatively new development with the Eurasian H5Nx clade lineage. 

Prior to 2020, we had only seen a few instances of this sort of species jump with the Eurasian H5Nx virus, most commonly to marine mammals (see EID Journal: Highly Pathogenic Avian Influenza A(H5N8) Virus in Gray Seals, Baltic Sea).  There were, however, reports suggesting that a couple of amino acid substitutions could greatly enhance its virulence in mammals (see J. Virulence : Altered Virulence Of (HPAI) H5N8 Reassortant Viruses In Mammalian Models). 

Starting about a year ago, we began seeing multiple reports of terrestrial mammals infected with the Eurasian H5Nx virus in Europe - often with neurological manifestations.  A few examples include:

CDC EID Journal: Encephalitis and Death in Wild Mammals at An Animal Rehab Center From HPAI H5N8 - UK

EID Journal: HPAI A(H5N1) Virus in Wild Red Foxes, the Netherlands, 2021

It was also only a year ago that we learned of the first human infections with H5N8 in Russia (see Russian Media Reports 7 Human Infections With Avian H5N8) which led to the classification of the Eurasian H5N8 as having some zoonotic potential (see CDC Adds Zoonotic Avian A/H5N8 To IRAT List).

Subsequently, a small number of H5N1 human infections have been reported in Nigeria, and in the UK.  But unlike the reports on mammalian infections above, have either been described as mild, or asymptomatic. 

We've previously seen neurological manifestations accompanying infection with some of the more pathogenic H5 subtypes in Asia, like clade 2.3.21.c (see Highly Pathogenic Avian Influenza A(H5N1) Virus Struck Migratory Birds in China in 2015), where the authors wrote:

This suggests that the novel Sanmenxia Clade H5N1 viruses possesses tropism for the nervous system in several mammal species, and could pose a significant threat to humans if these viruses develop the ability to bind human-type receptors more effectively.

But these Asian clade H5N1 viruses are genetically different from the European H5Nx clade viruses, making these recent reports of neurological presentations unexpected, and worthy of our attention.

We've a new report (Jan 20th), released by the Dutch Wildlife Health Centre, of yet another H5N1 infected mammal with severe neurological symptoms, this time involving a polecat (Mustela putorius) found in South Holland.  European polecats are ferret-like mammals, often called foul martens. 

There is a brief video on the side (warning: some may find it disturbing) showing the animal in distress. I'll have a postscript after the break. 

Polecat and foxes infected with bird flu
January 20, 2022

A polecat ( Mustela putorius ) was found in South Holland with bird flu. Elsewhere in the Netherlands, foxes ( Vulpes vulpes ) also appear to be infected with the virus, according to research by DWHC , NVWA and WBVR.

On January 8, 2022, a polecat was found near Dirklandse Sas on the South Holland island of Goeree-Overflakkee that was behaving very strangely. The animal turned its head uncontrollably and was completely disoriented. Such behavior often points to a nervous system disorder. The polecat was taken by animal ambulance to Vogelklas Karel Schot in Rotterdam, a shelter for wild birds and mammals. Because the symptoms were very severe, it was decided to euthanize the animal after 24 hours and to spare her further suffering. Such neurological symptoms also occur in waterfowl that are sick with bird flu. It was therefore decided to have the dead polecat tested in the lab of Wageningen Bioveterinary Research (WBVR).

bird flu

The test results showed that the polecat was indeed infected with the highly pathogenic avian flu variant H5N1. The virus was detected in the animal's brain, but samples from the throat and rectum tested negative. There is currently a bird flu epidemic going on among wild waterfowl in the Netherlands and abroad. In December large numbers of dead knotted sandpipers were found along the coast of the Wadden Sea that tested positive for H5N1, and barnacle geese and swans also suffer many victims, such as in the Oostvaardersplassen , Friesland and North and South Holland.

Aggravated Mammals and Birds

It is now clear that wild mammals can also be infected with H5N1. In May 2021, infected young foxes were found in Groningen and another sick fox was found last December, now in the south of the Netherlands . For the time being, these are predators that probably contract the virus by eating infected wild birds. This way of contamination has also been shown in raptors and scavengers, such as in 2015 in a white- tailed eagle that was found to have bird flu variant H5N8 . This avian flu variant was also detected in buzzard, kestrel and peregrine falcon in the winter of 2020/2021 .

Caution is advised

The cases of bird flu in mammals now demonstrated indicate that caution is advised during this bird flu epidemic. It is known that dogs and cats are also sensitive to bird flu. Therefore, as a precaution, keep dogs on a lead in places where dead (water) birds may lie. This prevents dogs from coming into contact with infected dead birds . For walkers, direct contact with sick and dead waterfowl should be avoided as much as possible.

Cleaning up and reporting sick animals

Animal carcasses usually remain in nature, after which scavengers clean up the carcasses. However, this is not a good idea for birds that have died from bird flu. The scavengers that eat it can also get sick themselves. For the removal of carcasses, the NVWA has therefore drawn up two hygiene protocols for site managers and animal ambulances, one for birds and one for mammals . Guidelines have been published for animal aid organizations that have to deal with sick and living animals via Stichting Dierenlot . If you spot dead animals yourself, consult the bird mortality map with a schematic overview of which birds must/can be reported where. And keep in mind that wild mammals can also have bird flu.

Text: André De Baerdemaeker, Bird class Karel Schot; Margriet Montizaan, DWHC; Nancy Beerens, WBVR; Maurice La Haye, Mammal Society.

Over the past 6 years we've seen a steady increase in H5Nx clade's host range, and pathogenicity, following a reassortment event in either Russia or China over the summer of 2016 (see EID Journal: Multiple Reassorted Avian H5N8 Viruses In The Netherlands, 2016).  

We've also seen this clade expand to include Eurasian H5N6, H5N1, H5N5 viruses as well. 

While once viewed as primarily a threat to wild birds and poultry, in late December the ECDC/EFSA Raised the Zoonotic Risk Potential Of Avian H5Nx.  While still not considered as big of threat to human health as the Asian H5N6/H5N1 virus, clade H5 viruses continue to evolve, making them an HPAI lineage to take seriously.

Thursday, January 20, 2022

Hong Kong CHP: 4 More Pet Shops Test Positive For COVID - 2 Customers COVID-Positive



Over the past 72 hours we've been following reports of COVID-positive hamsters detected at a Hong Kong pet store and warehouse, and several human infections which may have been the result of hamster-to-human transmission of the virus.  

This has led to a controversial culling order by the AFCD (Hong Kong Detects COVID In Pet Store Hamsters - Suspends Sales & Orders Cull), and compulsory quarantine for those who have been exposed to infected hamsters (see Hong Kong: Compulsory Quarantine For Those Exposed To COVID-Positive Hamsters).

Today the plot thickens as  environmental samples from 4 more Hong Kong pet shops have tested positive for COVID, and two more cases believed related to pet shops have emerged.  The government is urging anyone who has purchased a hamster since December 22nd to get tested immediately. 

Two reports, first from the CHP.

CHP follows up on cases tested preliminarily positive for SARS-CoV-2 virus related to pet shops and announces environmental samples results of relevant pet shops

The Centre for Health Protection (CHP) of the Department of Health (DH) today (January 20) said it is following up on two cases tested preliminarily positive for SARS-CoV-2 related to pet shops.

The first case tested preliminarily positive for SARS-CoV-2 virus involves a 30-year-old female living in Shing Him House (Block H), Tin Shing Court, 3 Tin Ching Street, Tin Shui Wai. She visited Little Boss pet shop in Causeway Bay on January 11 and bought a hamster and had contact with case 13047 (staff of Little Boss pet shop in Causeway Bay). She was classified as a close contact and was arranged to undergo quarantine at the Penny's Bay Quarantine Centre on January 18. She tested preliminarily positive on January 19. She received two doses of COVID-19 vaccination (Comirnaty) on May 14 and June 12, 2021 in Hong Kong.

The second case tested preliminarily positive involves a 23-year-old female living in Mei Yue House, Shek Kip Mei Estate, Shek Kip Mei. She visited one of the Little Boss shops at Tung Choi Street, Mong Kok and bought a hamster on January 4. She developed runny nose on January 17 and went to a community testing centre for test on January 19. She tested preliminarily positive subsequently. She received two doses of COVID-19 vaccination (Comirnaty) on July 13 and August 4, 2021 in Hong Kong.

The CHP earlier collected 88 environmental samples from the Little Boss pet shop in Causeway Bay and its warehouse in Tai Po. To follow-up the related infection situation, the CHP has, as at January 20 evening, collected a total of 604 environmental samples from 31 pet shops and relevant warehouses. Apart from the positive test results of the 18 environmental samples collected at the Little Boss pet shop in Causeway Bay and its warehouse in Tai Po as announced earlier, the latest laboratory testing results revealed that seven of the samples collected from four additional pet shops (I Love Rabbit at 87-99 Kau Yuk Road, Yuen Long; I Love Rabbit at 25-27 Lee Garden Road, Causeway Bay; Little Boss at 187 Tung Choi Street, Mong Kok; and Little Boss at Kai Wan Building, 142-146 Tung Choi Street, Mong Kok) also tested positive.

The Agriculture, Fisheries and Conservation Department collected samples from hamsters at the pet shop earlier which tested positive. Based on the results of epidemiological investigation and laboratory findings the CHP possesses at this stage, it could not be ruled out preliminarily that the positive test results of the environmental samples are caused by the pets infected with the virus.

Also, as a prudent measure, the four newly added pet shops will be included in a compulsory testing notice. Specified persons who were present at the relevant venues from January 7 to January 18 need to undergo compulsory testing on the specified date. The staff members of the four shops will be arranged to undergo compulsory quarantine at the quarantine centre.

Meanwhile, the Government has made a "restriction-testing declaration" (RTD) tonight for the building where the aforementioned 30-year-old female patient resided (Shing Him House (Block H), Tin Shing Court, 3 Tin Ching Street, Tin Shui Wai) and persons who resided or worked at the building will be subject to increased compulsory testing frequency. The places where the patient had visited during the incubation periods will also be included in a compulsory testing notice. Specified persons who were present at the relevant venues at specified periods need to undergo compulsory testing on the specified date.

​The CHP strongly reminds relevant residents that they must comply with the RTD operation. Any person who fails to present an SMS notification with a test result or wear a wristband as proof of having undergone testing breaches the compulsory testing notice and may be liable to a fine of $5,000. The person will also be issued with a compulsory testing order, requiring him/her to undergo testing within a specified time frame. Failure to comply with the compulsory testing order or the RTD is an offence and the offender may be liable to a fine of level 4 ($25,000) and imprisonment for six months.

Ends/Thursday, January 20, 2022
Issued at HKT 23:40

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The Center for Protection urges those who have purchased hamsters to get tested as soon as possible

January 20, 2022

There were 14 new positive test cases for the novel coronavirus in Hong Kong , and there were more than 20 preliminary positive cases, many of which were local infections, and the source of infection in some cases was unknown. The Centre for Health Protection of the Department of Health urges those who purchased hamsters on or after the 22nd of last month to be tested for the virus as soon as possible.

Zhang Zhujun, director of the Infectious Diseases Division of the Centre for Health Protection, said at a briefing today that of the 14 new cases, 12 involved the Omicron variant strain, one involved the Delta variant strain, and the test results of the remaining one variant strain were pending.

The source of the initial positive cases is unknown. Among them, a 24-year-old patient is a social worker assistant who works in Kwai Chung and lives in Cheung Sha Wan Village Cheung Yan Building; a 37-year-old female patient lives in Block 1, Mingyi Residence, Tsuen Wan, and is engaged in sales in Kwun Tong work; another 82-year-old male patient lives in Kong Cheong Court, Aberdeen Centre.

Some of the preliminary positive cases are related to previous cases. Among them, the cases in Yat Kwai House, Kwai Chung Estate are distributed on different floors and orientations and involve multiple units.

Zhang Zhujun also pointed out that a kindergarten teacher living in Phase 3 of Mei Foo New Village and a student of Delia Memorial School (Broadway) had the same results of whole genome sequencing of the virus. The Center for Protection is investigating the connection between the two cases.

In addition, there are four differences in the results of the full-gene analysis of the virus between the confirmed salesperson of the Causeway Bay pet store Little Boss and the store's customers. The Centre for Protection took samples from 11 pet stores yesterday, and the samples from the i love rabbit hamster cages from the Yuen Long pet store tested positive.

Zhang Zhujun said that if the virus is transmitted from human to human, the genetic analysis results are similar; if it is transmitted from animals to human, there will be different analysis results. The above results show that the possibility of virus transmission from animals to humans increases. She urged anyone who bought a hamster on or after the 22nd of last month to get tested for the virus as soon as possible.

In the evening, the government made a restriction and testing announcement, and listed Shing Him House, Tin Shing Court , Tin Shui Wai, Block 1 , Tsuen Wan Prestige Residence , and Cheung Sha Wan Village Chief Yan House as restricted areas. Those who were inspected were required to undergo compulsory testing before the designated time.

The Government has set up a dedicated webpage to provide relevant information and health advice on COVID-19.