Sunday, September 20, 2020

Viruses: PA From Recent H9N2 AIV Enhances H5N1 Infection In Mammalian Systems


In March of 2013 - just two weeks before we learned of the first H7N9 outbreak in humans in China - a study appearing in the EID Journal: Predicting Hotspots for Influenza Virus Reassortment, found  that both Eastern China and the Nile River Valley of Egypt were at the top of the list of areas likely to spawn the next novel flu virus.

EID Influenza Hotspots For Reassortment - 2013

China had spawned H5N1 in the mid-1990s, followed by a long  line of descendants, and within two years would launch not only H7N9, but also H10N8, H5N8, and H5N6.  Of those, only H5N8 has not infected humans.

Egypt, meanwhile, was becoming a hotbed of H5N1 activity and evolution, and starting in late 2014 - and lasting for about 6 months - became the scene of the large human outbreak of H5N1 on record (see EID Dispatch: Increased Number Of Human H5N1 Infection – Egypt, 2014-15). 

Both countries lie beneath major migratory flyways, both are major poultry producers (with many backyard flocks), and both have numerous LPAI and HPAI subtypes circulating in local birds. 

While China has gained better control of avian flu the past few years following their roll out of a new experimental H5+H7 poultry vaccine in 2017, Egypt continues to struggle with spotty poultry vaccination campaigns that often rely on older, mismatched vaccines (see Egypt: A Paltry Poultry Vaccine)which can potentially drive vaccine escape mutations.

As a result, multiple clades of HPAI H5 viruses (H5N1 and H5N8) - along with H9N2 - have all become endemic in Egyptian poultry.

As we've discussed often  (see The Lancet: H9N2’s Role In Evolution Of Novel Avian Influenzas), the avian H9N2 virus is a highly promiscuous virus, reassorting with many other subtypes easily.  In addition, we've seen the H9N2 continue to evolve towards a more `humanized' virus (see Virology: Receptor Binding Specificity Of H9N2 Avian Influenza Viruses).

While H9N2 has circulated in the Middle East for more than two decades, it was only first detected in Egyptian poultry in 2010 (cite), prompting concerns over how it might interact with HPAI H5N1.
The H5N1 virus already carries some internal genes from the H9N2 virus, and so the concern is another exchange - of more recent, potentially more `mammalian adapted'  H9N2 genes - could happen again with uncertain results. 

In early 2019, in J. Virology:Genetic Compatibility of Reassortants Between Avian H5N1 & H9N2 Influenza Viruses, we looked at the results of experimental reassortments of Egyptian H5N1 and H9N2 viruses in the laboratory, which warned:
In conclusion, our analyses indicated a substantial emergence potential of influenza virus reassortants derived from the H5N1 and H9N2 viruses currently cocirculating in Egypt, as well as the possibility of their high public health risk for humans relative to the parental H5N1 and H9N2 viruses. Cocirculation of the two influenza virus subtypes in birds may accelerate the emergence of novel viruses that may be a public health risk.
Last December, in EID Journal: Novel Reassortant HPAI A(H5N2) Virus in Broiler Chickens, Egyptwe saw a new proof of concept in the field, after an HPAI H5N8 virus reassorted with an LPAI H9N2 virus, and produced a new HPAI H5N2 virus in Egyptian poultry.

A reminder that while avian flu activity has been subdued globally for the past 3 years, the threat has not gone away.  

While a far less virulent virus than HPAI H5N1, LPAI H9N2 raises pandemic concerns because it continues to evolve towards a more mammalian-adapted virus. Add in its legendary ability to reassort with other influenza subtypes, and it becomes a virus to watch.

Which brings us to a new study that experimentally reassorts a recent LPAI H9N2 virus - carrying a mutated PA segment (Lysine 367) - with a recently circulating Egyptian H5N1 virus. 

Not only were these two viruses genetically compatible, their reassortant offspring showed enhanced replication in Madin-Darby canine kidney (MDCK-II) cells at 33 °C and 39 °C,  increasing their fitness to replicate in human hosts. 

While this reassortant combination has not been observed in the wild, with both viruses circulating in Egyptian poultry, there are legitimate concerns that they could someday conspire to spawn a more dangerous (to humans) H5Nx virus. 

I've only included the link, the Abstract, and an excerpt from the study's conclusion. Follow the link to read the paper in its entirety. 

by Ahmed Mostafa 1,2,*,,Sara H. Mahmoud 1,†,Mahmoud Shehata ,Christin Müller ,Ahmed Kandeil ,Rabeh El-Shesheny 1,3,Hanaa Z. Nooh 4,Ghazi Kayali 5,6,Mohamed A. Ali 1,* and Sephan Pleschka 2,*

Viruses 202012(9), 1046; (registering DOI)
Received: 26 August 2020 / Revised: 15 September 2020 / Accepted: 18 September 2020 / Published: 20 September 2020

Egypt is a hotspot for H5- and H9-subtype avian influenza A virus (AIV) infections and co-infections in poultry by both subtypes have been frequently reported. However, natural genetic reassortment of these subtypes has not been reported yet.
Here, we evaluated the genetic compatibility and replication efficiency of reassortants between recent isolates of an Egyptian H5N1 and a H9N2 AIV (H5N1EGY and H9N2EGY). All internal viral proteins-encoding segments of the contemporaneous G1-like H9N2EGY, expressed individually and in combination in the genetic background of H5N1EGY, were genetically compatible with the other H5N1EGY segments.
At 37 °C the replication efficiencies of H5N1EGY reassortants expressing the H9N2EGY polymerase subunits PB2 and PA (H5N1PB2-H9N2EGY, H5N1PA-H9N2EGY) were higher than the wild-type H5N1EGY in Madin-Darby canine kidney (MDCK-II) cells. This could not be correlated to viral polymerase activity as this was found to be improved for H5N1PB2-H9N2EGY, but reduced for H5N1PA-H9N2EGY. At 33 °C and 39 °C, H5N1PB2-H9N2EGY and H5N1PA-H9N2EGY replicated to higher levels than the wild-type H5N1EGY in human Calu-3 and A549 cell lines.
Nevertheless, in BALB/c mice both reassortants caused reduced mortality compared to the wild-type H5N1EGY. Genetic analysis of the polymerase-encoding segments revealed that the PAH9N2EGY and PB2H9N2EGY encode for a distinct uncharacterized mammalian-like variation (367K) and a well-known mammalian signature (591K), respectively. Introducing the single substitution 367K into the PA of H5N1EGY enabled the mutant virus H5N1PA-R367K to replicate more efficiently at 37 °C in primary human bronchial epithelial (NHBE) cells and also in A549 and Calu-3 cells at 33 °C and 39 °C. Furthermore, H5N1PA-R367K caused higher mortality in BALB/c mice.
These findings demonstrate that H5N1 (Clade reassortants carrying internal proteins-encoding segments of G1-like H9N2 viruses can emerge and may gain improved replication fitness. Thereby such H5N1/H9N2 reassortants could augment the zoonotic potential of H5N1 viruses, especially by acquiring unique mammalian-like aa signatures.


Taken together, our results demonstrate that the co-circulation of H5N1-subtype HPAIV and H9N2-subtype LPAIV in Egyptian poultry may result in co-infection and viral reassortment, thus H5N1 reassortants with an increased zoonotic potential may emerge and pose a public health risk. Specifically the lysine at position 367 of the PA seems to have a strong impact.
The data presented here question the role of genetic compatibility or viral replication fitness of H5N1/H9N2 reassortants to the low or rare detection of natural genetic reassortment events among HPAI H5N1 and LPAI H9N2 viruses in Egypt. Additionally, the ability of H9N2 strains to potentiate other AIVs may be attributed to the fact that H9N2 viruses accommodate for several human adaptation markers in their genome, which may enable the reassortant AIVs to cross the species barrier.

Even as we struggle to deal with a roughly 1% CFR (Case Fatality Rate) COVID-19 pandemic, there are other threats in the wild that could prove far more challenging.  Whether its avian influenza, a new swine-origin novel flu, or perhaps another exotic bat-borne virus, the specter of another pandemic is always on the horizon. 

We pretend it isn't at our own risk. 


Saturday, September 19, 2020

#NatlPrep: When Evacuation Is The Better Part of Valor


Note: This is day 19 of National Preparedness Month. Follow this year’s campaign on Twitter by searching for the #NatlPrep #BeReady or #PrepMonth hashtags.

This month, as part of NPM20, I’ll be rerunning some updated preparedness essays, along with some new ones.


Although I've had a couple of close calls over the years, 2017's brush with Hurricane Irma was the first time I've actually been forced to leave my home in the face of a natural disaster. I wrote about my decision in #NatlPrep: Disaster Buddies - The Most Important Prep Of All.

It is not a pleasant prospect, but sometimes circumstances and common sense dictate that you must leave your home - and the bulk of your belongings - behind. 

Luckily, I had several prearranged places I could go. Friends, who are also disaster buddies (see In An Emergency, Who Has Your Back?), who know my couch is always available to them should they need it.

Being able to leave in a hurry when an evacuation has been ordered means having a plan, a destination, and an emergency `to go’ kit or `BOB’ already equipped, and standing by. 

bob 001a
Bug-out-bag, Canteen, & Toiletry kit

In the vernacular, a `bug-out bag' or `BOB’ (or sometimes GOOD bag for `Get Out Of Dodge’) a bag of emergency supplies, ideally kept at the ready, that one can grab on the way out the door during an emergency. Every hurricane season I go through my personal bug out bag, and replace flashlight and radio batteries from last year, and swap out older emergency rations for newer ones.

A BOB isn't supposed to be a survival kit, but rather, is supposed to provide the essentials one might need during the first 72 hours of a forced, and sometimes unexpected, evacuation.

It should contain food, water, any essential prescription medicines, copies of important papers (ID's, insurance, important Phone #s), a first aid kit, portable radio, flashlight, extra batteries, and ideally blankets and extra clothes. While having to evacuate your home may seem like an unlikely event, every years hundreds of thousands of Americans are forced to do so. 

Rivers spill their banks, dams break, brush fires rage out of control, even sudden industrial accidents can force evacuations. And unlike with a hurricane, you won’t always have advance warning. 

The bug out bag pictured above is my immediate `grab' in case of a house fire, or some other abrupt emergency. But if I've got a few minutes to get out, I've also got a couple of larger duffel bags at the ready that can be tossed into the trunk of my car, containing extra clothes, and longer term disaster supplies.   

On top of that, I always keep a first aid kit in my car (see #NatlPrep : First Aid Kits - Don't Leave Home Without One), along with a small survival kit (containing tools, `space blanket', tarp, water, etc.).   Obviously, if I've a few hour to leave, I'll load my car to the gills. 

As we've discussed previously (see Why Preparing For This Year's Hurricane Season Will Be `Different'), evacuation during our COVID-19 pandemic will require more planning and preparation than usual. has the following advice on how to prepare for an evacuation.

Plan to Evacuate
Many kinds of emergencies can cause you to have to evacuate. In some cases, you may have a day or two to prepare while other situations might call for an immediate evacuation. Planning is vital to making sure that you can evacuate quickly and safely no matter what the circumstances.
Before an Evacuation
  • Learn the types of disasters that are likely in your community and the local emergency, evacuation and shelter plans for each specific disaster.
  • Plan how you will leave and where you will go if you are advised to evacuate.
  • Check with local officials about what shelter spaces are available for this year. Coronavirus may have altered your community’s plans.
  • If you evacuate to a community shelter, follow the latest guidelines from the Centers for Disease Control and Prevention (CDC) for protecting yourself and your family from possible coronavirus: people over 2-years-old should use a cloth facial covering while at these facilities.
  • Be prepared to take cleaning items with you like masks, soap, hand sanitizer, disinfecting wipes or general household cleaning supplies to disinfect surfaces.
  • Maintain at least 6 feet of space between you and people who aren’t in your immediate family.
  • Identify several places you could go in an emergency such as a friend’s home in another town or a motel. Choose destinations in different directions so that you have options during an emergency.
  • If needed, identify a place to stay that will accept pets. Most public shelters allow only service animals.
  • Be familiar with alternate routes and other means of transportation out of your area.
  • Always follow the instructions of local officials and remember that your evacuation route may be on foot depending on the type of disaster.
  • Come up with a family/household plan to stay in touch in case you become separated; have a meeting place and update it depending on the circumstance.
  • Assemble supplies that are ready for evacuation. Prepare a “go-bag” you can carry when you evacuate on foot or public transportation and supplies for traveling longer distances if you have a car. 
  • If you have a car:
    • Keep a full tank of gas if an evacuation seems likely. Keep a half tank of gas in it at all times in case of an unexpected need to evacuate. Gas stations may be closed during emergencies and unable to pump gas during power outages. Plan to take one car per family to reduce congestion and delay.
    • Make sure you have a portable emergency kit in the car.
  • If you do not have a car, plan how you will leave if needed. Decide with family, friends or your local emergency management office to see what resources may be available.
During an Evacuation
  • Download the FEMA app for a list of open shelters during an active disaster in your local area.
  • Listen to a battery-powered radio and follow local evacuation instructions.
  • Take your emergency supply kit.
  • Leave early enough to avoid being trapped by severe weather.
  • Take your pets with you but understand that only service animals may be allowed in public shelters. Plan how you will care for your pets in an emergency now.
  • If time allows:
    • Call or email the out-of-state contact in your family communications plan. Tell them where you are going.
    • Secure your home by closing and locking doors and windows.
    • Unplug electrical equipment such as radios, televisions and small appliances. Leave freezers and refrigerators plugged in unless there is a risk of flooding. If there is damage to your home and you are instructed to do so, shut off water, gas and electricity before leaving.
    • Leave a note telling others when you left and where you are going.
    • Wear sturdy shoes and clothing that provides some protection such as long pants, long-sleeved shirts and a hat.
    • Check with neighbors who may need a ride.
  • Follow recommended evacuation routes. Do not take shortcuts, they may be blocked.
  • Be alert for road hazards such as washed-out roads or bridges and downed power lines. Do not drive into flooded areas.
After an Evacuation
If you evacuated for the storm, check with local officials both where you’re staying and back home before you travel.
  • If you are returning to disaster-affected areas, after significant events prepare for disruptions to daily activities and remember that returning home before storm debris is cleared is dangerous.
  • Let friends and family know before you leave and when you arrive.
  • Charge devices and consider getting back-up batteries in case power-outages continue.
  • Fill up your gas tank and consider downloading a fuel app to check for outages along your route.
  • Bring supplies such as water and non-perishable food for the car ride.
  • Avoid downed power or utility lines, they may be live with deadly voltage. Stay away and report them immediately to your power or utility company.
  • Only use generators outside and away from your home and NEVER run a generator inside a home or garage or connect it to your home's electrical system.

The following aerial photo was taken of Crystal Beach,Texas after Hurricane Ike in 2008. It proves that staying home in the face of a flood, a hurricane, or other natural disaster can have deadly consequences.


As hard as it might be, sometimes evacuation is truly the better part of valor. 

Friday, September 18, 2020

WHO Influenza Update #376 & MMWR: Decreased Influenza Activity During COVID-19 Pandemic


One of the intriguing side effects of the COVID-19 pandemic has been the concurrent and dramatic drop in influenza activity around the globe.  Within weeks of COVID's emergence - and the imposition of social distancing and NPI measures - influenza activity in the northern hemisphere plummeted, and never took off in the southern hemisphere during their winter (see below)

While some of this drop-off was initially attributed to a redirection of reporting and surveillance assets due to COVID-19, subsequent testing has confirmed that influenza has been greatly suppressed globally for the past 6 months. 

The most recent WHO Influenza update (below) shows a blank flu map, and indicates only 34 positive flu samples were received by their laboratories over a two-week period in August (a 120-fold decrease over the same time period a year ago). 


  • The current influenza surveillance data should be interpreted with caution as the ongoing COVID-19 pandemic have influenced to varying extents health seeking behaviours, staffing/routines in sentinel sites, as well as testing priorities and capacities in Member States. The various hygiene and physical distancing measures implemented by Member States to reduce SARS-CoV-2 virus transmission have likely played a role in reducing influenza virus transmission.
  • Globally, influenza activity was reported at lower levels than expected for this time of the year. In the temperate zones of the southern hemisphere, the influenza season has not started. Despite continued or even increased testing for influenza in some countries in the southern hemisphere, very few influenza detections were reported.
  • In the temperate zone of the northern hemisphere, influenza activity remained below inter-seasonal levels.
  • In the Caribbean and Central American countries, no influenza detections were reported. Severe acute respiratory infection (SARI) activity, likely due to COVID-19, appeared to decrease in some reporting countries.
  • In tropical South America, tropical Africa and Southern Asia there were sporadic or no influenza detections across reporting countries.
  • In South East Asia, influenza A(H3N2) virus detections were reported in Cambodia.
  • Worldwide, of the very low numbers of detections reported, seasonal influenza A viruses accounted for the majority of detections.

National Influenza Centres (NICs) and other national influenza laboratories from 52 countries, areas or territories reported data to FluNet for the time period from 17 August 2020 to 30 August 2020 (data as of 2020-09-11 02:38:29 UTC). The WHO GISRS laboratories tested more than 1450681 specimens during that time period: 34 were positive for influenza viruses, of which 19 (55.9%) were typed as influenza A and 15 (44.1%) as influenza B. Of the sub-typed influenza A viruses, 0 (0%) were influenza A(H1N1)pdm09 and 11 (100%) were influenza A(H3N2). Of the characterized B viruses, 3 (37.5%) belonged to the B-Yamagata lineage and 5 (62.5%) to the B-Victoria lineage.

WHO encourages the testing of routine influenza surveillance samples from sentinel and non-sentinel sources for influenza and SARS-CoV-2 virus where resources are available and report this information, separate data from sentinel and non-sentinel sites if possible, to established regional and global platforms (See the Operational considerations for COVID-19 surveillance using GISRS guidance)

While ostensibly a `good thing', this reduction in flu activity around the world could have unexpected impacts (see When Epidemic Viruses Collide). For better or worse, the evolutionary trajectory of seasonal influenza viruses have been disrupted by our COVID-19 pandemic, and potentially changed as a result. 

Case in point - next week, the WHO is scheduled to convene an expert panel to select the vaccine components for next year's Southern Hemisphere flu vaccine. With so little flu data to go on, predicting next year's dominant flu strains will be even more daunting than usual. 

While there are fears of a `twindemic' this winter of seasonal flu and COVID-19, it is possible that influenza will remain suppressed this winter as well.  We are literally in uncharted territory, as we've never dealt with a flu season and a coronavirus pandemic before. 

Yesterday's MMWR delves deeper into this decreased global influenza activity, and suggests that while flu activity may be suppressed or delayed this winter, it will still be important to get the flu vaccine this fall. 

Decreased Influenza Activity During the COVID-19 Pandemic — United States, Australia, Chile, and South Africa, 2020

Weekly / September 18, 2020 / 69(37);1305–1309

Sonja J. Olsen, PhD1; Eduardo Azziz-Baumgartner, MD1; Alicia P. Budd, MPH1; Lynnette Brammer, MPH1; Sheena Sullivan, PhD2; Rodrigo Fasce Pineda, MS3; Cheryl Cohen, MD4,5; Alicia M. Fry, MD1 (View author affiliations)


What is already known about this topic?

Influenza activity is currently low in the United States and globally.

What is added by this report?

Following widespread adoption of community mitigation measures to reduce transmission of SARS-CoV-2, the virus that causes COVID-19, the percentage of U.S. respiratory specimens submitted for influenza testing that tested positive decreased from >20% to 2.3% and has remained at historically low interseasonal levels (0.2% versus 1–2%). Data from Southern Hemisphere countries also indicate little influenza activity.

What are the implications for public health practice?

Interventions aimed against SARS-CoV-2 transmission, plus influenza vaccination, could substantially reduce influenza incidence and impact in the 2020–21 Northern Hemisphere season. Some mitigation measures might have a role in reducing transmission in future influenza seasons.

PDF pdf icon[257K]



In the United States, influenza virus circulation declined sharply within 2 weeks of the COVID-19 emergency declaration and widespread implementation of community mitigation measures, including school closures, social distancing, and mask wearing, although the exact timing varied by location (2). The decline in influenza virus circulation observed in the United States also occurred in other Northern Hemisphere countries (3,4) and the tropics (5,6), and the Southern Hemisphere temperate climates have had virtually no influenza circulation.

Although causality cannot be inferred from these ecological comparisons, the consistent trends over time and place are compelling and biologically plausible. Like SARS-CoV-2, influenza viruses are spread primarily by droplet transmission; the lower transmissibility of seasonal influenza virus (R0 = 1.28) compared with that of SARS-CoV-2 (R0 = 2–3.5) (7) likely contributed to a more substantial interruption in influenza transmission. These findings suggest that certain community mitigation measures might be useful adjuncts to influenza vaccination during influenza seasons, particularly for populations at highest risk for developing severe disease or complications.

Initially, declines in influenza virus activity were attributed to decreased testing, because persons with respiratory symptoms were often preferentially referred for SARS-CoV-2 assessment and testing. However, renewed efforts by public health officials and clinicians to test samples for influenza resulted in adequate numbers tested and detection of little to no influenza virus. Further, some countries, such as Australia, had less stringent criteria for testing respiratory specimens than in previous seasons and tested markedly more specimens for influenza but still detected few with positive results during months when Southern Hemisphere influenza epidemics typically peak. A new Food and Drug Administration–approved multiplex diagnostic assay for detection of both SARS-CoV-2 and influenza viruses could improve future surveillance efforts (

It is difficult to separate the effect that individual community mitigation measures might have had on influenza transmission this season. Although school-aged children can drive the spread of influenza, the effectiveness of school closures alone is not clear because adults have other exposures (8). There is evidence to support the use of face masks by infected persons to reduce transmission of viral respiratory illnesses to others and growing evidence to support their use (in the health care setting, in households, and in the community) to protect the healthy wearer from acquiring infection. More data are needed to assess effectiveness of different types of masks in different settings (9). Data from the current pandemic might help answer critical questions about the effect of community mitigation measures on transmission of influenza or other respiratory diseases. In addition, assessing acceptability of effective measures would be critical, because acceptability is likely to be inversely correlated with the stringency of the measure.

The findings in this report are subject to at least four limitations. First, an ecologic analysis cannot demonstrate causality, although the consistency of findings across multiple countries is compelling. Second, other factors, such as the sharp reductions in global travel or increased vaccine use, might have played a role in decreasing influenza spread; however, these were not assessed. Third, viral interference might help explain the lack of influenza during a pandemic caused by another respiratory virus that might outcompete influenza in the respiratory tract (10). This possibility is less likely in the United States because influenza activity was already decreasing before SARS-CoV-2 community transmission was widespread in most parts of the nation. Finally, it is possible that the declines observed in the United States were just the natural end to the influenza season. However, the change in the decrease percent positivity after March 1 was dramatic, suggesting other factors were at play.

The global decline in influenza virus circulation appears to be real and concurrent with the COVID-19 pandemic and its associated community mitigation measures.

Influenza virus circulation continues to be monitored to determine if the low activity levels persist after community mitigation measures are eased. If extensive community mitigation measures continue throughout the fall, influenza activity in the United States might remain low and the season might be blunted or delayed. In the future, some of these community mitigation measures could be implemented during influenza epidemics to reduce transmission, particularly in populations at highest risk for developing severe disease or complications.

However, in light of the novelty of the COVID-19 pandemic and the uncertainty of continued community mitigation measures, it is important to plan for seasonal influenza circulation this fall and winter. Influenza vaccination for all persons aged ≥6 months remains the best method for influenza prevention and is especially important this season when SARS-CoV-2 and influenza virus might cocirculate (1).

Regardless of how this year's flu season plays out - being part of a `vulnerable demographic' - I have every intention of getting the flu shot this month.  I will also continue to social distance, practice stringent hand hygiene, and wear a face cover in public as part of a `layered' protection scheme. 

I recognize the flu vaccine probably only provides my age group with 30%-40% protection, but given the long list of things that can go wrong during or following flu infection (see CDC: Another Study Linking Severe Influenza To Heart Damage), I'll take whatever advantage I can get.

Like wearing a seat belt in a car crash, getting the vaccine doesn't guarantee you'll walk away unscathed . . . but it does increase your chances.

Thursday, September 17, 2020

NHC: Watching Southern Gulf Of Mexico For Development


Even as the remnants of Hurricane Sally spread flooding rains across the Southeastern states, and residents in Florida and Alabama begin to assess and deal with the damage, the tropics continue to brew new threats.   

Closest to home, and the most likely to develop into something, is an area of disturbed weather in the southwestern Gulf of Mexico, which the National Hurricane Center gives a 90% chance of development over the next few days. 

From the 8 am EST Tropical Outlook:


Tropical Weather Outlook
NWS National Hurricane Center Miami FL
800 AM EDT Thu Sep 17 2020

For the North Atlantic...Caribbean Sea and the Gulf of Mexico:

The National Hurricane Center is issuing advisories on Hurricane Teddy, located over the central tropical Atlantic and on Tropical Storm Vicky, located over the eastern tropical Atlantic. The National Hurricane Center has issued its last advisory on Tropical Depression Sally, located inland over eastern Alabama.

1. Thunderstorm activity has continued to increase and become better organized this morning in association with a well-defined low pressure system located over the southwestern Gulf of Mexico.

Upper-level winds are gradually becoming more conducive for development and, if this recent development trend continues, a tropical depression or a tropical storm could form later today.
The low is expected to meander over the southwestern Gulf of Mexico for the next day or so before moving slowly northward to northeastward on Friday and Saturday. An Air Force Reserve reconnaissance aircraft is scheduled to investigate the disturbance this afternoon.

* Formation chance through 48 hours...high...90 percent.

* Formation chance through 5 days...high...90 percent.

If this system develops, it will be named Wilfred - the 21st named storm of the season.  After Wilfred, the NHC will use the names of the letters from the Greek Alphabet to identify the rest of the storms of the 2020 Atlantic hurricane season. 

While steering currents are expected to be weak for the next couple of days, if this storm develops, it is expected to move north or northeastward in a few days, and could eventually threaten our already battered Gulf Coast. 

Stay tuned.

Kazakhstan MOA: Avian Epizootic Reported In 7 Northern Districts


Six weeks ago in A Disturbing Dearth Of Data, we looked at a report of HPAI H5N8 detected among wild birds found dead on the shores of Peschanoe and Tabinsha lakes, in (Chelyabinsk region) Russia.

Since then, we've seen numerous reports of HPAI H5 avian influenza outbreaks (see Russia's Worsening HPAI H5 Outbreak (in Poultry)spreading across several western Siberian oblasts, very near their border with Kazakhstan.

A little over a week ago, in DEFRA: High Pathogenicity Avian Influenza (H5N8) in Russia we looked at the the UK's latest report on avian flu activity in Russia, and the potential for migratory birds to spread the virus into Europe, Africa, or the Middle East this fall and winter. 

The DEFRA report warned:

The genotype of the current H5N8 viruses in Russia is not yet known, and importantly it is not known whether this virus is showing further genetic reassortment compared to the 2016/17 and 2019/20 forms of the virus that spread to Europe. Increased fitness of these viruses for wild birds through such exchange is possible.

While there have been scattered mentions in the Russian media for several days, today the Ministry of Agriculture of the Republic of Kazakhstan has announced they are dealing with a large epizootic of avian influenza. 


Epizootic situation in North Kazakhstan under the control of the Ministry of Agriculture of the Republic of Kazakhstan

NKR is taking measures against the spread of highly pathogenic avian influenza: vaccines are imported, territories are disinfected, dead animals are destroyed, and the export of poultry and related products is banned.

In seven districts of the North Kazakhstan region ( Timiryazevsky, Tayynshinsky, Zhambyl, Kyzylzharsky, Shal akyn, named after G. Musrepov, named after M. Zhumabaev ) from September 9 to 16 this year. the death of poultry of various species was registered.

The National Reference Center determined that highly pathogenic avian influenza was the cause of the death. In accordance with the adopted rules, the Republic of Kazakhstan notified the World Organization for Animal Health about the outbreak.

To urgently restore the safe status of the country and prevent the spread of HPAI, the Committee for Veterinary Control and Supervision of the Ministry of Agriculture of the Republic of Kazakhstan, from September 17, 2020, introduced temporary restrictions on the export of live poultry and hatching eggs, down and feathers, poultry meat and all types of poultry products, feed and feed additives for poultry , as well as used equipment for keeping, slaughtering and cutting birds from Timiryazevsky, Zhambylsky, Kyzylzharsky, Tayinshinsky, Shal akyn, them. G. Musrepov, them. M. Zhumabayev districts of the North Kazakhstan region .

To eliminate a particularly dangerous disease, the Republican Anti- Epizootic Detachment and the North Kazakhstan Territorial Inspectorate of the KVKN are currently carrying out a set of mandatory measures, incl. destruction of corpses of birds, disinfection of premises and courtyard areas.

873 thousand doses of domestic drugs against highly pathogenic avian influenza have been allocated for the vaccination of animals in the territories bordering the Russian Federation .

By the decision of the special commission, the Republican antiepizootic detachment of the KVKN Ministry of Agriculture of the Republic of Kazakhstan will pay compensation to the owners of dead birds in the amount of the average monthly market value of animals .

The epizootic situation in the region is under the control of the ministry.

Let us remind you that on August 26 this year. The KVKN Ministry of Agriculture of the Republic of Kazakhstan introduced restrictions on the import of live birds, poultry products and related products from the Omsk region of the Russian Federation to Kazakhstan due to the outbreak of highly pathogenic avian influenza virus ( / details / minselhoz-ogranichil-vvoz-nekotoryh-tovarov-iz-omskoy-oblasti-rf? lang = ru ). However, according to experts and scientists, the HPAI causative agent can spread not only through these categories of goods, but also with the help of wild migratory birds. 


While global avian flu activity has been greatly suppressed since the last great epizootic in 2017, big outbreaks are often followed by periods of quiescence. This summer's uptick in activity in Russia, and parts of Asia bears watching. 

Some excerpts from the most recent (21 Aug - Sept 10th) OIE Avian flu activity summary  follow:

In the reporting period, 34 new HPAI outbreaks were reported in domestic birds in Asia, Europe and Oceania involving different HPAI subtypes namely H5N2, H5N5, H7N7 and H5 (neuraminidase subtype pending). 1 new outbreak of H5 was reported in non-poultry in Europe. In addition, 120 HPAI outbreaks in poultry and non-poultry are still ongoing in Oceania, Europe, Asia and Africa involving different subtypes, namely H5, H5N1, H5N5, H5N6, H5N8, H7N3, H7N7 and H7N9. 

• Outbreaks of H5N1, H5N6 and H7N9 are still continuing in a few Asian countries with Chinese Taipei reporting recurrence of new H5N2 and H5N5 outbreaks. 

• Australia experienced recurrence of H7N7 outbreaks after six years and the situation is continuing with fresh outbreaks. 

• In South Africa ongoing outbreaks of H5N8 are still continuing. Russia, already experiencing ongoing outbreaks of H5N8 in non-poultry, also reported new H5 outbreaks in poultry and non-poultry. It is more likely that the source of infection in these outbreaks is contact with wild birds and followed by limited local spread. 

Veterinary Authorities in the affected countries have responded to contain outbreaks in poultry with stamping out measures, heightened surveillance, and recommendations to poultry owners to increase biosecurity. The OIE Standards, and the transparency of reporting through the OIE’s World Animal Health Information System, provide the framework for Veterinary Services to implement effective surveillance, reporting, and controls for avian influenza. 

Wild bird surveillance can indicate periods of heightened risk, and at these times measures to improve on-farm biosecurity may reduce the likelihood of exposure of poultry.

MMWR: Two New Reports On Pregnancy & COVID-19


Twice over the last six weeks we've looked at the thorny issue of COVID-19's impact on pregnancies, starting with a look back at the impacts from past influenza pandemics and a review of several recent studies (see Pregnancy & COVID-19: Still More Questions Than Answers), followed up 10 days later with a PAHO Epi Alert: COVID-19 During Pregnancy - 13 August 2020.

The CDC maintains a Data on COVID-19 during Pregnancy website, but cautions that:
Because only about a quarter of case report forms include information on pregnancy status, these numbers likely do not include all pregnant women with COVID-19 in the United States and must be interpreted with caution. The completeness of this variable continues to improve each week.

Hispanic and non-Hispanic black pregnant women appear to be disproportionately affected by SARS-CoV-2 infection during pregnancy. 

While the data remains incomplete, we've two new early releases from the CDC's MMWR that attempt to better quantify the impact and risks from COVID-19 in pregnancy.  Both reports are detailed and lengthy, and so I've only reproduced the links and summaries below.

Early Release / September 16, 2020 / 69

Lakshmi Panagiotakopoulos, MD1; Tanya R. Myers, PhD1; Julianne Gee, MPH1; Heather S. Lipkind, MD2; Elyse O. Kharbanda, MD3; Denison S. Ryan, MPH4; Joshua T.B. Williams, MD5,6; Allison L. Naleway, PhD7; Nicola P. Klein, MD, PhD8; Simon J. Hambidge, MD, PhD5,6; Steven J. Jacobsen, MD, PhD4; Jason M. Glanz, PhD9; Lisa A. Jackson, MD10; Tom T. Shimabukuro, MD1; Eric S. Weintraub, MPH1 (View author affiliations)View suggested citation

What is already known about this topic?

Pregnant women might be at increased risk for severe illness from SARS-CoV-2 infection.

What is added by this report?

Prevalences of prepregnancy obesity and gestational diabetes were higher among pregnant women hospitalized for COVID-19–related illness (e.g., worsening respiratory status) than among those admitted for pregnancy-related treatment or procedures (e.g., delivery) and found to have COVID-19. Intensive care was required for 30% (13 of 43) of pregnant women admitted for COVID-19, and one pregnant woman died from COVID-19.
What are the implications for public health practice?

Antenatal counseling emphasizing preventive measures, including use of masks, frequent hand washing, and social distancing, might help prevent COVID-19 among pregnant women, especially those with prepregnancy obesity and gestational diabetes.

Early Release / September 16, 2020 / 69
Miranda J. Delahoy, PhD1,2; Michael Whitaker, MPH1,3; Alissa O’Halloran, MSPH1; Shua J. Chai, MD1,4; Pam Daily Kirley, MPH4; Nisha Alden, MPH5; Breanna Kawasaki, MPH5; James Meek, MPH6; Kimberly Yousey-Hindes, MPH6; Evan J. Anderson, MD7,8; Kyle P. Openo, DrPH7,8,9; Maya L. Monroe, MPH10; Patricia A. Ryan, MS10; Kimberly Fox, MPH11; Sue Kim, MPH11; Ruth Lynfield, MD12; Samantha Siebman, MPH12; Sarah Shrum Davis, MPH13; Daniel M. Sosin, MD14; Grant Barney, MPH15; Alison Muse, MPH15; Nancy M. Bennett, MD16; Christina B. Felsen, MPH16; Laurie M. Billing, MPH17; Jessica Shiltz, MPH17; Melissa Sutton, MD18; Nicole West, MPH18; William Schaffner, MD19; H. Keipp Talbot, MD19; Andrea George, MPH20; Melanie Spencer, MPH20; Sascha Ellington, PhD1; Romeo R. Galang, MD1; Suzanne M. Gilboa, PhD1; Van T. Tong, MPH1; Alexandra Piasecki, MPH1,21; Lynnette Brammer, MPH1; Alicia M. Fry, MD1; Aron J. Hall, DVM1; Jonathan M. Wortham, MD1; Lindsay Kim, MD1; Shikha Garg, MD1; COVID-NET Surveillance Team (View author affiliations)
What is already known about this topic?

Information on the clinical characteristics and birth outcomes of hospitalized U.S. pregnant women with COVID-19 is limited.

What is added by this report?

Among 598 hospitalized pregnant women with COVID-19, 55% were asymptomatic at admission. Severe illness occurred among symptomatic pregnant women, including intensive care unit admissions (16%), mechanical ventilation (8%), and death (1%). Pregnancy losses occurred for 2% of pregnancies completed during COVID-19-associated hospitalizations and were experienced by both symptomatic and asymptomatic women.

What are the implications for public health practice?

Pregnant women and health care providers should be aware of potential risks for severe COVID-19, including adverse pregnancy outcomes. Identifying COVID-19 during birth hospitalizations is important to guide preventive measures to protect pregnant women, parents, newborns, other patients, and hospital personnel.

The CDC's `living document' Evidence used to update the list of underlying medical conditions that increase a person’s risk of severe illness from COVID-19continues to list pregnancy as a 2nd tier (mixed evidence) risk group for severe illness due to COVID-19.  But their guidance for People with Certain Medical Conditions advises:

Based on what we know at this time, pregnant people might be at an increased risk for severe illness from COVID-19 compared to non-pregnant people. Additionally, there may be an increased risk of adverse pregnancy outcomes, such as preterm birth, among pregnant people with COVID-19.

Actions to take
  • Do not skip your prenatal care appointments.
  • Make sure that you have at least a 30-day supply of your medicines.
  • Talk to your healthcare provider about how to stay healthy and take care of yourself during the COVID-19 pandemic.
  • If you don’t have a healthcare provider, contact your nearest community health centerexternal icon or health department.
  • Call your healthcare provider if you have any questions related to your health.
  • Seek care immediately if you have a medical emergency.
  • You may feel increased stress during this pandemic. Fear and anxiety can be overwhelming and cause strong emotions. Learn about stress and coping.

A decade after the last influenza pandemic (2009), our understanding of long-term impacts of maternal influenza infection on the unborn child remains limited (see Study: Outcomes Of Infants Born To Women With Influenza A(H1N1)pdm09), and it will likely take years to fully assess and appreciate the impact of COVID-19.

Practically every day we learn about more non-trivial complications from SARS-CoV-2 infection (see PAHO Epi Alert: Complications & Sequelae Of COVID-19), and that until we know a lot more, avoiding infection if you can - particularly if you are in a high risk group - just makes sense.

For now, you'll find the latest pregnancy-related guidance from the CDC below.