Wednesday, July 26, 2017

Texas DSHS: Probable Local Zika Infection In South Texas


Last October - although no local cases had been reported at the time - Texas health officials warned of a heightened risk of locally acquired Zika infection in six specific south Texas counties (Cameron, Hidalgo, Starr, Webb, Willacy, and Zapata).
Subsequently 6 local cases were detected in Brownsville (Cameron County) in November and December. 
In April, as temperatures warmed, the DSHS updated their Testing Recommendations for Rio Grande Valley. Today, as a result of that enhanced surveillance, Texas Health authorities announced the detection of their first (likely) locally acquired Zika infection of 2017. 

Health officials find probable local Zika infection
News Release
July 26, 2017

The Texas Department of State Health Services and Hidalgo County Health and Human Services have determined a Hidalgo County resident who previously had a Zika infection was most likely infected in Texas. Because the individual has not recently traveled outside the area or had any other risk factors, the infection was probably transmitted by a mosquito bite in South Texas sometime in the last few months. Laboratory testing shows the individual is no longer at risk of spreading the virus to mosquitoes.

Thousands of Zika tests have been done since a DSHS recommendation in April expanded testing of pregnant women and people with Zika symptoms in six South Texas counties. The additional testing led to the identification of this infection, the first this year that appears to have been transmitted by a mosquito in Texas. There is no evidence of ongoing Zika transmission in the state at this time, but public health officials are continuing to conduct human and mosquito surveillance to find any future Zika infections as early as possible.

Hidalgo County Health and Human Services has alerted health care providers, reminding them of the testing recommendations, and DSHS and the county are asking everyone in the area to be aware of the most common Zika symptoms: rash, fever, joint pain and eye redness. People should contact their provider about testing if they experience a rash plus one of the other symptoms.

Local officials have also responded by increasing mosquito control and surveillance activities and going door-to-door to share information about Zika and ensure pregnant women and people with symptoms have had the appropriate testing.

People throughout the Rio Grande Valley and Texas should continue to protect themselves from mosquito bites by
  • Using EPA-approved insect repellent every time they go outside.
  • Using air conditioning or window and door screens that are in good repair to keep mosquitoes out.
  • Limiting outdoor activities during peak mosquito times.
  • Covering exposed skin with long pants and long-sleeved shirts whenever possible.
  • Removing standing water in and around homes, including in trash cans, toys, tires, flower pots and any other containers so mosquitoes can’t lay their eggs.
  • Using a larvicide in water that can’t be drained to keep mosquitoes from developing into biting adults.
Texas previously had six locally-transmitted cases of Zika in Brownsville in November and December 2016. More information on Zika for the public and health care providers is available at

J. Clin. Vir.: Ιnfluenza A(H3N2) Genetic Variants In Vaccinated Patients In Northern Greece


Last Saturday in The Enigmatic, Problematic H3N2 Influenza Virus we looked at the nearly 50 year history and growing diversity of the H3N2 virus in humans, and recent reports of an emerging subclade 3C.2a1 with amino acid (aa) substitutions (including N121K) that may have adversely affected the influenza Vaccine's Effectiveness (VE) over the last winter's flu season.
Influenza viruses evolve via two well established routes; Antigenic drift & Antigenic Shift (reassortment).
Shift requires the co-infection of a host with two different influenza viruses which then swap chunks of their genetic code, creating a new `reassorted' virus (see NIAID Video: How Influenza Pandemics Occur). 
While viable reassortments are rare, as any virologist will tell you . . . Shift Happens.
Far more common is Antigenic drift, which is driven by replication errors that are common with single-stranded RNA viruses (see NIAID Video: Antigenic Drift).  While most of these biological accidents are evolutionary failures, every once in a while a more biologically `fit' virus is produced, and it is able to compete with its parental viruses.
This is the reason why influenza vaccines must be updated so often. 
Unfortunately, it takes six months to create and produce enough influenza vaccine for each flu season, and during this time the virus continues to evolve. For the northern hemisphere, vaccine strain selections must be made in February (see WHO: Recommended Composition Of 2017-2018 Northern Hemisphere Flu Vaccine).
Despite this production lag, most years the vaccine is still a pretty good match. But as we saw in the 2014-2015 flu season, sometimes the virus is able to evade the vaccine (see CDC HAN Advisory On `Drifted’ H3N2 Seasonal Flu Virus).
We never know just how good a match the vaccine will be until well into the flu season. Starting about six months ago we began to get interim reports on last year's vaccine effectiveness (VE). 
But at the same time we've been seeing reports of much lower VE - particularly among those over 65 - who were infected with some recently emerging variants of the H3N2 virus (see Changes in genetically drifted H3N2 influenza A viruses and vaccine effectiveness in adults 65 years and older during the 2016/17 season in Denmark),
Today we've another study, this time from Greece, focusing on genetic variants of the H3N2 virus isolated from both vaccinated  and unvaccinated patients during the last flu season.
Among those who were unvaccinated, H3N2 subclade 3C.2a - which is recognized as a pretty good antigenic match to last year's vaccine - was most commonly detected.  But among those who received the flu vaccine last year, the emerging subclade 3C.2a1 was far most common, suggesting it may be better at evading the vaccine.

Ιnfluenza A(H3N2) genetic variants in vaccinated patients in northern Greece

A. Melidou'Correspondence information about the author A. MelidouEmail the author A. Melidou Email the author A. Melidou , G. Gioula, M. Exindari , E. Ioannou, K. Gkolfinopoulou, T. Georgakopoulou, S. Tsiodras, A. Papa 


    •Common aa substitutions T135K and D122N on viral antigenic and glycosylation sites.
    •These variant strain has been observed in vaccinated patients.
    •Possible antigenic drift in northern Greek A(H3N2) circulating viruses.
    •Continuous monitoring of A(H3N2) evolution and circulation of variant strains is essential to monitor their effect on vaccine effectiveness.



Influenza A(H3N2) viruses predominated during the influenza 2016/2017 season and showed extensive genetic diversification. A high vaccination failure rate was noticed during the 2016/17 season in Greece, especially among the elderly.


The scope of the study was to investigate the genetic characteristics of A(H3N2) circulating viruses and viruses detected in vaccinated patients.

Study design

Virus samples originated from vaccinated and unvaccinated patients, obtained at the National Influenza Centre for northern Greece. Phylogenetic analysis and comparison of the haemagglutinin gene of the viruses to the vaccine virus A/Hong Kong/4801/2014 was performed.


The majority of analysed viruses are clustering in the genetic clade 3C.2a, and in a newly emerged subclade, designated as 3C.2a1. The highest proportion of viruses detected in vaccinated patients fell into a distinct subcluster within the 3C.2a1 subclade, which is characterised by the amino acid substitutions N122D and T135 K in haemagglutinin.


Viruses that belong to the 3C.2a clade are generally considered to resemble antigenically to the northern hemisphere vaccine component A/Hong Kong/4801/2014 that was recommended by WHO to be included also into the 2017/18 vaccine.
However, viruses belonging to a specific 3C.2a1 subcluster was extensively circulating in northern Greece and among vaccinated individuals. Both substitutions carried by this strain were located on antigenic sites and caused losses of N-linked glycosylation sites of the virus, which could potentially affect viral antigenicity. Further studies are needed to determine the antigenicity of this variant strain and its possible implication in vaccine effectiveness.

The 64$ question is which subclade of H3N2 will dominate the northern hemisphere this fall and winter.  Clade 3C.2a should be a pretty good match to this fall's vaccine, while there are nagging questions over the vaccine's effectiveness against some variants of clade 3C.2a1.

The most recent Influenza Virus Characterization from the ECDC  - based on very limited virus sampling this summer - writes:
Genetic characterization

For specimens collected between weeks 21/2017 and 26/2017, genetic characterization of 3 viruses has been reported. Two were B/Yamagata lineage viruses and one fell into the A(H3N2) 3C.2a1 subclade defined by N171K amino acid substitution, often with N121K, in the haemagglutinin.
Viruses in this clade have been antigenically similar to the vaccine component clade (3C.2a), but both clades are evolving rapidly with the emergence of several virus clusters defined by additional amino acid substitutions in the haemagglutinin, thereby requiring continued monitoring of antigenic characteristics. See also the WHO CC London February 2017 report.

As we go into each year’s flu season, we are always presented with a  `Forrest Gump’ moment, as we never really know what we are going to get.  This year appears no different.

Stay tuned.

Tuesday, July 25, 2017

Taiwan's Summer H3N2 Epidemic Continues Near Peak

Credit Taiwan's Flu Express Week 28


While not as severe as what is being reported in Hong Kong (see HKU Experts Call For Deploying Prophylactic Tamiflu To Avert Crisis) - after a lackluster winter flu season - Taiwan has been dealing with its own out-of-season summer flu surge since early May.    
Like Hong Kong, their current epidemic is primarily due to H3N2. Two weeks ago, Taiwan's CDC announced that their flu had peaked, and was beginning to decline.
While that trend continues, today Taiwan's CDC warns that flu continues near its peak, and  announced that over the past week local ERs saw more than 106,000 flu cases, 101 were diagnosed as `severe', and that 13 people died from flu-related illness.

Domestic influenza epidemic continues to decline, but still in the epidemic peak, people do not take it lightly

UNDCP said the domestic influenza flu epidemic for three consecutive weeks of decline, the other influenza and severe cases and confirmed cases also decreased for 2 weeks; but the number of influenza treatment is still more, and continued severe cases, the overall epidemic is still popular peak, To remind people to ignore the symptoms of influenza, such as signs of severe risk, please seek medical attention as soon as possible to reduce the risk of concurrent serious illness, and please keep a good hand and respiratory health, and the implementation of sick at home to rest.

According to the monitoring data, the number of visits was 106,005 last week (July 16 to July 22), down 8.6% from the previous week (115,987 person-times) and has been falling for 3 consecutive weeks. The upper respiratory tract / The number of cases reported in the past three weeks was flat, but the number of new notifications was lower than that in mid to late June, among which 16 were positive for influenza test, and the population was densely located (12). Laboratory data showed that H3N2 was predominantly in community epidemic virus type, and only about 9% of influenza virus was detected in influenza B virus. The antigenicity monitoring data showed that 95% H3N2 virus coincided with the influenza vaccine group.

101 cases of influenza infection last week to determine the case, to determine the number of cases for 2 consecutive weeks of decline, the case of infection type to H3N2 for more; another 13 cases of severe death cases, the age of onset ranging from 54 to 96 years old, Have a chronic history, infection type 11 cases of H3N2 and 2 cases of type B. July 1, 2016 so far accumulated 1,194 cases of influenza complicated with severe cases, of which 121 died. At present, the flu epidemic has been the highest point, showing a downward trend, according to the trend of the epidemic over the years, the number of new cases of severe disease is expected to slow down with the mild epidemic after the decline.

The KPC reiterates its appeal that if people have flu-like symptoms, please go to the nearest public influenza influenza antiviral contract clinic for medical treatment, to avoid concentrating on the emergency hospital, where the doctor to determine compliance with the use of public drug use conditions, without fast screening, The use of public anti-viral agents; but if there are breathing difficulties, rapid, cyanosis (hypoxia), blood sputum or sputum thickening, chest pain, changes in consciousness, hypotension and other signs of influenza risk, you should try to the largest hospital for treatment The Information can be found on the UNDG Global Information Network (influenza area) ( or by calling the Free Epidemic Prevention Line 1922 (or 0800-001922).

The exact reasons behind this summer's unusually severe flu in Hong Kong, Macao, Taiwan, and (reportedly) Southeast China isn't known, although last week researchers at the University of Hong Kong suggested it might be due to small mutation in the virus (see The Enigmatic, Problematic H3N2 Influenza Virus).

Mutation or not, this is a reminder that seasonal influenza can be quite deadly, and that it doesn't always follow the `rules'.

Turkish Media Reporting large Die Offs Of Poultry - Facilities Quarantined


With the dual caveats that a decade ago Turkey had quite a bad time with hundreds of outbreaks of H5N1 (including a dozen human infections and four deaths) - and that their press can be a bit hyperbolic on the subject of bird flu (Kuş Gribi) - overnight numerous Turkish media outlets are reporting on large poultry die offs in the eastern part of the country.

A few (translated) headlines include:
Bird Flu Panic in Kars! Kaz hundreds darkly dying 

Avian flu is going back to the nightmare?  

Bird flu suspected in Kars: Quarantine decision was taken    

It should be noted that the quarantining towns and poultry facilities has long been a part of Turkey's bird flu control playbook (see 2007 Turkey: Three Villages Quarantined? & Turkey : 4 More Villages Quarantined, & 2008 Turkey Quarantines Three Villages). 
A pattern which should make today’s headlines and story slightly less urgent sounding that it might at first appear.  At this point, bird flu (subtype not provided) is only suspected.  
The following syntax-challenged media report (cobbled together using 2 different translators) indicates that the poultry deaths began in Kars 10 days ago, and that the town of Ardahan - 60 km further north - is also reporting poultry deaths.

Both towns are located within about 30 km of the Georgian and Armenian borders.  

Kars and Ardahan in bird flu alert: Facility were quarantined

Internal News Service -
July 25, 2017

In the last 10 days in Kars headquarters and villages, the goose and poultry deaths took place in succession, and many facilities were quarantined. A large number of poultry were killed in Ardahan, no doubt bird flu.

The deaths of poultry living in Kars in 10 days, the authorities took action. Bird-blowing is, of course, putting a large number of poultry into living birds.

According to the EHA; In the last 10 days in Kars headquarters and the villagers, the deaths of goose and poultry were followed by the authorities. The teams affiliated to the Provincial Directorate of Food, Agriculture and Livestock put the geese in vigorous state by quarantining their districts in the Mezra village of the center. It was learned that the samples taken from the animals were sent with a lot of people, especially Erzurum to be examined.

On the other hand, the citizens who claimed that the poultry had died, claimed that their animals were killed by bird flu.

The alarm in Ardahan

In Ardahan, a large number of poultry were slaughtered by birds in the branches of the Provincial Directorate of Food, Agriculture and Livestock and the Directorate of Animal Health Branch.

Suspected Bird flu in poultry in the city, officials are alarmed. Directorate for food, agriculture and livestock and animal health branch teams, wearing special clothing, some businesses in the neighborhood suspected Central Ardahan Habeeb seen goose, chicken, duck and Turkey has culled poultry as animals.

The markets ' bird flu ', the outdoor areas in neighboring provinces of unsupervised brought sold poultry caused by citizens who claim "brought from the outside, ducks and poultry are sold. That the authorities do not intervene. But without test chickens in the village, collecting without the vaccine without analysis. We also we sin, i.e. the citizen is cut off, "he said.

Sales of poultry in public areas on the Peddler who citizens protests started to escape by leaving the area where they are located.

We'll have to await official word from the FAO or OIE to know if HPAI is the true cause of these bird deaths.

OIE Notification: H5N1 In Poultry - Myanmar


Myanmar has only reported a couple of scattered outbreaks of H5N1 in recent years, last reporting an outbreak in April of 2016  in the north central region of their country.  Before that we have to go back to February of 2015, and prior to that to the summer of 2012.
Earlier this year, in OIE Notification: H5N6 Arrives In Myanmar, we learned - somewhat belatedly - that H5N6 had been detected in market birds sampled nearly a year earlier in Shan State, near the Chinese border.
Today, however, Myanmar has notified the OIE of an outbreak of HPAI H5N1 in Dawei in the south-eastern part of the country, only about 40 miles from the Thai border. Affected are roughly 5000 Lohmann layers.

In it's epidemiological comments, the report cites:  Lack of bio security of the farm and a small holder has an illegal processing place located in front of the farm.

Monday, July 24, 2017

Journal AEM : US Feral Swine Were Exposed To Both Avian & Swine Influenza A Viruses

Feral Swine - Credit USDA


While scientists monitor commercial swine herds for signs of influenza evolution, relatively little is known about the carriage of influenza A viruses by feral swine in the United States, and around the globe.   
With U.S. feral hog populations tripling over the past 25 years (now est. at 6 million ) scattered across 38 states, these invasive and incredibly destructive creatures are expected to expand to all 50 states in the next few decades  (see 2017 study  Interpreting and predicting the spread of invasive wild pigs).

Swine, as we've discussed often, can be infected by many types of influenza (including swine, human and avian strains), and may be co-infected by two or more viruses at the same time.  This  susceptibility - along with influenza's ability to reassort into new subtypes - makes pigs excellent `mixing vessels' for influenza.

Despite less-than-robust surveillance of commercial swine around the globe, over the past couple of years we've seen a number of new `reassortant' viruses detected in pigs. A few recent blogs include:
I&ORV: Triple-Reassortant Novel H3 Virus of Human/Swine Origin Established In Danish Pigs

Emerg. Microbes & Inf.: Pathogenicity & Transmission Of A Swine Influenza A(H6N6) Virus - China

Front. Microbiol.: A Novel H1N2 Reassorted Influenza Virus In Chinese Pigs
PNAS: The Pandemic Potential Of Eurasian Avian-like H1N1 (EAH1N1) Swine Influenza  

Compared to commercial swine, our understanding of what is going on with influenza in feral pigs is almost non-existent.  We have seen a handful of studies over the years, including a 2008 survey in the Journal of Wildlife Diseases (see Influenza exposure in United States feral swine populations.) which found:
Of the 271 IAV-positive samples, 236 cross-reacted with swine IAVs, 1 with avian IAVs, and 16 with avian and swine IAVs, indicating that feral swine were exposed to both swine and avian IAVs but predominantly to swine IAVs. Our findings suggest that feral swine could potentially be infected with both avian and swine IAVs, generating novel IAVs by hosting and reassorting IAVs from wild birds and domestic swine and facilitating adaptation of avian IAVs to other hosts, including humans, before their spillover. 
 A 2013 EID Journal Dispatch (see Influenza A Subtype H3 Viruses in Feral Swine, United States, 2011–2012), which from 1,989 serum samples collected from 31 states, found that 182 samples were IAV (Influenza A Virus) positive.  They concluded: 
Our study demonstrated that subtype H3N2 IAVs are periodically infecting feral swine in the United States. Feral swine are a potential source of IAVs with bidirectional transmission to domestic swine or humans. Detection of an H3N2v-like IAV in the feral swine population demonstrates a potential threat to human health. Continued surveillance is recommended to monitor the distribution and the genomic and antigenic diversities of IAVs in feral swine to better assess the risk.
All of which serves as prelude to a new study, published last week in the Journal of Applied Environmental Microbiology, that finds U.S. feral hogs have been exposed to a variety of influenza A viruses, including avian subtypes.
US feral swine were exposed to both avian and swine influenza A viruses
Brigitte E. Martina, Hailiang Suna, Margaret Carrelb, Fred L. Cunninghamc, John A. Barochd, Katie C. Hanson-Dorrc, Sean G. Younge, Brandon Schmitd, Jacqueline M. Noltingf, Kyoung-Jin Yoong, Mark W Lutmanh, Kerri Pedersenh, Kelly Lageri, Andrew S. Bowmanf, Richard D. Slemonsf, David R. Smithj, Thomas DeLibertod* and Xiu-Feng Wana*  


Influenza A viruses (IAVs) in swine can cause sporadic infections and pandemic outbreaks among humans, but how avian IAV emerges in swine is still unclear. Unlike domestic swine, feral swine are free ranging and have many opportunities for IAV exposure through contacts with various habitats and animals, including migratory waterfowl, a natural reservoir for IAVs.

During 2010--2013, 8,239 serum samples were collected from feral swine across 35 US states and tested against 45 contemporary antigenic variants of avian, swine, and human IAVs; of these, 406 (4.9%) samples were IAV-antibody positive. Among 294 serum samples selected for antigenic characterization, 271 cross-reacted with ≥1 testing virus whereas the other 23 did not cross-react with any testing virus. Of the 271 IAV-positive samples, 236 cross-reacted with swine IAVs, 1 with avian IAVs, and 16 with avian and swine IAVs, indicating that feral swine were exposed to both swine and avian IAVs but predominantly to swine IAVs. 

Our findings suggest that feral swine could potentially be infected with both avian and swine IAVs, generating novel IAVs by hosting and reassorting IAVs from wild birds and domestic swine and facilitating adaptation of avian IAVs to other hosts, including humans, before their spillover. Continued surveillance to monitor the distribution and antigenic diversities of IAVs in feral swine is necessary to increase our understanding of the natural history of IAVs.
        (Continue . . . )

While agricultural exhibitions at state and county fairs make up the vast majority of the swine-human contact in the United States (followed by commercial farms and abattoirs), feral pigs - which are hunted for meat, sport, and animal control - are increasingly in contact with humans. 
Being omnivorous, and free ranging, they also have significant opportunities for contact with IAV infected birds. 
While the odds of that happening may seem long here in the United States, it was only 7 months ago we were following an outbreak of a rarely reported avian H7N2 virus among hundreds of cats (and 1 veterinarian) across several New York City animal shelters (see J. Virology: Virulence Of A Novel H7N2 Virus Isolated From Cats In NYC - Dec 2016).
The H7N2 virus was likely acquired when an unlucky feline dined on the wrong bird in what is arguably the most urban area of the United States.
It that can happen in mid-winter in Manhattan, then it isn't that much of a stretch to imagine it happening among feral hogs in Texas, Florida, or Tennessee.

Just one of the many reasons why I never bet against flu.