Thursday, July 27, 2017

Saudi MOH Reports 2 MERS Cases Over 2 Days


After a two-week lull, Saudi Arabia reported a single primary MERS case from Riyadh yesterday listed in stable condition, and today is reporting a single primary (with camel contact) case from Buraidah, who is listed in critical condition.

After seeing 50+ cases in June, this slowdown is welcomed given the start of this year's Hajj (August 30th) is just a little over a month away.

COCA Call Today: Zika - Updated Clinical Guidance & Recommendations for Pregnant Women and Infants


Later today  the CDC will hold a COCA (Clinicians Outreach and Communication Activity) caall with their latest guidance and recommendations on Zika Virus infection in pregnant women and infants.
Primarily of interest to clinicians and healthcare providers, COCA (Clinician Outreach Communication Activity) calls are designed to ensure that practitioners have up-to-date information for their practices.
Follow the link below to review the different ways you can access this webinar.

Zika Virus: Updates to Clinical Guidance and Recommendations for Pregnant Women and Infants

Free Continuing Education 
Date:Thursday, July 27, 2017
Time: 2:00-3:00 pm (Eastern Time)
Please join the COCA Call webinar with digital audio, video and presentation formats from a PC, Mac, iPad, iPhone or Android device:

If you cannot join through digital audio, you may join by phone in listen-only mode: 1 646-558-8656 or 1 408-638-0968

Passcode: 974 205 265
International numbers are available:


CDC has updated its interim guidance for pregnant women with possible exposure to Zika virus to include separate recommendations for pregnant women with symptoms and pregnant women without symptoms. In addition, CDC recently released its latest findings from the Zika pregnancy and infant registries on pregnancy outcomes for pregnant women with Zika virus infection in the U.S. territories and has new updates for healthcare providers on pediatric ophthalmologic findings in infants with possible congenital Zika virus exposure. During this COCA Call, clinicians will learn about the recent updates to CDC’s interim guidance for pregnant women with possible exposure to Zika virus; hear about the latest findings on pregnancy outcomes in the U.S. territories, based on the Zika pregnancy and infant registries; and receive new information on pediatric ophthalmologic findings to assist in caring for patients based on currently available data.

Russia: Rosselkhoznadzor Finds More HPAI Contaminated Meat In Retail Stores


During April and May we followed a number of outbreaks of HPAI H5N8 in western Russia (see here, here, and here), with the largest reported at one of Russia's biggest turkey producing facilities in Rostov (see Link).
By mid-May Russia's Federal Service for Veterinary and Phytosanitary Surveillance (Rosselkhoznadzor) announced that HPAI Contaminated Poultry Had Been Shipped To At Least 9 Regions Of Russia.
During May and June we saw numerous reports of contaminated meat being found in the food chain (see Rosselkhoznador Investigation Into HPAI Contaminated Meat Distribution & Sale), along with allegations of illegalities on the part of Rostov's Regional Veterinary Laboratory which was charged with testing these products and overseeing the issuance of food safety certificates.

Although reports of bird flu outbreaks have diminished over the past two months, we continue to see scattered reports of the discovery of contaminated meat in the food chain.  Today, we get this out of Vladivosiok:

In Primorye, discovered and thwarted the realization of retail chains products with the genome of avian influenza

According to Rosselkhoznadzor (Moscow), at this year's poultry farms of the Rostov region LLC "Evrodon-South" observed mass death of turkey stock. In selected pathological material was discovered gene of influenza A virus of birds, and identified the H5 subtype. In this regard, all terupravleniya Rosselkhoznadzor and veterinary services of the Russian Federation was ordered to strengthen the veterinary control measures in respect of products from this manufacturer, as well as for enterprises and commercial organizations that have economic ties with it.

In this regard, the Office of Rosselkhoznadzor for the Primorsky Krai and the Sakhalin Oblast unscheduled inspections of a number of wholesale food stores, retail chains and stores the Primorsky Territory was organized in order to prevent trafficking and sale of dangerous poultry products.

In the course of supervisory activities the inspectors Rosselkhoznadzor in Vladivostok in one of the hypermarkets and large food warehouse was discovered products produced on the affected bird flu Rostov company. Immediately after the discovery of potentially unsafe poultry meat has been placed on isolated storage, precluding any unauthorized traffic.

Conducted FGBU "Maritime Interregional Veterinary Laboratory" Rosselkhoznadzor tests have shown that 2 tons of steaks of turkey, who were in the wholesale food warehouse, as well as 300 kg of products of turkey meat in assortment (splint, ase, steak, medallions, sets for fire , wings and steaks), found in urban hypermarket, contains the genetic material of the virus avian influenza A, subtype H5.

Subsequently conducted FGBU "Federal Center for Animal Health" Rosselkhoznadzor (ARRIAH) testing of selected production samples confirmed the presence in them of the influenza virus genome of birds.

However, without waiting for the results ARRIAH, all dangerous products were destroyed (burned) its owners at the complex for the destruction of bio-waste "Factor-Primorye" Vladivostok under the control of Rosselkhoznadzor inspectors.

As previously reported, in May of this year, inspectors Rosselkhoznadzor, in collaboration with the staff of the department of economic security and countering corruption Russian Ministry of Internal Affairs for the city of Vladivostok in the Soviet area was prevented by turnover and, accordingly, the implementation of the population of 3 tons of turkey genome with avian influenza, produced at the plant OOO "Evrodon" Rostov region. Dangerous products have been found on one of the wholesale food warehouses and subsequently destroyed (burned).

While HPAI H5N8 isn't as big of a health concern as H5N1 or H5N6 - both of which have a track record of infecting humans - this illustrates how easily avian flu can make its way into some country's food supply.
A little over a month ago, in Appl Environ Microbiol: Survival of HPAI H5N1 In Infected Poultry Tissues, we looked at the viability (via viral isolation) of H5N1 in experimentally infected chicken's feathers, muscle tissue, and liver stored at various temperatures ( +4°C or +20°C).
Refrigerated (+4°C) feathers retained viable virus for 8 months, tissue for 6 months, and in the liver for nearly 3 weeks. But even at the higher temperature (68F), the virus remained viable for a month in feathers, and just under 3 weeks in muscle tissue.

Beyond contaminated food concerns, this sort of prolonged viral persistence provides opportunities for dead birds in the wild to infect scavengers, and reinforces the need for people in contact with dead birds to take safety precautions.

HK Flu Express Wk 29: Influenza Activity Remains At A Very High Level


Fourteen weeks ago Hong Kong's CHP declared the end of last winter's mild flu epidemic, with their Flu Express Week 15 reporting a `low level' of flu activity by mid-April. Two weeks later, quite unexpectedly, the Hong Kong CHP Reported A Late Season Flu Surge, and reinstated their enhanced surveillance for severe seasonal influenza.
Since then we've seen a nearly continuous rise in severe seasonal flu cases - mostly H3N2 - which has claimed more than two hundred lives, and has severely impacted Hong Kong's hospital system. 
While Hong Kong is known for having a biphasic or `double peaked’  flu season, their heaviest activity usually occurs from February–April with a less severe season in mid to late summer (see Seasonality of Influenza A(H3N2) Virus: A Hong Kong Perspective (1997–2006).

This summer's flu epidemic has lasted longer, and has been far more severe, than their last two flu epidemics (see chart at top of blog), and shows no signs of abatement. According to the latest Hospital Authority Hospital Key Statistics daily report, inpatient occupancy rates range from 96% to 124% across 17 local hospitals.

Since last week an additional 67 severe cases, and 47 deaths, have been recorded due to flu-related illness. With 255 deaths since May 5th, this summer's flu outbreak has claimed 6 times the number of lives caused by Hong Kong's 2017's winter flu (n=41). 
Although a few indicators have slowed slightly over the past week, it is too soon to say whether Hong Kong has reached the peak of their epidemic. The CHP warns to expect a `high level' of flu activity over the coming weeks.
Some excerpts from today's Flu Express report, and the I'll return with a bit more.
Flu Express is a weekly report produced by the Respiratory Disease Office of the Centre for Health Protection. It monitors and summarizes the latest local and global influenza activities.

Local Situation of Influenza Activity (as of Jul 26, 2017)
Reporting period: Jul 16 – 22, 2017 (Week 29)
  • The latest surveillance data showed that the local influenza activity remained at a very high level in the past week. It is foreseen that the influenza activity will remain at a very high level in the coming weeks.
  • The Centre for Health Protection (CHP) has collaborated with the Hospital Authority (HA) and private hospitals to reactivate the enhanced surveillance for severe seasonal influenza cases (i.e. influenza-associated admissions to intensive care unit or deaths) among patients aged 18 or above since May 5, 2017. As of Jul 26, 361 severe cases (including 252 deaths) were recorded. Separately, 18 cases of severe paediatric influenza-associated complication/death (including three deaths) (aged below 18 years) were recorded in the same period.
  • Apart from adopting personal, hand and environmental hygiene practices against respiratory illnesses, those members of the public who have not received influenza vaccine may get the vaccination as soon as possible for personal protection.
Surveillance of severe influenza cases

(Note: The data reported are provisional figures and subject to further revision)

Since the activation of the enhanced surveillance for severe influenza infection on May 5, 2017, a total of 379 severe cases (including 255 deaths) were recorded cumulatively (as of Jul 26) (Figure 9). These included:

  • 361 cases (including 252 deaths) among adult patients aged 18 years or above. Among them, 316 patients had infection with influenza A(H3N2), 21 patients with influenza A(H1N1)pdm09, 13 patients with influenza B and 11 patients with influenza A pending subtype. 131 (36.3%) were known to have received the influenza vaccine for the 2016/17 season. Among the 252 fatal cases, 113 (44.8%) were known to have received the influenza vaccine. In the winter season in early 2017, 66 adult severe cases (including 41 deaths) were filed.
  • 18 cases (including three deaths) of severe paediatric influenza-associated complication/ death. Sixteen (88.9%) cases did not receive the influenza vaccine for the 2016/17 season. To date in 2017, 26 paediatric cases (including four deaths) were filed.
Enhanced surveillance for severe seasonal influenza (Aged 18 years or above)
In week 29, 65 cases of influenza associated ICU admission/death were recorded (including 39 deaths), which was lower than 72 cases (including 52 deaths) recorded in week 28. In the first 4 days of week 30 (Jul 23 to 26), 37 cases of influenza associated ICU admission/death were recorded, in which 29 of them were fatal.
Surveillance of severe paediatric influenza-associated complication/death (Aged below 18 years)
 In week 29, four cases of severe paediatric influenza-associated complication were reported. In the first 4 days of week 30 (Jul 23 to 26), one case of severe paediatric influenza-associated complication was reported. The case details are as follow:

            (Continue . . .)

We have been following similar, albeit less severe, reports from other regions of eastern Asia (see Taiwan's Summer H3N2 Epidemic Continues Near Peak and Macao, Hong Kong & Guangdong Province All Reporting Heavy Flu Activity) in recent weeks. 

Getting good numbers out of Mainland China is difficult, but Sharon Sanders of Flutrackers has been monitoring media reports in their China Seasonal Flu Tracking forum and has posted the following threads in the past few days.
China - Pediatric flu patients up significantly in July in Heyuan, Guangdong province - July 27, 2017

China - Recent high incidence of flu patient overcrowding in Hengfeng, Jiangxi Province - July 26, 2017

China - Major hospitals in Dongguan reporting overcrowding due to flu patients - up 20-30% in July - Guangdong province - July 21, 2017

The cause of this year's out-of-season heavy flu activity remains unclear, although several theories have been advanced, including waning late-season effectiveness of last year's flu vaccine, and a possible antigenic change in the H3N2 virus.

For more on those possibilities, you may want to revisit these recent blogs:
The Enigmatic, Problematic H3N2 Influenza Virus
Hong Kong: HKU Experts Call For Deploying Prophylactic Tamiflu To Avert Crisis
J. Clin. Vir.: Ιnfluenza A(H3N2) Genetic Variants In Vaccinated Patients In Northern Greece

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.