A Russian Influenza Epidemiology Report To Ponder

UPDATED:  See An Update On The Russian Influenza Epi Report

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Every winter since the end of the 2009 H1N1 pandemic we've seen frequent, vague, often hyperbolic reports of H1N1 outbreaks around the world carrying an unusually high mortality, often suggesting that a `mutation' was responsible.

In India and the Middle East, the (now) seasonal H1N1pdm virus is still regarded as a `swine flu' by the media, and is always good for a headline.  Doubly so if the `M' word can be incorporated.

Yet despite this yearly hype, over the seven years since it appeared A/H1N1pdm09 has remained remarkably stable. While the H3N2 vaccine strain has been changed repeatedly, nearly all circulating H1N1 viruses have remained antigenically similar to the H1N1 strain that appeared back in 2009.

We have seen some limited, sporadic mutations (see 2014's  EID Journal: Emergence of D225G Variant A/H1N1, 2013–14 Flu Season, Florida) linked to enhanced virulence, and recently the ECDC reported that a genetic subcluster of viruses within the 6B subgroup has emerged, defined by HA1 amino acid substitutions S162N and I216T (see  Influenza virus characterisation, Summary Europe, December 2015).

Despite these changes, the H1N1 viruses that have been examined have all reportedly been antigenically similar to the vaccine virus A/California/07/2009. 

Once again this winter we've been seeing numerous reports of large H1N1 outbreaks - mostly in the Middle East and Eastern Europe -  with supposedly high mortality rates. Over the past couple of weeks, there have been multiple reports coming out of Russia and the Ukraine.

This morning Sharon Sanders on FluTrackers posted the following (translated) report: 

Russia - Government says "high incidence" of flu is due to H1N1pdm09 mutation not covered by vaccine - January 26, 2016

Today, 05:44 AM

In Russia, died from the flu 50 people, a high incidence is related to a mutation of the H1N1 virus Society January 26th, 16:19 UTC + 3, 24 people died this week, said Head of the Laboratory of Biotechnology and Research Institute of Influenza diagnostic preparations


PETERSBURG, January 26. / Correspondent. Natalia Mihalchenko TASS /. High morbidity and mortality from influenza in certain regions of Russia is associated with a mutation of the virus H1N1 (Swine Flu). This was reported by TASS Head of the Laboratory of Biotechnology and Research Institute of Influenza diagnostic preparations Anna Sominina.

Total of 50 Russians died of influenza, including 24 this week," - she said. "Among the isolated and studied in laboratories around 40% of viruses are changes in the genome that do not contain the vaccine. All in all today was able to identify three mutations" - added Sominina. According to the Institute of influenza in the country weekly epidemic threshold was exceeded by 48.8%, the baseline - 32%. Among the types of circulating influenza virus H1N1 predominant (96%). 

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Granted, Tass isn't always the most reliable source.   But Sharon also found and posted the following (week 3) Epidemiological report from the WHO National Influenza Centre Of Russia, which lends some credence to the above report.

Week 11.01.2016-17.01.2016
Influenza and ARI morbidity data

Epidemiological data show increase of influenza and other ARI activity in Russia in comparison with previous week. The nationwide ILI & ARI morbidity level (60.6 per 10 000 of population) was lower than the national baseline (69.5 per 10 000) by 12.8%.

ILI and ARI epidemic thresholds were exceeded in 9 of 59 cities collaborating with two WHO NICs in Russia.

Cumulative number of diagnosed influenza cases

Cumulative results of influenza laboratory diagnosis by different tests were submitted by 50 RBLs and two WHO NICs. According to these data as a result of 2580 patients investigation the overall proportion of respiratory samples positive for influenza virus was estimated as 25.3% including 615 (94.1%) influenza A(H1N1)pdm09 cases, 17 (2.6%) influenza A(H3N2) cases, 10 (1.5%) influenza A cases and 12 (1.8%) influenza B case.
Results of influenza diagnosis

Conclusion

Influenza and ARI morbidity data.  Increase of influenza and other ARI activity was registered during the week 03.2016 in traditional surveillance system in Russia. The nationwide ILI & ARI morbidity level (60.6 per 10 000 of population) was lower than the national baseline by 12.8%.

Etiology of ILI & ARI morbidity. The overall proportion of respiratory samples positive for influenza  was estimated as 25.3%. Percent of positive ARI cases of non-influenza etiology (PIV, adeno- and RSV) was estimated as 22.2% of investigated patients by IFA and 16.0% by PCR.

Antigenic characterization. Totally 45 influenza A(H1N1)pdm09 and 2 A(H3N2) viruses were characterizated antigenically in two NICs of Russia since the beginning of the season. 35 (76.6%) influenza A(H1N1)pdm09 strains were related closely to influenza A/California/07/09 virus, 10 (23.4%) influenza A(H1N1)pdm09 viruses had decreased up to 1/16 titers. Two A(H3N2) strains were similar to influenza A/Hong-Kong/4801/2014 virus but reacted with antiserum to influenza A/Switzerland/9715293/2013  vaccine strain up to 1/4 - 1/8 of homological titer only.

Genetic characterization. Three influenza A(H1N1)pdm09 viruses were identical for 97.8% to A/California/07/09 virus and for 99.0% to influenza A/South Africa/3626/13  virus. All investigated strains had  substitutions S84N, S162N+ and I216T in HA.

In sentinel surveillance system clinical samples from 57 SARI and 50 ILI/ARI patients were investigated by rRT-PCR. 24 (35.6%) influenza SARI cases were detected including 21 influenza A(H1N1)pdm09, 1 influenza A(H3N2) and 2 influenza B cases. 5 (10.0%) influenza ILI/ARI cases were detected including 4 influenza A(H1N1)pdm09 and 1 influenza A(H3N2) cases.

 

Two of the amino acid substitutions mentioned in the above report (S162N+ & I216T) are associated with the new genetic subcluster within subgroup 6B mentioned by the ECDC, while the third change (S84N) has been linked to reduced antigenic reactivity (cite).

Going back through the Russian Epi Weekly reports, as of the last week of 2015, they reported 23 of the 23 viruses H1N1 viruses examined to be antigenically similar to the vaccine strain, meaning that these reduced titer samples have all appeared over the past three weeks.

It would not be a huge surprise to finally see some significant antigenic drift in the H1N1pdm09 virus.  It has remained stable far longer than anyone expected. But it remains to be seen whether these `reduced titer' viruses will spread beyond the region.



The reports of increased `morbidity and mortality' from these viruses  - while possible - appear to be anecdotal at this time, and are not reflected in the data provided by the Russian Epi report. 

Influenza viruses  - `mutated' or otherwise - are responsible for hundreds of thousands of deaths each year, and so these statements will require additional  data to substantiate. 

The timing here is important, as decisions on what vaccine strains to include in next fall's North American Influenza vaccine are normally made by the end of February.


So we'll keep an extra close eye on the Russian Influenza reports in the weeks to come.

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CDC Adds Two Destinations To Zika Travel Advisory

Credit PAHO - Epi Week 3

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Twelve days ago the CDC issued a Level-II travel advisory for 14 countries and territories over the Zika Virus threat, asking pregnant women to considered postponing travel to regions that were affected. Seven days later they added 8 additional countries and/or territories.  

Last night two more travel destinations were added to the list (United States Virgin Islands and Dominican Republic) both having recently reported confirmed local transmission of the virus.  

It should be noted that while evidence of a tentative link between the introduction of Zika to the Americas and the sharp rise in microcephalic births in Brazil continues to grow, a causal link has yet to be established.  Doing so could take months.

Given the potentially dire outcome of maternal infection, the CDC is acting out of an abundance of caution and is recommending that pregnant women avoid travel to these affected regions until more is known.

This rapid expansion of the virus is expected to continue, and there are likely countries in the Americas where the virus is already circulating but it has yet to be confirmed.  Four months ago, only two countries in the Americas (Brazil & Columbia) were reporting cases.


On Monday in PAHO Statement On Zika Transmission & Prevention, it was postulated that other than in Canada and perhaps Chile, the virus would likely find suitable mosquito vectors (at least part of the year) across much of the Western Hemisphere. 

The following CDC statement was released last night. 

CDC adds 2 destinations to interim travel guidance related to Zika virus

Media Statement

For Immediate Release: Tuesday, January 26, 2016Contact: Media Relations, (404) 639-3286

CDC is working with other public health officials to monitor for ongoing Zika virus‎ transmission. Today, CDC added the following destinations to the Zika virus travel alerts: United States Virgin Islands and Dominican Republic.  Previously, CDC issued a travel alert (Level 2-Practice Enhanced Precautions) for people traveling to regions and certain countries where Zika virus transmission is ongoing: the Commonwealth of Puerto Rico, a U.S. territory; Barbados; Bolivia; Brazil; Cape Verde; Colombia; Ecuador; El Salvador; French Guiana; Guadeloupe; Guatemala; Guyana; Haiti; Honduras; Martinique; Mexico; Panama; Paraguay; Saint Martin; Samoa; Suriname; and Venezuela.  Specific areas where Zika virus transmission is ongoing are often difficult to determine and are likely to continue to change over time.

As more information becomes available, CDC travel alerts will be updated. Travelers to areas where cases of Zika virus infection have been recently confirmed are at risk of being infected with the Zika virus. Mosquitoes that spread Zika are aggressive daytime biters, prefer to bite people, and live indoors and outdoors near people. There is no vaccine or medicine available for Zika virus. The best way to avoid Zika virus infection is to prevent mosquito bites.

Some travelers to areas with ongoing Zika virus transmission will become infected while traveling but will not become sick until they return home. Some people who are infected do not have any symptoms. Symptoms include fever, rash, joint pain, and red eyes. Other commonly reported symptoms include muscle pain and headache. The illness is usually mild with symptoms lasting from several days to a week. Severe disease requiring hospitalization is uncommon and case fatality is low. Travelers to these areas should monitor for symptoms or illness upon return. If they become ill, they should tell their healthcare professional where they have traveled and when.

Until more is known, CDC continues to recommend that pregnant women and women trying to become pregnant take the following precautions:

• Pregnant women should consider postponing travel to the areas where Zika virus transmission is ongoing. Pregnant women who must travel to one of these areas should talk to their doctor or other healthcare professional first and strictly follow steps to avoid mosquito bites during the trip.
• Women trying to become pregnant should consult with their healthcare professional before traveling to these areas and strictly follow steps to prevent mosquito bites during the trip. 

Guillain-Barré syndrome (GBS) has been reported in patients with probable Zika virus infection in French Polynesia and Brazil. Research efforts will also examine the link between Zika and GBS.

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NIH Director's Blog On Zika: An Emerging Health Threat

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The geographic range of two type of Aedes mosquitoes known to transmit the Zika virus includes much of the United States, and according to a blog post today by NIH Director Dr. Francis Collins, that conceivably puts as many as 200 million Americans at risk - at least during the summer months.  

Another  22.7 million Americans live in parts of the country (primarily Southern Florida and Texas) where one or both of these mosquito breeds can live year round. 

While the Zika virus is not currently circulating in North American mosquito populations, all it requires is for a Zika infected individual to arrive on our shores and provide a blood meal to the right kind of mosquito.

Assuming that mosquito goes on to bite another person within a reasonable period of time, they have the potential to pass on the virus.  

In reality, it likely takes multiple introductions over time, and under the right conditions, before a virus like Zika (or Dengue, or Chikungunuya) can successfully establish itself (at least temporarily) in a new location.  But, as we've already seen with Dengue in Florida, Texas, and Hawaii . . .  when provided enough opportunities . . . it can and does happen.

According to a study sponsored by the NIH, 2.7 million travelers arrive in the United States each year from Brazil (and many more from other endemic regions), providing ample opportunities for the virus to be imported.

All of which makes it of paramount importance for researchers to determine if there is a causal link between maternal Zika infection and microcephalic birth defects, to develop better diagnostics and (hopefully) effective therapeutics, and perhaps find ways to mitigate the spread of the virus.


NIH Director Dr. Francis Collins discusses all of this, and more, in his blog today. Follow the link to read:

Zika Virus: An Emerging Health Threat

Posted on January 26, 2016 by Dr. Francis Collins

 

Credit: Kraemer et al. eLife 2015;4:e08347

For decades, the mosquito-transmitted Zika virus was mainly seen in equatorial regions of Africa and Asia, where it caused a mild, flu-like illness and rash in some people. About 10 years ago, the picture began to expand with the appearance of Zika outbreaks in the Pacific islands. Then, last spring, Zika popped up in South America, where it has so far infected more than 1 million Brazilians and been tentatively linked to a steep increase in the number of babies born with microcephaly, a very serious condition characterized by a small head and brain [1]. And Zika’s disturbing march may not stop there.

In a new study in the journal The Lancet, infectious disease modelers calculate that Zika virus has the potential to spread across warmer and wetter parts of the Western Hemisphere as local mosquitoes pick up the virus from infected travelers and then spread the virus to other people [2]. The study suggests that Zika virus could eventually reach regions of the United States in which 60 percent of our population lives. This highlights the need for NIH and its partners in the public and private sectors to intensify research on Zika virus and to look for new ways to treat the disease and prevent its spread.

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WHO MERS Updates - Saudi Arabia & UAE

Credit WHO

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Normally when we get MERS updates from the WHO involving multiple cases it is a mixed bag; primary cases with no known exposure, primary cases with camel contact, and household or nosocomial infections from exposure to previously identified cases. 

Today, we've reports on 6 cases from two countries (4 from KSA & 2 from UAE), and five are listed as no known exposure other than having frequent contact with camels, and four of those are consumers of camel's milk.   

The 6th case is a contact of one of the five camel contacts.  Not included in today's report are 4 recent MERS cases reported in connection with a camel market in Jeddah.


The good news is we've not seen any reports of secondary nosocomial transmission from any of these cases.

Middle East respiratory syndrome coronavirus (MERS-CoV) – United Arab Emirates

Disease outbreak news
26 January 2016

Between 11 and 14 January 2016, the National IHR Focal Point of the United Arab Emirates notified WHO of 2 additional cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection, including 1 death.

Details of the cases

• A 73-year-old male from Abu Dhabi developed symptoms on 27 December and visited a health care clinic in Abu Dhabi. He was treated symptomatically and sent home on the same day. On 31 December, the patient travelled to Oman with family members and returned back to Abu Dhabi on 1 January. On the same day, he developed symptoms and was admitted to hospital. The patient, who had no comorbidities, tested positive for MERS-CoV on 10 January. He passed away on 25 January. The patient had a history of frequent contact with camels. He consumed raw camel milk once in the 14 days prior to the onset of symptoms. He had no history of exposure to other risk factors in Abu Dhabi and in Oman in the 14 days prior to onset of symptoms.
• An 85-year-old female from Abu Dhabi was detected through the tracing of contacts. The patient is a contact of a laboratory-confirmed MERS-CoV case (see above). She has no history of exposure to other risk factors in the 14 days prior to detection. The patient, who has comorbidities, tested positive for MERS-CoV on 13 January. Currently, she is asymptomatic admitted to a negative pressure isolation room on a ward. 

Middle East respiratory syndrome coronavirus (MERS-CoV) – Saudi Arabia

Disease outbreak news
26 January 2016

Between 27 December 2015 and 13 January 2016, the National IHR Focal Point for the Kingdom of Saudi Arabia notified WHO of 4 additional cases of Middle East respiratory syndrome coronavirus (MERS-CoV) infection.

Details of the cases

• A 50-year-old male from Madinah city developed symptoms on 3 January and, on 10 January, was admitted to hospital in Madinah. The patient, who has comorbidities, tested positive for MERS-CoV on 12 January. Currently, he is in critical condition in ICU. The patient has a history of frequent contact with camels and consumption of their raw milk. He has no history of exposure to other known risk factors in the 14 days prior to the onset of symptoms.
• An 85-year-old male from Bisha city developed symptoms on 3 January. On the same day, the patient visited a hospital where he was treated symptomatically and sent home. On 9 January, the patient travelled by airplane to Riyadh to seek medical care. Once in Riyadh, he was admitted to hospital. The patient, who has comorbidities, tested positive for MERS-CoV on 11 January. Currently, he is in stable condition in a negative pressure isolation room on a ward. The patient has a history of frequent contact with camels and consumption of their raw milk. He has no history of exposure to other known risk factors in the 14 days prior to the onset of symptoms.
• A 59-year-old male from Onizah city developed symptoms on 18 December and, on 27 December, was admitted to hospital. The patient, who is a heavy smoker and has comorbidities, tested positive for MERS-CoV on 28 December. Currently, he is in critical condition in ICU. The patient has a history of frequent contact with camels and consumption of their raw milk. He has no history of exposure to other known risk factors in the 14 days prior to the onset of symptoms.
• A 54-year-old male from Jeddah city developed symptoms on 14 December and, on 24 December, was admitted to hospital. The patient, who has comorbidities, tested positive for MERS-CoV on 26 December. Currently, he is in stable condition in a negative pressure isolation room on a ward. The patient has a history of frequent contact with camels.

Globally, since September 2012, WHO has been notified of 1,630 laboratory-confirmed cases of infection with MERS-CoV, including at least 586 related deaths.

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#CascadiaEQ Tweetchat Today - Earthquake Preparedness

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The graphic above says it all.  Today at 10am (PST)  1pm EST there will be a tweetchat on the Cascadia Earthquake threat, and how to prepare.  Use hashtag #CascadiaEQ to follow along and participate.

Today is the 316th Anniversary of the Magnitude 9 mega thrust quake that struck the Pacific Northwest in 1700.   A quake that was only the latest in a long line of seismic events that tend to occur in that region every few hundred years. 

 

I've written a number of Cascadia quake related blogs over the years which you may wish to revisit.

OSU: Pragmatic Action - Not Fatalism - In Order To Survive The `Big One’

Tsunami Preparedness Week: Because It Has Happened Here

Just A Matter Of Time

 

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MMWR: Evaluation and Testing of Infants with Possible Congenital Zika Virus Infection

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As the Zika virus continues to spread across the Americas it is inevitable that U.S. doctors will be called upon to evaluate and test pregnant women and infants for (congenital) Zika virus infection. 

While a conclusive link between maternal Zika virus infections and microcephaly has yet to be established, the CDC views the risks as too great to ignore and has already produced a good deal of guidance. 

Ten days ago the CDC released a HAN advisory for clinicians on Recognizing, Managing & Reporting ZIka Virus Infections In Travelers, while last week the CDC's MMWR published Interim Guidelines For Pregnant Women During A Zika Outbreak, along with reports on Zika's Spread & Its Possible Association With Microcephaly.

The word `interim' features prominently in nearly all of these documents as the threa from Zika infection is still poorly understood, and our understanding of how to best handle its challenges may change over time.

Today, another major MMWR Early Release that provides interim guidance to clinicians on evaluating and dealing with possible maternal Zika virus infection. First the description from the CDC of this release, followed by a link to the report (which is too large to excerpt properly).

Interim Guidelines for the Evaluation and Testing of Infants with Possible Congenital Zika Virus Infection

The CDC has developed, in consultation with the American Academy of Pediatrics, interim guidance for the evaluation, testing, and management of infants born to mothers who traveled to or resided in an area with Zika virus transmission during pregnancy.

The document provides guidance to healthcare providers caring for 1) infants with microcephaly or intracranial calcifications detected prenatally or at birth or 2) infants without these findings whose risk is based on maternal exposure and testing for Zika virus infection.

Briefly, pediatric healthcare providers should ask mothers of newborns with microcephaly or intracranial calcifications about their residence and travel while pregnant as well as symptoms of illness compatible with Zika virus disease (acute onset of fever, maculopapular rash, arthralgia, and conjunctivitis). In addition, results of any Zika virus testing performed prior to delivery should be obtained.  Interim guidance includes consideration of clinical issues that might be encountered in caring for infants who might have been infected with Zika virus infection. Certain actions (e.g., cranial ultrasound and ophthalmologic examination) are recommended for all infants being tested for Zika virus infection, and other actions (e.g., repeat hearing screening, developmental monitoring) are recommended for all infants with Zika virus infection, regardless of the presence or absence of symptoms.

Interim Guidelines for the Evaluation and Testing of Infants with Possible Congenital Zika Virus Infection — United States, 2016
 
JANUARY 26, 2016
 
CDC has developed interim guidelines for health care providers in the United States who are caring for infants born to mothers who traveled to or resided in an area with Zika virus transmission during pregnancy.

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WHO: Influenza at the Human-Animal Interface - January 2016

 A(H5N1) cases in humans by week of onset, 2004-2016

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Reports to the World Health Organization from China and Egypt on human avian flu cases are dramatically lower this winter over last, although it is not yet certain whether that has more to do with delays in reporting than with the actual level of activity.

Despite almost daily headlines in Arabic papers announcing H5N1 cases (confirmed or suspected), Egypt's MOH continues to deny finding any H5N1 infections (see Egyptian MOH Statement: No Bird Flu Cases Since Last Summer).

Similarly, China has substantially reduced (or delayed) their reporting on H7N9 cases since February of last year, preferring to release information in batches, often weeks after the fact.


Today's update from the WHO does provide us with information on several human infections (H5N6 & H9N2) we had not seen previously announced.

Influenza at the human-animal interface

Summary and assessment as of 20 January 2016

Human infection with avian influenza A(H5) viruses

Since the last WHO Influenza update on 14 December 2015, two new laboratory-confirmed human cases of avian influenza A(H5N1) virus infection were reported to WHO.

A 60-year-old male from Mymensing District in Bangladesh was hospitalized on 12 October 2015 with severe acute respiratory infection (SARI). Nasopharyngeal and throat swabs were collected upon hospital admission as part of SARI surveillance, and tested positive for A(H5N1) virus. The patient fully recovered. Prior to illness onset, the patient was exposed to live backyard poultry. The second case was in a 42-year-old male from Sichuan Province in China who had an onset of illness on 27 December 2015. He was hospitalized on 31 December 2015 and remains in a critical condition. This case had history of exposure to poultry.

From 2003 through 20 January 2016, 846 laboratory-confirmed human cases of avian influenza A(H5N1) virus infection have been officially reported to WHO from 16 countries (Figure 1). Of these cases, 449 have died.

In this reporting period, five laboratory-confirmed human cases of avian influenza A(H5N6) virus infection were reported to WHO from China (Table 1). All were sporadic cases and with no further transmission among contacts.
 

Cases of avian influenza A(H5N6) reported in 14 December 2015 till 20 January 2016

Since 2013 through to 20 January 2016, ten cases of avian influenza A(H5N6) have been detected of which nine were notified to WHO and one was reported in the scientific literature.1 All nine cases notified to WHO had clinically severe disease. The case reported in the literature, a five-year-old female, was a mild case detected through routine surveillance activities.

Various influenza A(H5) subtypes, such as influenza A(H5N1), A(H5N2), A(H5N3), A(H5N6), A(H5N8) and A(H5N9), continue to be detected in birds in West Africa, Europe and Asia, according to recent reports received by OIE. Since last month’s report on detections of avian influenza A(H5) viruses in birds in France, no human infections have been identified. Although the influenza A(H5) viruses might have the potential to cause disease in humans, so far no human cases of infection have been reported, with exception of the human infections with influenza A(H5N1) and A(H5N6) viruses in China.

Overall public health risk assessment for avian influenza A(H5) viruses: Overall, the public health risk assessment for avian influenza A(H5) viruses remains unchanged since the assessment of 17 July 2015.
 
http://www.who.int/influenza/human_animal_interface/HAI_Risk_Assessment/en/


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This report also adds ten human cases of avian influenza A(H7N9) virus infection were reported to WHO from Guangdong, Jiangsu, Jiangxi and Zhejiang provinces of China, last December's novel H3N2v infection in New Jersey (see my report here), and a single H9N2 infection in a poultry worker in a market in Dhaka City, Bangladesh last October.


While it is entirely possible that the actual number of human infections this winter is lower than last year, the lack openess on the part of the Chinese and Egyptian Ministries of Health over the past year make it difficult to place a lot of confidence in the numbers we're seeing.

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