JID: Evolutionary Dynamics Of Influenza A Viruses In US Exhibition Swine

Credit Wikipedia

 

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Although bird flu  has captured most of our attention over the past year, scientists are abundantly aware of the potential for seeing novel swine-origin influenza viruses emerge as well. 

 

Just last week in Live Markets & Novel Flu Risks In The United States, we looked at some of the zoonotic exposure risks and two weeks ago in Novel (H3N2v) Flu Case Reported In Minnesota, we saw the latest reported human infection with a swine-variant virus.

 

Swine are considered excellent `mixing vessels’ for influenza, as they are susceptible to a wide variety (swine, human, avian) of flu strains, they may be co-infected by more than one virus at a time, and they not only have ample contact with other pigs, but with humans as well.

Since pigs can be infected by more than one flu virus at the same time, it is possible for two viruses to swap genetic material (reassort), resulting in a new hybrid strain. 

 

The 2009 H1N1 pandemic evolved from numerous reassortments in swine over a period of years, finally jumping species when it had become well enough adapted to human physiology. 

 

Here in North America we’ve been watching the evolution of several swine variant viruses (H1N1v, H1N2v, H3N2v) over the past few years, all of which have reassorted with - and picked up the M gene segment from – the 2009 H1N1 virus (see Keeping Our Eyes On The Prize Pig). 

 

All of which serves as prelude to a new study, and an accompanying editorial, published today in the Journal of Infectious Diseases that looks at the ongoing evolution of swine origin influenza viruses and the threats they pose to human health. 

 

First the abstract (slightly reformatted for readability) to the study (a preliminary PDF version of the whole study is available).

 

 

Evolutionary dynamics of influenza A viruses in US exhibition swine

Martha I. Nelson1, David E. Wentworth2,∧, Suman R. Das2, Srinand Sreevatsan3, Mary L. Killian4, Jacqueline M. Nolting5, Richard D. Slemons5 and Andrew S. Bowman5,*

 

Abstract

The role of exhibition swine in influenza A virus (IAVs) transmission was recently demonstrated by over 300 human infections of H3N2v viruses while attending agricultural fairs. Through active IAV surveillance in US exhibition swine and whole-genome sequencing of 380 isolates, we demonstrate that exhibition swine are actively involved in the evolution of IAVs, including zoonotic strains.

• First, frequent introduction of IAVs from commercial swine populations provides new genetic diversity in exhibition pigs each year locally.
• Second, genomic reassortment between viruses co-circulating in exhibition swine increases viral diversity.
• Third, viral migration between exhibition swine in neighboring states demonstrates that movements of exhibition pigs contributes to the spread of genetic diversity.

The unexpected frequency of viral exchange between commercial and exhibition swine raises questions about the understudied interface between these populations. Overall, the complexity of viral evolution in exhibition swine indicates novel viruses are likely to continually re-emerge, presenting threats to humans.

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JID also published an accompanying editorial by Tiana Baranovich and Justin Bahl  called  Influenza A Virus diversity and transmission in exhibition swine (full text available) that warns `The manners in which these H3N2v viruses have become established in exhibition swine suggest that exhibition swine should be considered a unique reservoir for influenza viruses with pandemic potential’

 

For more on swine-origin influenza viruses and the potential threats they pose, you may wish to revisit:

 

EID Journal: Influenza A Viruses of Human Origin in Swine, Brazil

USDA IAV-S Surveillance Program Detects Novel H3N1 In US Swine

Study: Reassortants of H1N1pdm & Swine H1 & H3 Viruses in Japan

EID Journal: H3N2v Swine To Human Transmission At Agricultural Fairs – 2012

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Saudi MOH: 1 New MERS Case In Riyadh

 

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Although Korea was an outlier event, in the short history of MERS in the Middle East, summers have been generally pretty quiet (see ECDC chart below).  Cases tend to pick up a bit in the fall and winter, and peak in the spring.

Credit ECDC RRA Report

We do continue to see a trickle of case reports out of Saudi Arabia this summer, with the 12th case reported from the Riyadh region in just over two weeks.  While details have been scant, the indications are that much of this uptick in cases has been due to a combination of both community and hospital exposures.

 

Unlike many of those cases, however, today’s entry is not listed as a contact of a known case.

 

While many MERS cases have pretty well defined exposure risks (nosocomial, family contact, camels, etc.), often there is no readily apparent source of infection, which has led to speculation that mildly symptomatic cases may be flying under the surveillance radar, and spreading the virus in the community.

 

In November of 2013, we looked at a study published in The Lancet Infectious Diseases, that attempted to quantify the likely extent of transmission of the MERS virus in the Middle East. (Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility).

 

They calculated  that for every case identified, there are likely 5 to 10 that go undetected.

 

More recently, last April in the Lancet’s Presence of Middle East respiratory syndrome coronavirus antibodies in Saudi Arabia: a nationwide, cross-sectional, serological study  by Drosten & Memish et al., researchers found MERS antibodies in 15 of 10009 serum samples analyzed from across Saudi Arabia.  They wrote:

 

Seroprevalence of MERS-CoV antibodies was significantly higher in camel-exposed individuals than in the general population. By simple multiplication, a projected 44 951 (95% CI 26 971–71 922) individuals older than 15 years might be seropositive for MERS-CoV in Saudi Arabia. These individuals might be the source of infection for patients with confirmed MERS who had no previous exposure to camels.

 

While a plausible source for some of these unexplained sporadic community infections, we are still badly hampered by the lack of a well mounted case control study out of Saudi Arabia. Last May, in WHO EMRO: Scientific Meeting Reviews MERS Progress & Knowledge Gaps we examined many of the deficits remaining in our understanding of this disease.

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CDC’s Vital Signs: A Coordinated Approach To Curb The Spread Of Antibiotic Resistance

 

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Although pandemics and disease outbreaks like MERS and Ebola tend to grab the headlines, there is arguably no greater threat to public health today than the inexorable rise in antibiotic resistant bacteria around the globe.  The CDC estimates that – in the United States alone – at least 23,000 people die each year due to antibiotic resistant infections.

 

In 2012 - less than 75 years after the first modern antibiotics were rolled out - World Health Director-General Margaret Chan expressed the dire warning that the World Faces A `Post-Antibiotic Era’, one where a minor scrape could prove deadly, and where many elective surgeries would simply be too risky with out prophylactic antibiotics.

We’ve looked at this growing threat dozens of times over the years, but a few highlights include:

 

WHO: Survey & Analysis On Global Response To Antimicrobial Resistance

CDC: Improving Antibiotic Prescribing Practices In Hospitals

The Lancet: Antibiotic Resistance - The Need For Global Solutions

UK CMO: Antimicrobial Resistance Poses `Catastrophic Threat’

CDC HAN Advisory: Increase In CRE Reports In The United States

 

While the number and variety of antibiotic resistant organisms continues to grow, among the most dangerous are MRSA, MDR-TB, resistant gonorrhea, NDM-1 (and other NDMs), and a growing list of Carbapenem-resistant Enterobacteriaceae (CREs) like K. pneumoniae.

 

Much of this medical nightmare has been brought on by the misuse, and over reliance on, antibiotics over the years (see CDC: Improving Antibiotic Prescribing Practices In Hospitals).  And one of the deadly side effects has been the rise in difficult to control  C. difficile infections, which carries with it a high mortality rate.

 
Yesterday the CDC released a major Vital Signs report that contains modeling showing the likely impact of CRE and C. difficile infections over the next 5 years, under a variety of control scenarios.  While too lengthy to post here, I’ve some excerpts and links for you to explore.

 

Our first stop is a CDC Press release on the mathematical modeling on the growth of resistant C. dif.

 

CDC modeling projects growth of drug-resistant infections and C. difficile

Improved infection control and antibiotic prescribing could save 37,000 lives over five years

Embargoed Until: Tuesday, August 4, 2015, 3:30 p.m. ET
Contact: Media Relations
(404) 639-3286

The latest CDC Vital Signs includes mathematical modeling that projects increases in drug-resistant infections and Clostridium difficile (C. difficile) without immediate, nationwide improvements in infection control and antibiotic prescribing.

The promising news is that CDC modeling projects that a coordinated approach—that is, health care facilities and health departments in an area working together—could prevent up to 70 percent of life-threatening carbapenem-resistant Enterobacteriaceae (CRE) infections over five years. Additional estimates show that national infection control and antibiotic stewardship efforts led by federal agencies, health care facilities, and public health departments could prevent 619,000 antibiotic-resistant and C. difficile infections and save 37,000 lives over five years.

Antibiotic-resistant germs, those that no longer respond to the drugs designed to kill them, cause more than 2 million illnesses and at least 23,000 deaths each year in the United States. C. difficile caused close to half a million illnesses in 2011, and an estimated 15,000 deaths a year are directly attributable to C. difficile infections.

The report recommends the following coordinated, two-part approach to turn this data into action that prevents illness and saves lives:

1. Public health departments track and alert health care facilities to drug-resistant germ outbreaks in their area and the threat of germs coming from other facilities, and
2. Health care facilities work together and with public health authorities to implement shared infection control actions to stop the spread of antibiotic-resistant germs and C. difficile between facilities.

Antibiotic resistant infections in health care settings are a growing threat in the United States, killing thousands and thousands of people each year,” said CDC Director Tom Frieden, M.D., M.P.H. “We can dramatically reduce these infections if health care facilities, nursing homes, and public health departments work together to improve antibiotic use and infection control so patients are protected.”

The Vital Signs report shows that C. difficile and drug-resistant bacteria—like CRE, MRSA (methicillin-resistant Staphylococcus aureus), and resistant Pseudomonas aeruginosa—spread inside of and between health care facilities when appropriate infection control actions are not in place and patients transfer from one health care facility to another for care. These infections can lead to serious health complications, including sepsis or death. Even facilities following recommended infection control and antibiotic use practices are at risk when they receive patients who carry these germs from other health care facilities.

(Continue . . .)

The full Vital Signs report can be accessed at the link below:

 

Making Health Care Safer

Stop Spread of Antibiotic Resistance

Overview

We're at a tipping point: an increasing number of germs no longer respond to the drugs designed to kill them. Inappropriate prescribing of antibiotics and lack of infection control actions can contribute to drug resistance and put patients at risk for deadly diarrhea (caused by C. difficile). Even if one facility is following recommended infection controls, germs can be spread inside of and between health care facilities when patients are transferred from one health care facility to another without appropriate actions to stop spread. Lack of coordination between facilities can put patients at increased risk. Now more than ever is the time for public health authorities and health care facilities to work together, sharing experiences and connecting patient safety efforts happening across the state.

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ECDC Vector Maps: Invasive Ticks, Mosquitoes & Sand Flies

CREDIT ECDC:   Yellow Areas = Recent Introduction Of Aedes Albopictus

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Although one doesn’t traditionally think of vector-borne diseases like Malaria, Leishmaniasis, Crimea-Congo Hemorrhagic Fever, and Malaria as being serious public health concerns for Europe, increasingly the arthropod vectors (mosquitoes, ticks, sand flies) for these diseases are showing up and establishing themselves  across the region. 

 

In 2007, Europe got a major wake-up call when a rare, tropical virus called Chikungunya arrived (via a traveler returning from India) in the province of Ravenna, in the northeast of Italy. While the virus isn't normally found in Europe, the vector, the Aedes mosquito, is (see It's A Smaller World After All).

 

All it took was one infected person to arrive with the virus, and the chain of transmission began, ultimately infecting nearly 300 people.

 

Since then, we’ve seen a procession of studies suggesting that Europe is increasingly becoming a suitable environment for many of these vector borne diseases to spread. In 2010 the journal Eurosurveillance devoted an entire issue to The Threat Of Vector Borne Diseases, with perhaps the biggest threat outlined in Yellow fever and dengue: a threat to Europe? by P Reiter (excerpt below).

 

The history of dengue and yellow fever in Europe is evidence that conditions are already suitable for transmission. The establishment of Ae. albopictus has made this possible, and the possibility will increase as the species expands northwards, or if Ae. aegypti is re-established.

 

In 2011, in ECDC: Local Malaria Acquisition In Greece we saw more reasons for concern with the return of a scourge that had – due to diligent mosquito control measures over the past 50 years – been all but eliminated across Europe.

While southern Europe has always been slightly vulnerable, just last October, in WHO: Locally Acquired Chikungunya In France, we saw another example of autochthonous transmission of a formerly tropical disease, this time in a Central European nation.

 

In 2012 the ECDC released a cautionary report on the Status & Importance Of Invasive Mosquito Breeds In Europe and last summer they announced a new joint ECDC-EFSA project called  “VectorNet”.  A network for sharing data on the geographic distribution of arthropod vectors capable of  transmitting human and animal diseases.

 

Today the ECDC has published a series of updated maps showing the distribution of a variety of mosquito, tick, and sandfly species capable of transmitting diseases.  As you will see as you examine the maps, some of these vectors are making substantial inroads across parts of Europe.

 

 

Vector maps: New information on ticks in Europe. Invasive mosquitoes in new areas in southern Europe

04 Aug 2015

​New information on the geographical distribution of ticks and invasive mosquitoes in Europe is made available through the latest vector maps. The maps, which are updated quarterly, show the latest data on the geographical distribution of tick, phlebotomines and exotic mosquito species in Europe, as of July 2015.

What’s new in the tick maps?
New information on the geographical distribution (presence/absence) has been added to the Dermacentor reticulatus, Hyalomma marginatum, Ixides ricinus maps:

• Dermacentor reticulatus: updated information about 61 administrative units, mainly in Germany, France and Spain. 
• Hyalomma marginatum: updated information about 35 administrative units, primarily in Romania. 
• Ixodes ricinus: updated information about 366 administrative units, mainly in Finland, Germany and Poland.

In addition, the new maps show the presence of tick species in Europe in greater detail. The maps on Hyalomma marginatum - a tick species which can transmit serious diseases such as Crimean-Congo haemorrhagic fever (CCHF), now distinguish between introduction and establishment: a new category ‘introduced’ describes the presence of imported ticks and indicates that the species has been found but there is no evidence that it has become established locally.

New areas with invasive mosquitoes in southern Europe
Two invasive mosquito species, important disease vectors, have been found in new areas in southern Europe:

• The mosquito species Aedes albopictus, a potential vector of dengue and chikungunya, is now present in new areas in northern and southern Spain, along the Mediterranean coast. 
• The new maps show that Aedes koreicus, a mosquito that can transmit Japanese encephalitis, has been introduced around the Black Sea, while there is no evidence yet of the establishment of the species.

The maps are the outcome of the collaborative work of VectorNet and are based on collecting existing data by the network members.  VectorNet is a joint initiative of the European Food Safety Agency (EFSA) and the European Centre for Disease Prevention and Control (ECDC), that started in May 2014. The project supports the collection of data on vectors, related to both animal and human health.

See and download latest maps on vector distribution (updated July 2015):

• Vector maps - Mosquitoes
• Vector maps – Sandflies
• Vector maps – Ticks

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Saudi MOH Announces 4 New MERS Cases, 4 Fatalities

 

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Although we’ve seen several lulls in reporting this summer – some lasting a week or more – we continue to see new MERS cases emerge – particularly from the Riyadh region.   Yesterday there were two new cases reported in the Capital city, and today we are notified of three more – plus one case in Najran.

Additionally, four recent cases – all from Riyadh – have died, including a 32 year-old who was admitted to the hospital on July 19th, and was listed having no comorbidities.

 

Of the five cases reported from Riyadh over the past 2 days, four are listed as contacts of known cases.   Recent WHO GAR updates have identified both family and nosocomial exposures as propelling this recent surge of cases in Riyadh.

 

 

While exposure risks in these clusters are often easy to identify, in far too many cases the source of infection isn’t known.  The 32-year-old who died had no known exposure risk, and simply presented himself at a local hospital with symptoms two weeks ago.

 

Last May, in WHO EMRO: Scientific Meeting Reviews MERS Progress & Knowledge Gaps we examined some of the deficits in our understanding of this disease, and the glaring lack of a well mounted case-control study, after more than three years.

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South Korean President Replaces MOH Over Handling Of MERS

 

 

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Although it is not listed as a known side effect on any of the the WHO FAQ sheets, one of the prominent side effects of large MERS outbreaks have been its chilling effects on the careers of a number of Minister’s of Health – first in Saudi Arabia (see Saudi Arabia Replaces Minister Of Health (Again)) – and now in South Korea .

 

With South Korea’s MERS epidemic now fully contained, the nation’s President has decided the time has come to replace her embattled Minister of Health.  First a brief report from the AP, followed by the Health & Human Welfare announcement on their proposed replacement:

 

 

South Korea to replace health minister after MERS outbreak

SEOUL, South Korea (AP) — South Korea's president has decided to replace her health minister, officials said Tuesday, in the wake of criticism over the government's handling of the MERS virus outbreak that killed 36 people and infected nearly 200 others.

Last week, South Korea announced that it was virtually free of Middle East respiratory syndrome, which had rattled the country since an outbreak was declared in May. More than 16,000 people had been isolated at hospitals and homes as the government tried to contain the disease's spread.

South Korean media have criticized the government for failing to swiftly cope with MERS in the initial stage of its landing in the country.

President Park Geun-hye nominated local medical professor Chung Chin Youb to replace Moon Hyung-pyo as health minister, Park's office said in a statement. The statement described Chung as a person who can bolster South Korea's public health care.

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The outgoing Minister – Dr. Moon Hyung-pyo – held the office since December of 2013.  The following short bio on his proposed replacement comes from the Ministry of Health & Welfare.
 

 

(machine translation)

Secretary of health and human services devoted to the candidate leaves □

❍ Name: Jung Jin leaves (鎭 燁) CHUNG CHIN YOUB

❍ Besides science classroom at Seoul National University position: Professor, Seoul National University bundang hospital, orthopaedic/orthopaedic faculty

Seoul National University bundang hospital former occupations: ❍

❍ Date of birth: March 10, 1955 (aged 60)

❍ Ex. Saint: Seoul

❍ E-mail : chin@snu.ac.kr

❍ Bell Bridge: Christian

❍ Blood output type: O type

❍ Education

1973-Seoul high school graduate

-Department of Seoul National University in 1980, aerosol

Seoul National University, graduate school of medicine, Ms aerosol-1988

Seoul National University, graduate school of medicine and Dr. Sol-1993

❍ Experience (note)

-Seoul National University Hospital in 1984, resident

Senior Hospital Physician-1988 nuclear

-In 1992, the United States, the children's Hospital the way Lett Fellow

-Assistant Professor, Seoul National University Hospital orthopedic classrooms in 1993, Associate Professor, Professor (County)

Seoul National University bundang hospital Education Center 2002

-Seoul National University bundang hospital care 2004, Deputy

Seoul National University bundang hospital 2008-2013-

-2008-2013 for the Managing Director and Finance Chairman of the Hospital Association's hospital information

2008-2009-2010 President of the Pediatric Orthopedic for craniocervical

Oversees the operation of the mutual medical devices Forum 2012-Chairman (present)

❍ Sang-Hoon

-The Prime Minister Award (2008), Korea global executives (2011), Korea health industry special prize (2011), industrial packaging (2011)

❍ Publications

Besides the Pediatric orthopaedic Sciences ' cradle ' (1996), ' Besides the science of orthopaedic for students ' (1998)

❍ Family

-(Spouse) on July 10, 1958, delayed

-(Daughter) stop on October 24, 1983, Yoon

-(Daughter) be suspended August 8 1988

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Updating The NYC Legionella Outbreak

Legionella Bacteria - Photo Credit CDC PHIL

 

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Last Wednesday, in NYC DOH: Investigating A South Bronx Legionella Outbreak, we saw a statement from the New York City Department of Health on an ongoing Legionnaire’s disease outbreak, which at that time had infected 31 people, and killed 2.

 

Today NYC media are reporting the number of cases has jumped to 71, and the number of deaths now sits at 4. 

 

Four dead in Legionnaires’ disease outbreak in New York

Posted 1:22 pm, August 3, 2015, by CNNwire

NEW YORK — The number of deaths in the New York City Legionnaires’ disease outbreak is up to four.

Seventy-one cases of the flu-like disease have been reported since mid-July in the South Bronx, up from 31 on Thursday, the city Department of Health and Mental Hygiene said Sunday.

Legionnaires’ disease is a respiratory bacterial infection usually spread through mist that comes from a water source, such as cooling towers, air conditioning or showers. It is not transmitted person to person. Symptoms of the disease include fever, chills and a cough.

Most people recover, but between 5% to 30% of those who get the disease die, according to the U.S. Centers for Disease Control and Prevention.

The four victims were all older adults with additional underlying medical problems, the city said. Fifty-five individuals are hospitalized.

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The Legionella bacteria thrives in warm water, such as is commonly found in air-conditioning cooling towers, hot tubs, and even ornamental water fountains. When water is sprayed into the air the bacteria can become aerosolized and inhaled.

 

Those who are susceptible (often smokers, immunocompromised, elderly, etc.) can develop serious – even life threatening – pneumonia.

 

Tonight, a town hall meeting is scheduled to inform residents on the progress of the investigation, and to assure them that this is not a contagious disease, and that it is not being spread by the city water supply.

 

The NYC Department of Health also posted the following update on their website today.

 

Updated 8/3/2015

South Bronx Legionnaires’ Disease Outbreak

Frequently Asked Questions

What is the difference between a water tank and a cooling tower?

A cooling tower contains water and is used by some buildings as part of their air conditioning, ventilation and/or heating systems.

A water tank is a totally separate system. Some taller buildings use a water tank to store water used for drinking, washing dishes and/or showering. No water tanks are associated with the current South Bronx outbreak.

Is the tap water in the South Bronx safe to drink, wash and bathe with?

Yes. It is safe to drink, wash and bathe with the tap water in the South Bronx and throughout the city.

What has the Health Department done at the South Bronx buildings with cooling towers that tested positive for Legionella?

There are five South Bronx buildings with cooling towers that tested positive for Legionella. These buildings have completed short-term cleaning and disinfection. The Health Department remains in constant contact with management at all five buildings and is working very closely with management on long-term procedures to keep those cooling towers free of Legionella.

Is it safe for people to remain in the five buildings that tested positive for Legionella, especially if they continue to run their air conditioning systems?

Yes. All cooling towers have been disinfected. That process immediately reduces or eliminates the likelihood of Legionella being released.

Will the Health Commissioner issue an order for the entire South Bronx or the entire City requiring all buildings with cooling towers to disinfect and clean their cooling towers, regardless of whether the towers were inspected/tested for Legionella?

The City is evaluating whether a wide-scale cleaning and disinfection program would be appropriate. Currently, only five buildings have tested positive for Legionella. All five have undergone rapid disinfection and cleaning. We will continue to monitor the outbreak and evaluate whether additional steps are necessary.

 

While large outbreaks of Legionella are often traced to specific causes, quite often the source of the infection for sporadic cases remains a mystery. 

 

A few outbreaks have been quite large, as with the 2001 Murcia, Spain outbreak that affected more than 800 people (killing 6), and last year’s outbreak in Portugal (see WHO: Legionnaire’s Disease Outbreak – Portugal) which saw at least 336 people infected and 11 fatalities.

 

Legionella got it’s name after it was identified as the bacterial cause of a large pneumonia outbreak at Philadelphia’s Bellevue Stratford Hotel during an American Legion convention in 1976. During that outbreak, 221 people were treated and 34 died.

 

We now know Legionella to be a major cause of infectious pneumonia, and that it can sometimes spark large outbreaks of illness. 

 

According to the CDC between 8,000 and 18,000 Americans are hospitalized with Legionnaire's Disease each year, although many more milder cases likely occur. For background information on the disease, the CDC maintains a fact sheet at Patient Facts: Learn More about Legionnaires' disease.

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