Tuesday, May 31, 2016

Texas DSHS Announces 1st Locally Acquired Chikungunya Case

Cameron County - Credit Wikipedia


While we wait to see when we get the first locally acquired vector transmitted Zika infection in the continental United States, two other mosquito borne viruses are also on our radar:

Dengue and Chikungunya.

Dengue Resurfaced In Key West in 2009 after a 70 year absence, and has periodically shown up in Texas since the early 2000's.  The handful of outbreaks reported in Florida and Texas  in recent years have been small, localized and short lived.

Chikungunya was introduced to the Caribbean by viremic travelers in 2013, who inadvertently `seeded’ the virus into the local mosquito population. Since then millions have been infected across the Americas, although Florida is the only state to have reported (a small number) of locally acquired cases.

That is, until today. 

Although we are just learning about it this afternoon, it appears Texas had a locally acquired case of CHKV back in November of last year, which was contracted in the southernmost county in the state.

Brownsville is the largest city, and county seat of Cameron County, which lies on the border with Mexico, where last November the CDC issued Updated Travel Notices: Chikungunya In Mexico & Central America.

Exactly why this case wasn't reported to health authorities until very recently isn't clear, but the DSHS reminds labs and doctors of the need to report cases promptly in today's announcement.

DSHS Announces First Texas-Acquired Chikungunya Case  

Recently reported case contracted in 2015

The Texas Department of State Health Services has confirmed the first locally acquired case of chikungunya, a mosquito borne illness. A Cameron County resident got sick with the illness in November 2015 and was diagnosed with a lab test in January 2016. The case, however, was not reported to the local health department until last month. The investigation performed by the Cameron County Department of Health and Human Services determined the patient had not traveled, and the case was confirmed last week by testing at the US Centers for Disease Control and Prevention.

Chikungunya disease is a viral illness spread by mosquitoes and was first detected in travelers returning to Texas from areas with local transmission in 2014. All previous Texas residents who contracted the illness were infected while traveling abroad. Because this case was contracted more than six months ago and mosquito surveillance has not found chikungunya in local mosquitoes, the primary risk of infection remains related to travel. DSHS encourages people to protect themselves from mosquito bites at home and while traveling to stop the spread of chikungunya, Zika and West Nile virus.

Chikungunya and most other viruses transmitted by mosquitoes are required to be reported to the local health department or DSHS regional office within one week. DSHS reminds laboratories and health care providers to report cases promptly so health officials will have the information they need to make decisions that will protect public health.
Chikungunya illness is rarely fatal but can cause severe joint pain, high fever, head and muscle aches, joint swelling and rash. Most people feel better within a week, though some may develop longer-term joint pain.

CDC Statement On 1st MCR-1 Colistin Resistant Infection in U.S.


Last Thursday, in MHRP: 1st Detection Of Colistin Resistant E. coli in U.S. Resident, we looked at a media release from the Military HIV Research Program and a link to a study in Antimicrobial Agents and Chemotherapy, both announcing the first discovery of an mcr-1 Resistant E. coli infection in a human on United States soil.

Today the CDC has released a statement on the finding, their ongoing epidemiological study to try to determine the origin of this patient's infection and possible spread, and the plan to bolster lab capacity around the country to test for this emerging resistance gene. 

First the statement, then I'll have a bit more.

Discovery of first mcr-1 gene in E. coli bacteria found in a human in United States

MCR-1 causes resistance to colistin, a last-resort drug for treating resistant infections

Media Statement

For Immediate Release: Tuesday, May 31, 2016 Contact: Media Relations,
(404) 639-3286

The Centers for Disease Control and Prevention is part of a coordinated public health response after the Department of Defense (DoD) announced the discovery of the first mcr-1 gene found in bacteria in a human in the United States. CDC is working with DoD, the Pennsylvania Department of Health, local health departments, and others to identify people who have had contact with the patient and take action to prevent local spread.

E. coli bacteria carrying the MRC-1 gene was found in a urine sample from a Pennsylvania woman with no recent travel outside of the U.S. The mcr-1 gene makes bacteria resistant to the antibiotic colistin, which is used as a last-resort drug to treat patients with multi-drug-resistant infections, including carbapenem-resistant Enterobacteriaceae (CRE).
The mcr-1 gene exists on a plasmid, a small piece of DNA that is capable of moving from one bacterium to another, spreading antibiotic resistance among bacterial species.  The CDC and federal partners have been hunting for this gene in the U.S. ever since its emergence in China in 2015. 

Despite some media reports, the Pennsylvania State Health Department investigation has determined that the woman did not have CRE and the bacteria identified is not resistant to all antibiotics (referred to as a pan-resistant infection). The presence of the mcr-1 gene, however, and its ability to share its colistin resistance with other bacteria such as CRE raise the risk that pan-resistant bacteria could develop. 

The investigation is currently focused on identifying close contacts, including household and healthcare contacts, of the Pennsylvania patient to determine whether any of them may have been at risk for transmission of the bacteria containing the mcr-1 gene.

Beginning in fall 2016, CDC’s Antibiotic Resistance Lab Network will provide the infrastructure and lab capacity for seven to eight regional labs, and labs in all states and seven major cities/territories, to detect and respond to resistant organisms recovered from human samples . State labs will be able to detect new forms of antibiotic resistance—including mutations that allow bacteria to survive the effects of the last-resort drugs like colistin—and report these findings to CDC. 

 With this comprehensive lab capacity, state health labs and regional labs that are part of the network will be able to investigate emerging resistance faster and more effectively, generating better data for stronger infection control among patients to prevent and combat future resistance threats. CDC will also provide new resources to state health departments to support their efforts to stop antibiotic-resistant outbreaks and prevent the spread of antibiotic-resistant pathogens across communities.  

Consistent with the National Action Plan for Combating Antibiotic-Resistant Bacteria, CDC and other government agencies will continue efforts to track, slow and respond to the emergence of antibiotic resistance.

For more information on the mcr-1 discovery, see http://www.hhs.gov/blog/2016/05/26/early-detection-new-antibiotic-resistance.html.

As stated in this release, this woman's infection was not Carbapenem resistant, and therefore still treatable.

But just two months ago The Lancet's Emergence of the mcr-1 colistin resistance gene in carbapenem-resistant Enterobacteriaceae, reported on two K pneumoniae isolates from China that carried both the MCR-1 gene and the gene for NDM-5 (Carbapenem-resistance), providing it near pan-drug resistance.

While still exceedingly rare, this is the kind of nightmare resistance combination that could someday propel us into a post-antibiotic era, one where even minor infections are no longer treatable.
Lest anyone think this hyperbole, that is the exact phrase used by WHO Director General Chan more than 4 years ago (see Chan: World Faces A `Post-Antibiotic Era’).

For more on this newest antimicrobial threat - MCR-1 - you may wish to revisit:

Eurosurveillance Editorial: Plasmid-Mediated Colistin Resistance (MCR-1 gene):The Story Unfolds

The Lancet: Dissemination Of The MCR-1 Colistin Resistance Gene 
MCR-1: The Return Of The Plasmids

WHO: Updated Interim Guidelines On The Prevention of Sexual Transmission of Zika Virus


Six months ago sexual transmission of Zika was considered a rarity, and viewed as unlikely to constitute much of a public health risk. But as time has gone on, evidence has accrued that sexual transmission is much more common than previously believed.

On Friday, Lisa Schnirring of CIDRAP News wrote Zika data point to sexual transmission in women on research that found women in the sexually active age-group (15-65) far more likely to be infected than men.
We've also seen studies on the persistence of Zika Virus (and Zika RNA) in semen, urine, and even saliva (see Fiocruz: Revisting Zika Virus Detection In Saliva & Urine), which have raised (as yet, unanswered) questions over the full range of sexual transmission of the virus. 

Today the WHO has released new, interim guidance, which doubles the length of time (from 4 week to 8 weeks) they recommend couples follow safe sex practices or abstain from sex after returning from Zika endemic regions. 

They also recommend if the male partner was symptomatic, the waiting period should be extended to six months.  

While there isn't sufficient evidence to support non-intercourse sexual transmission of the virus, they do acknowledge the findings of the Zika virus in both saliva and urine, writing:

 3. Presence of Zika virus in other body fluids

Publications on the presence of Zika virus in other body
fluids that may be involved in sexual transmission have also been considered. Studies have reported the presence of Zika virus by RT-PCR in saliva 17, 18 and urine 14, 15, 18-25 .
The persistent shedding of Zika virus ribonucleic acid
(RNA) in both fluids has been found up to 29 days after
the onset of infection. Culture of Zika virus in urine 14, 18, 20,26 and saliva 18 has also been reported, with the virus cultured at day six after symptom onset for both fluids.

Follow the link below to download the full 4-page PDF guidance document.

Publication details

Number of pages: 5 Publication date: Updated 30 May 2016 Languages: English WHO reference number: WHO/ZIKV/MOC/16.1 Rev.1



The primary transmission route of Zika virus is via the Aedes mosquito. However, mounting evidence has shown that sexual transmission of Zika virus is possible and more common than previously assumed. This is of concern due to an association between Zika virus infection and adverse pregnancy and fetal outcomes, including microcephaly, neurological complications and Guillain-Barré syndrome. 

The current evidence base on Zika virus remains limited. This guidance will be reviewed and the recommendations updated as new evidence emerges.

ECDC Updated Risk Assessment On Africa's Yellow Fever Epidemic


Parts of Africa are seeing their worst Yellow Fever outbreak in decades, and we've seen a small number of exported cases turning up in places like China, raising concerns of international spread.

Two months ago the ECDC issued a rapid risk assessment on the Angola outbreak (see Yellow Fever In Angola & The Risk Of International Spread - ECDC), which warned:

As yellow fever and dengue fever share the same mosquito vector, Aedes aegypti, any area where dengue has been transmitted could be suitable for establishment of local transmission of yellow fever if the virus is introduced by a viraemic traveller.

Theoretically, this shouldn't be much of a problem, as countries with competent vectors (Aedes mosquitoes) are supposed to require a yellow fever vaccination for travelers going to or returning from areas were the virus is endemic. 

But in actual practice, some countries have been less than diligent in enforcing this requirement, and fake Yellow Fever vaccination certificates are reportedly pretty common. 

Today the ECDC has published a new, updated risk assessment, which finds `the risk of exporting the virus to other countries is high'.

Rapid risk assessment: Outbreaks of yellow fever in Angola, Democratic Republic of Congo and Uganda, first update

30 May 2016
Available as PDF in English


​The current epidemic of yellow fever, an acute viral haemorrhagic vector-borne disease, which has seen outbreaks in Angola, Democratic Republic of Congo and Uganda, highlights the risk of infection for unvaccinated travellers. There is also a risk of further international spread through introduction of the virus into areas with a competent vector and susceptible populations.

Given that outbreaks of yellow fever in urban settings have the potential for rapid spread and that significant yellow fever epidemics are ongoing in Angola, DRC and Uganda, this risk assessment evaluates the risk of yellow fever infection being introduced into Europe and sets out a range of options for response.

Hunan Province Reports A New H5N6 Infection


Although case reports remain widely scattered and sporadic, we continue to see new cases of H5N6 crop up infection in China.  During its 1st 18 months of circulation (April 2014-Nov 2015), it was only diagnosed in 4 people.

But over the past six months (Dec 2015-May 2016), China has reported 11 new cases spread across 4 provinces.

In April Hunan Province reported their first case (see China Reports 2nd H5N6 Case in A Week), that of an 11 year-old girl from Lusong district, Zhuzhou city, who was said to be recovering after a serious bout of pneumonia.

Today Hunan Province reports their 2nd case, in a brief statement offered by their provincial CDC.

Hunan Diagnose H5N6 cases

Update Time: 2016-5-30

May 28, 2016, Hunan Diagnose H5N6 cases. Patients Tian Moumou, male, 50 years old, Xiangxi Autonomous Prefecture Guzhang County. When the disease in Jishou city workers, currently in critical condition, the hospital for treatment.

H5N6 avian-derived influenza virus is a virus, limited its ability to infect humans, there is no evidence of sustained human-to-human transmission.    

Over the past couple of months we've looked at the continuing evolution of H5N6 viruses (see Novel Reassortant H5N6 Viruses In Humans, Guangdong China and J. Virology: H5N6 Receptor Cell Binding & Transmission In Ferrets).

A little over a week ago the WHO released an assessment which noted not only the increase in human infections, but the ongoing evolution of the virus as well.

Avian influenza A(H5) viruses
According to the animal health authorities in China 3,4 , influenza A(H5N6) viruses have been detected in poultry in recent months in many provinces in the country, including those reporting human cases. Recent publications indicate ongoing evolution of avian influenza A(H5N6) viruses through reassortment with other avian influenza viruses resulting in viruses with different internal genes. 5,6

To date, no changes in transmissibility in humans have been detected as a result of these reassortant 1viruses. Surveillance is continuing in both human and animal populations to monitor for further virus evolution. All recent avian influenza A(H5N6) viruses that have been tested remain susceptible to the neuraminidase inhibitor class of antiviral drugs.

While the overall case counts remain low, and we've seen no indication of human-to-human spread, this upward trend in cases is of concern, as are the detections of H5N6 in poultry in Vietnam and Laos, and the virus showing up in migratory birds in Hong Kong.

For more background on this emerging avian flu threat, you may wish to revisit some of these blogs from last year:

H5N6: The Other HPAI H5 Threat
H5N6 Rising: Infecting Birds, Humans, & Even Cats
EID Journal: Influenza A(H5N6) Virus Reassortant, Southern China, 2014

Monday, May 30, 2016

Detection Of Airborne H9 Nucleic Acid In Chinese Live Poultry Market


In China the link between live poultry markets (LPMs) and the spread (and reassortment of) avian flu strains is already well established, and it is easy to understand why.

Large quantities of birds of varying species (chickens, ducks, geese, quail, and others) are brought in from different farms, housed together in cramped quarters, and then slaughtered (and often de-feathered) in open air booths as thousands of people walk by. 

Not only does this expose humans to avian viruses, it facilitates the sharing of different avian flu subtypes (H5, H7, H9) among the birds, promoting continual reassortment and the creation of new clades, or subtypes.

In 2014, a year after the H7N9 virus emerged in China, in CDC: Risk Factors Involved With H7N9 Infection, we looked at a case-control study that pretty much nailed LPMs as the prime  risk factor for infection.

While even casual exposure to poultry in live bird markets was cited as the primary risk factor, people who owned, raised, or slaughtered birds at home, on farms, or in the wild were not found to be at any increased risk.

Last December, a Who's Who of avian flu experts, writing in The Lancet: Interventions To Reduce Zoonotic & Pandemic Risks From Avian Flu In Asia listed immediate actions that should be taken by LPMs to curb the evolution and spread of avian flu in Asia.

The detection of viral RNA (or sometimes live virus) in LPMs isn't new (see Macao Detects H7 In Poultry Market - Live Sales Halted 3 Days), and some studies (see H5N1: Hiding In Plain Sight) have shown these viruses may survive for days or even weeks under the right conditions.

But these detections have generally been on fomites (inanimate objects like knives, table tops, cages, etc.) or in environmental contamination from chicken manure, feathers, entrails, or dust.  

Less well defined is the airborne spread of avian viruses in these markets, although it may explain how a few people just walking past a live market have reportedly been infected.

Three years ago, in How to Aerosolize A Chicken, we looked at one plausible way this can happen, through the use of mechanical de-feathering machines used in some chicken stalls.
And there is some evidence that avian viruses can be spread from farm to farm - at least over short distances - by prevailing winds (see Bird Flu’s Airborne `Division).

Adding more weight to this idea, a year ago, in CIDRAP: H5N2 Roundup & Detection In Environmental Air Samples, we looked at air sampling conducted by the University of Minnesota around infected poultry farms that found evidence of airborne virus particles.

But until now, little has been published on the search for airborne avian flu viruses in and around live poultry markets in China.  

Which brings us to a study, published last week in the Chinese Medical Journal, which describes two years of environmental and air testing from one of the hundreds of LPMs in Nanning, China (Guangxi province).

They collected Aerosol samples from one (of 12) random stalls (including chickens, geese, and ducks) every week.  At the same time they collected floor sewage and feathers, and swabbed poultry cages and chopping blocks.

Samples were cataloged and tested for influenza A viral RNA and positive samples were then analyzed to determine their (H5/H7/H9) subtype.

RT-PCR testing is very sensitive, and the detection of viral RNA is a much lower bar than isolating live virus, and doesn't tell us about the viability of the viruses they detected.

The (open access) study found ample environmental evidence of viral contamination, and reports the first positive detection of Airborne H9 (presumably H9N2) in a Chinese LPM. 

Although not a huge threat to human health, H9N2 is increasingly on our radar because the number of human infections appear to be increasing, we've seen signs of increasing mammalian adaptations, and because it has contributed its internal genes to a number of reassorted avian flu viruses.

Guangxi Province has only reported 3 cases of H7N9, and so it isn't terribly surprising that H7 viruses were not detected, and while H5 viruses were found in roughly 20% of environmental samples, no airborne H5 was detected.

The full report can be read at the link below, I've included some excerpts from the discussion:

First Positive Detection of H9 Subtype of Avian Influenza Virus Nucleic Acid in Aerosol Samples from Live Poultry Markets in Guangxi, South of China.



Overall,  the present results suggest that AIV  nucleic  acid exist in aerosol and other environmental samples from LPMs of  Guangxi.  Aerosol  transmission  might  be  an  important  mode of human infected by AIV after visiting LPMs; thus, it is needed to monitor virus distribution in aerosol sample from LPMs.
Previous studies have shown that LPMs were closely linked to H9N2, H5N1, and H7N9 infection in human in 2003,[4]  2006, and 2013,[5] respectively.

LPMs promote the transmission of AIV from avian to human. It is still needed to confirm the transmitted mechanism through exposure  or  visiting  LPMs.  Chickens  were  successfully  infected  with  AIV  H5N1and  H9N2  by  aerosol  and  caused  higher titers of virus. [6,7]
Avian influenza H9 has been isolated animals  from  LPMs[8‑11]  and  from  air  in  chicken  houses  in  China. Our results first reported H9 subtype of AIV nucleic acid existing in aerosol sample from LPM of Guangxi, China, providing support for aerosol transmission of AIV in LPM.
H5 subtype of AIV nucleic acid was not detected positive in  aerosol  while  it  was  positive  in  other  four  styles  of  environmental samples. H9 subtype was positive in aerosol and other four styles of environmental samples in 2014.

It is still needed further study to investigate whether there are differences in viral viability between H5 and H9 subtypes in aerosol and other environmental samples. As  LPMs  play  an  important  role  in  the  dissemination  of  AIVs, active surveillance to monitor AIV in LPMs should be carried out as an early warning system for AIV outbreaks.