H7N9: Video Chat Via Science Live

 

 

 

# 7215

 

Each week Science Magazine holds an online chat with top experts on the hottest topics in science as part of their ScienceLive Series. Later this morning (10 am EDT) they will hold a live video Chat on the H7N9 virus, with guests Yuelong Shu, Marion Koopmans, and  moderator Jon Cohen. 

 

Here are the details for what should prove a very interesting discussion.

 

Live Chat: The Threat of H7N9 Bird Flu (Video)

by Jon Cohen on 1 May 2013, 8:47 AM | See below for the chat box. Join us this Thursday at 10 a.m. EDT for a live conversation with leading scientists and expert reporters.

 

Today's Topic

When Chinese public health officials announced last month that people were sick and dying from a bird flu virus never before seen in humans, researchers immediately began hunting for answers to a deluge of pressing questions. How did the humans become infected? How deadly was the bug? Had it spread to people outside of China? Would anti-influenza drugs work? And how long would it take to make a vaccine?

 

Join us at a special time, 10 a.m. EDT, on Thursday, 2 May, on this page for a live video chat when we discuss H7N9 with experts. They’ll tackle the questions above and take yours. Be sure to leave your queries in the comment box below.

Today's Guests

Yuelong Shu

Marion Koopmans

Moderator

hCoV-EMC: Saudi Arabia Reports 7 Cases, 5 Fatal

Photo Credit NIAID

UPDATED: Confirmed at 7:20am EDT by Gregory Hartl, spokesperson for WHO.

 

# 7214

 

It’s being widely reported this morning (see Reuters, AFP, Al Jazeera stories) that 5 Saudis have died in recent days from the novel coronavirus (hCoV-EMC aka NCoV), and that two more remain in Intensive Care.

 

Caveat: Thus far, I’ve not been able to find an official announcement from the KSA Ministry of Health. All of the media reports read as if they are based on the same report, and so I’ve been trying (without success) to find alternate corroboration (see UPDATE above).

 

Crucial details - such as patient descriptions, onset dates, and epidemiological links (if any)  - are not provided at this time.  About all we really know are the numbers, and a generic location (Ahsaa province).

 

First, a report from Al Jazeera, then I’ll return with a bit more.

 

Five die of SARS-like virus in Saudi Arabia

Health ministry says it is taking "precautionary measures" with two more people being treated in intensive care unit.

Last Modified: 02 May 2013 08:31

Saudi Arabia's health ministry has said that five Saudis have died from a new SARS-like virus and that two more are being treated in an intensive care unit.

 

In a statement cited by the Saudi SPA agency late on Wednesday, the ministry said that all the deaths occurred in the Ahsaa province in the oil-rich eastern region of the kingdom, according to the AFP news agency.

 

Known as novel coronavirus or hCoV-EMC, the virus was first detected in mid-2012 and is a cousin of Severe Acute Respiratory Syndrome (SARS), which triggered a scare 10 years ago when it erupted in east Asia, leaping to humans from animal hosts.

 

The health ministry said it was taking "all precautionary measures for persons who have been in contact with the infected people ... and has taken samples from them to examine if they are infected".

 

However, the ministry gave no figures for how many people have been examined to see if they have the lethal disease.

(Continue . . .)

 

This novel coronavirus (hCoV-EMC) appeared just over a year ago in a cluster of patients at a Jordanian Hospital, since then, there have been 17 lab confirmed cases, and roughly a dozen `suspected’ cases.   

 

While a couple of `mild’ cases have been reported, most of the known hCoV-EMC cases have progressed to severe pneumonia, and renal failure.  Until today, 12 of the 17 confirmed cases have proved fatal.

 

Four  clusters support the idea that some, limited, human-to-human transmission has occurred.

 

Although the H7N9 virus had temporarily pushed this novel coronavirus off the front page, pretty much everyone in the EID world has been expecting that more cases would crop up. 

 

The World Health Organization – in their recent GAR (Global Alert & Response) update of April 24th, described the current status of the NCoV Investigations this way:

 

 

Novel coronavirus summary and literature update – as of 24 April 2013

Summary

The available evidence related to novel coronavirus continues to suggest a zoonotic origin for the virus. However, the cluster of cases reported by the United Kingdom provides strong evidence of human-to-human transmission, confirming suspicions that were raised in the previously reported clusters. Investigations around cases have not thus far uncovered evidence of sustained transmission in the community, and transmission between humans appears to be relatively uncommon. The availability of serological tests and the recently acquired capacity to test for the virus using sensitive PCR techniques provide an opportunity to expand our knowledge of the occurrence of the virus in the community.

 

Many questions remain to be answered. The most important are the source of the virus, the exposures that result in human infection, and the mode of transmission. Some features of the cases such as the predominance of males among the confirmed cases may provide important clues to relevant exposures. In addition, although all cases to date have had some connection with the Arabian peninsula, more information is needed about the true geographic extent of the virus. Available evidence suggests that the virus may have its origin in bat species. However, experience with Nipah virus in Malaysia and SARS in China both illustrate that intermediate hosts may sometimes play an important role in transmission to humans and that direct exposure to reservoir species is not needed for infection. The experience of Nipah virus in Bangladesh, in which consumption of raw palm sap contaminated by bat feces has been identified as the mode of transmission, also illustrates the sometimes complex route by which virus may be transmitted from source to human. Finally, if more cases occur, it will be important to study clinical management methods in light of new research demonstrating the effect of certain antiviral agents on laboratory growth of the virus. Protocols for clinical management trials should be developed in anticipation of future cases.

 

In addition to the kinds of investigations described above, there continues to be a need for vigilance and surveillance, both within the affected area and for unusual clusters of respiratory disease in other parts of the world.

WHO: Updated H7N9 FAQ

 

 

 

# 7213

 

While a lot of the questions still cannot be answered with much more than - `we don’t know yet’ - the World Health Organization has updated their extensive H7N9 FAQ page, with the latest information available.

 

Sometimes the hardest things for officials to do is to admit the limits of their knowledge of, or ability to control, a potentially risky situation.

 

WHO has, quite commendably, been consistently straightforward and open about what they know – and don’t know – about this emerging viral threat.

I’ve only posted the link, and a small fraction of the FAQ. Follow the link to read it in its entirety.

 

 

Frequently Asked Questions on human infection caused by the avian influenza A(H7N9) virus

Update as of 30 April 2013

Note that this document supersedes the previous version. Updates will be posted as new information becomes available.

1. What is the avian influenza A(H7N9) virus?

Avian influenza A H7 viruses are a group of influenza viruses that normally circulate among birds. The avian influenza A(H7N9) virus is one subgroup among the larger group of H7 viruses. Although some H7 viruses (H7N2, H7N3 and H7N7) have occasionally been found to infect humans, no human infections with H7N9 viruses have been reported until recent reports from China.

2. What are the main symptoms of human infection caused by avian influenza A(H7N9) virus?

Thus far, most patients with this infection have had severe pneumonia. Symptoms include fever, cough and shortness of breath. However, information is still limited about the full spectrum of illness that infection with avian influenza A(H7N9) virus might cause.

3. How many human cases of avian influenza A(H7N9) virus have been reported in China to date?

New cases that are reported are now being compiled and posted daily. The most current information on cases can be found in Disease Outbreak News.

4. Why is this virus infecting humans now?

We do not know the answer to this question yet, because we do not know the source of exposure for these human infections. However, analysis of the genes of these viruses suggests that although the viruses have evolved in birds, they may infect mammals more easily than other avian viruses.

<SNIP>

7. How are people becoming infected with the avian influenza A(H7N9) virus?

At this point it is not known how persons are becoming infected. Some of the confirmed cases had contact with animals or with environments where animals are housed. The virus has now been found in chickens, ducks, and captive-bred pigeons at live bird markets near locations where cases have been reported. The possibility of an animal source of the infection is being investigated, as is the possibility of person-to-person transmission.

<SNIP>

12. Is the source of infection poultry and live poultry markets?

Although some evidence points to live poultry as a source of infection, it cannot yet be confirmed that live poultry is the primary or the only source of infection. Neither is there enough evidence to exclude other possible animal or environmental sources of infection.

<SNIP>

16. Is the general population at risk from the avian influenza A(H7N9) virus?

We do not yet know enough about these infections to determine whether there is a significant risk of community person to person spread. This possibility is the subject of epidemiological investigations that are now taking place.

17. Are health care workers at risk from the avian influenza A(H7N9) influenza virus?

Health care workers often come into contact with patients with infectious diseases. Therefore, WHO recommends that appropriate infection prevention and control measures be consistently applied in health care settings, and that the health status of health care workers be closely monitored. Together with standard precautions, health care workers caring for those suspected or confirmed to have avian influenza A(H7N9) infection should use additional precautions (see:
http://www.who.int/csr/resources/publications/swineflu/WHO_CDS_EPR_2007_6/en/index.html ).

18. What investigations have begun?

Local and national health authorities are taking the following measures, among others:
• Enhanced surveillance for pneumonia cases of unknown origin to ensure early detection and laboratory confirmation of new cases;
• Epidemiological investigation, including assessment of suspected cases and contacts of known cases;
• Close collaboration with animal health authorities to determine the source of the infection.

19. Does this influenza virus pose a pandemic threat?

An animal influenza virus that develops the ability to infect people could theoretically carry a risk of causing a pandemic. However, whether the avian influenza A(H7N9) virus could actually cause a pandemic is unknown. Other animal influenza viruses that have been found to infect people occasionally have not gone on to cause a pandemic.

(Continue . . .)

 

Lancet: Origin and Diversity of Novel Avian Influenza A H7N9

 

The H7N9 Reassortment – Credit Eurosurveillance

 

# 7212

 

 

Two weeks ago, in Eurosurveillance: Sequence Analysis Of H7N9 Suggests `Widespread Circulation’, we looked at research that examined 7 early H7N9 virus samples collected in China’s outbreak and calculated the genetic distance between them.

 

Simply put, the genetic distance is the accumulated genetic difference between species or between different samples taken within a species.

 

We know that viruses circulating in the wild pick up mutations at a roughly determinable rate. Once you figure out that rate (it varies among viruses), you can compare two similar viruses, and count the number differences between them.

 

With that information you can get an idea of how long it has been since their  tMRCA  (Time To Most Recent Common Ancestor).

 

The Eurosurveillance study (above) – which utilized mutation rates from two previous H7 outbreaks (in 1999 and 2003) – calculated that H7N9 may have been widely circulating for months before it was finally detected.

But, in exactly what host, remains a subject of debate.

 

Today the Lancet has the most complete phylogenic analysis of the H7N9 virus to date, that not only suggests this virus evolved through multiple reassortments (likely involving wild birds -> wild ducks -> domesticated ducks -> poultry), it pushes back its estimated tMRCA to roughly January 2012.

 

doi:10.1016/S0140-6736(13)60938-1

Origin and diversity of novel avian influenza A H7N9 viruses causing human infection: phylogenetic, structural, and coalescent analyses

Di Liu PhD , Weifeng Shi PhD , Yi Shi PhD, Dayan Wang PhD , Haixia Xiao , Wei Li MSc , Yuhai Bi PhD , Ying Wu PhD , Xianbin Li BS, Prof Jinghua Yan PhD , Prof Wenjun Liu PhD, Prof Guoping Zhao PhD , Prof Weizhong Yang MD , Prof Yu Wang MD , Prof Juncai Ma PhD , Prof Yuelong Shu PhD , Prof Fumin Lei PhD , Prof George F Gao DPhil

Summary

Background

On March 30, 2013, a novel avian influenza A H7N9 virus that infects human beings was identified. This virus had been detected in six provinces and municipal cities in China as of April 18, 2013. We correlated genomic sequences from avian influenza viruses with ecological information and did phylogenetic and coalescent analyses to extrapolate the potential origins of the virus and possible routes of reassortment events.

<SNIP>

 

Findings

The novel avian influenza A H7N9 virus originated from multiple reassortment events. The HA gene might have originated from avian influenza viruses of duck origin, and the NA gene might have transferred from migratory birds infected with avian influenza viruses along the east Asian flyway. The six internal genes of this virus probably originated from two different groups of H9N2 avian influenza viruses, which were isolated from chickens. Detailed analyses also showed that ducks and chickens probably acted as the intermediate hosts leading to the emergence of this virulent H7N9 virus. Genotypic and potential phenotypic differences imply that the isolates causing this outbreak form two separate subclades.

Interpretation

The novel avian influenza A H7N9 virus might have evolved from at least four origins. Diversity among isolates implies that the H7N9 virus has evolved into at least two different lineages. Unknown intermediate hosts involved might be implicated, extensive global surveillance is needed, and domestic-poultry-to-person transmission should be closely watched in the future.

 

There is a lot here to digest (and I’ve only hit the highlights), so follow the link to read this paper in its entirety (free registration req.).

 

There also remains a lot we don’t know about this virus, including where it spends its time when its not infecting people. While linked to poultry exposure, questions remain over exactly what host (or hosts) are silently carrying this virus and giving it to humans.

 

The authors conclude by writing:

 

. . .  on the basis of available evidence, we believe that the novel avian influenza A H7N9 virus was a multiple reassortant. The HA and NA genes might originate from duck avian influenza viruses, which might have obtained the viral genes from migratory birds a year previously, whereas the internal genes might come from chicken avian influenza viruses. We believe that the estimated times to most recent common ancestor for the eight genomic fragments and the frequent poultry transportation in China account for the increased number of confirmed sporadic cases of human infection. In particular, this novel H7N9 virus has diversified into different lineages since its emergence several months ago.

 

H7N9: Hunan, Fujian Report New Cases

Heat map – Credit Laidback Al FluTrackers

 

 

# 7211

 

 

There’s been a welcome slowing of new H7N9 case announcements out of China this week, most noticeably from Shanghai, which closed their live poultry markets very early in this outbreak, and has not reported a new case in the past 10 days.

 

Nevertheless, the geographic range of this virus has increased profoundly over the past week, and testing continues to find new, albeit sporadic, infections.

 

Today, Hunan and Fujian province have each reported new cases. As we’ve seen so often with this virus  (see Eurosurveillance: H7N9 Virus-Host Interactions & Age Shift) - both are male, and both from an older age cohort (58 & 69).

 

Up first, via Xinhua News, details on Hunan Province’s latest reported H7N9 case.

 

Hunan new case of human infection of H7N9 avian influenza confirmed cases

May 1, 2013 18:17:48
Source: China News Network

The official website of the Health Department of Hunan Province on May 1 announced that the province's new case of human infection of H7N9 avian influenza confirmed cases. Currently, patients in critical condition, is actively rescuing.

 

According to reports, the patient Zhao, male, aged 69, the Shaoyang City Wugang people, farming. Patients no obvious incentive on the afternoon of April 23, chills, fever, cough, Wugang City, a village health treatment in April 24 -26, 2011, the body temperature of 39 ° C -39.5 ° C. Treatment in Wugang City People's Hospital on April 27, temperature 41 ° C, "lobar pneumonia" admitted Wugang City People's Hospital. 29 April sicker patients, of Wugang City People's Hospital "unexplained pneumonia Wugang CDC report.

 

Wugang City CDC immediately carry out epidemiological investigations, and samples were collected swabs, serum specimens were sent to the Shaoyang City CDC detected. At 12 o'clock on the April 30, Shaoyang City CDC test results for people infected with the H7N9 avian influenza virus nucleic acid positive. At 14:00 pm, the patient transferred to the Central Hospital of Shaoyang treatment. At 19:00 Hunan Provincial Center for Disease Control results of the review is positive. May 1, in accordance with the "human infection of H7N9 avian flu, 2nd Edition (2013)", Hunan comprehensive case of the Group of Experts clinical manifestations, laboratory and epidemiological findings, the diagnosis of human infection of H7N9 avian influenza confirmed cases.

 

After investigation, the patients prior to the onset of the poultry exposure history, its close contact with a total of 50 people, to take timely medical observation. Up to now, all close contacts of the cases were not unusual. (Reporter Liu column)

 

And details on Fujian Province’s third case, again from Xinhua News.

 

 H7N9 case reported in SE China

English.news.cn   2013-04-30 13:24:58

FUZHOU, April 30 (Xinhua) -- Health authorities in southeast China's Fujian Province reported a new human infection of the H7N9 avian flu on Tuesday, bringing the total number of cases in the province to three.

 

A 58-year-old man surnamed Xu from the city of Fuzhou tested positive for the flu on Tuesday at the provincial center for disease control and prevention, according to a statement from the provincial health department.

 

Xu developed a fever and cough before seeking treatment at the Fujian Provincial Hospital on April 28. Xu was in critical condition, it said.

 

People who have had close contact with Xu are being monitored for flu symptoms.

 

This slowdown in cases, while encouraging, may not be truly reflective of the events on the ground in China.

 

This week is one of the major National holidays celebrated in Asia (Labor Day), and it is unclear whether that may be affecting reporting from the provinces.

Nature: The Row Over H7N9 Sequencing Data

Photo Credit – CDC 

 

 

# 7210

 

There is an old adage of uncertain parentage – but most often attributed to political scientist Wallace Sayre – that (paraphrased) states, `Academic infighting is so bitter, because the stakes are so small’.

 

Of course, that isn’t nearly as true as it once was.

 

The stakes in academia now extend far beyond the publish or perish incentive in order to achieve tenure.  In addition to prestige, the fruits of research today can be worth millions in terms of government and private grants, patents, or licensing agreements to individuals, universities, organizations, and even governments.

 

These incentives have often led to research being closely held until papers can be published and proper credit bestowed to the originators.

 

In the fast moving world of virology, where – as we’ve recently witnessed – new, and potentially dangerous viruses can pop up and begin to spread quickly, delays in releasing data can have serious consequences for public health.

 

To overcome this hoarding of data - which can impede other researcher's progress for months or even years - GISAID was set up in 2008 to allow researchers to deposit, and get credit for, genetic sequences they have worked out.

 

But as the following  Nature article from Declan Butler & David Cyranoski explains, once sequences are deposited, the process gets complicated and things don’t always go as well as planned. 

 

Follow the link to read:

 

 

Nature | News

Flu papers spark row over credit for data

Rush to publish on H7N9 avian flu upsets Chinese scientists.

• Declan Butler
• & David Cyranoski

01 May 2013

On 31 March, China reported the first human cases of infection with a new H7N9 avian flu virus. The same day, a team at the Chinese National Influenza Center (CNIC) in Beijing uploaded to a research database the genetic sequences of viruses isolated from the first three human cases. But Nature has learned that in the days that followed, Chinese scientists and officials grew increasingly concerned that China might lose credit for its work in isolating and sequencing the virus.

 

(Continue . . . )