H5N1

China: Scientists make new H7N9 claim

Via People's Daily Online, a Shanghai Daily report: Scientists make new H7N9 claim. Excerpt:

Scientists at Fudan University claimed yesterday that the H7N9 bird flu virus originated from poultry or wild bird in eastern China instead of the previous theory that the virus's two major proteins - HA and NA - come from fowl in China and South Korea respectively. 

The scientists said their findings were based on generic research and analysis through advanced bioinformatics and it can be important to prevent bird flu in the future. 

The new results were published in the latest edition of the US-based Clinical Infectious Diseases. 

Since February 19, the flu-like symptoms first started to appear in eastern China and the National Health and Family Planning Commission announced the discovery of the new H7N9 virus on March 31. 

Previously, scientists - both at home and abroad - believed that the virus's HA of the H7 subtype came from duck in Hangzhou, Zhejiang Province, and NA of the N9 subtype was from fowl in South Korea. 

But Fudan researchers said from gene sequencing they discovered that NA of the N9 subtype had its origins in Baikal Teal in Hongze Lake in Jiangsu Province.

The original CID article is behind a paywall, or I would link to it.

Alabama: Now 10 cases, 1 death linked to H1N1 (updated)

Via the Dothan Eagle: One illness fatality linked to H1N1 flu virus. Excerpt:

Officials with the local office of the state Department of Public Health said Wednesday that one of the two deaths that are part of a recent respiratory illness outbreak could be associated with the H1N1 flu virus. 

Lesa C. Smith, a registered nurse with state Department of Public Health, also said the number of people admitted to local hospitals during the recent respiratory illness outbreak has increased from seven to nine. 

“We can’t say that the person died with H1N1, but we can say it was a death associated with it,” Smith said. “A total of nine have been admitted. We know some people are recovering, and are going home.” 

Corey Kirkland, a health department spokesperson, said the two deaths occurred Saturday and Sunday. 

Several local state Department of Public Health officials held a press conference Tuesday morning to release information about a recent outbreak or “cluster” of respiratory illnesses to hit Southeast Alabama. 

Smith said the three key symptoms area residents need to be on the lookout for includes shortness of breath, coughing and fever. 

“We’re looking at those three things, but so far we don’t have a common factor among all of them,” Kirkland said. “There are many different types of respiratory disease. We haven’t pinned it down to one specific illness. Right now we’re looking for patients who are showing these symptoms.” 

Kirkland said two of the people tested positive for specific viruses, which included the H1N1 flu virus. He said another person tested positive for the type A flu virus, which Smith said was the typical seasonal flu virus. 

“We’re still in the investigative state, and we’re still waiting other tests to come back,” Kirkland said. 

Health department officials have said all nine people admitted to local hospitals were within an eight-county southeast region, which includes Barbour, Coffee, Crenshaw, Dale, Geneva, Henry, Houston and Pike County.

Update: As soon as I posted this item, with 9 cases, I found a report from WSFA.com saying the number of cases is now 10.

ECDC: Disease threats report for week 20

ECDC has published Monitoring current threats: ECDC Communicable Disease Threats Report (CDTR), week 20. The summary:

The CDTR reports this week on an ongoing outbreak of hepatitis A virus (HAV) affecting individuals from various northern countries in the EU. Since the beginning of the outbreak on 1 October 2012 until 17 May 2013 a total of 85 cases were reported, of which 34 are confirmed. No cases have travel history outside of the EU during their potential exposure period. 

The source of the outbreak has not yet been identified but preliminary investigations point to frozen berries as the vehicle of infection. Public health authorities in the affected countries and ECDC are actively collaborating to identify the vehicle of the infection in order to prevent the occurrence of additional cases. 

Between April 2012 and 16 May 2013, 40 laboratory-confirmed cases of Middle East respiratory syndrome coronavirus (MERS-CoV), including 20 deaths, have been notified. All cases worldwide remain associated (including indirect association following secondary person-to-person transmission in the UK and France) with transmission in the Arabian Peninsula. 

ECDC published an update of its risk assessment on 17 May. ECDC is closely monitoring the situation in collaboration with the World Health Organization and the European Union Member States.

CIDRAP: New MERS-CoV case reported as puzzles persist

Via CIDRAP, Robert Roos writes: New MERS-CoV case reported as puzzles persist. Excerpt:

Saudi Arabia reported today that a foreigner died yesterday of a MERS-CoV (Middle East respiratory syndrome coronavirus) infection, while health officials in Jordan offered new details—some of them puzzling—about a hospital cluster of cases that occurred there in April 2012. 

In a brief statement, the Saudi Ministry of Health (MOH) announced "the demise of a non-Saudi case of novel Coronavirus in al-Qassim region," a province in the central part of the country. The person was hospitalized a few days ago with a severe respiratory illness and died yesterday, the statement said. 

The MOH gave no information on the patient's age, gender, nationality, previous health status, occupation, residency status, or possible exposures to the virus. The statement noted that no new cases have emerged in the past 5 days in the Al-Ahsa region in Eastern province, site of a hospital-centered MERS-CoV outbreak involving 22 cases. 

The announcement comes a day after a press report that a World Health Organization (WHO) expert, Anthony Mounts, MD, expressed concern that guest workers in the Middle East could spread the novel virus to their home countries, particularly India and the Philippines. 

The WHO said today that the death toll in the Al-Ahsa outbreak has increased to 10 with the death of a patient whose case was announced earlier. The WHO gave no other information about the patient, and it wasn't immediately clear if the death is the same one that was noted by the Saudi MOH in a May 20 statement.

Click through for Roos's whole post, which includes more on the Tunisian cases as well as a summary of the Jordanian outbreak in 2012 that launched this whole thing.

Live-animal markets and H7N9

Thanks to Greg Folkers for this NEJM letter, published today: Live-Animal Markets and Influenza A (H7N9) Virus Infection. Maybe I've been doing this too long, but it reads like a medical thriller. Excerpt:

A recent outbreak of a previously unrecognized novel reassortant avian influenza A (H7N9) virus in China had resulted in 131 documented cases and 36 deaths as of May 16. Although some patients had a history of contact with live poultry or visiting live-animal markets before the onset of illness, the source of infection remains unclear. 

A 45-year-old woman was admitted to a hospital on March 23, 2013, with a 5-day history of fever (temperature, 41.0°C), cough, expectoration, malaise, and shortness of breath. Computed tomography of the chest that was performed 2 days before admission showed infection in the right lung. On March 28, a specimen of tracheal secretion from the patient was collected for laboratory testing. Epidemiologic investigation showed that the patient was otherwise healthy except for a positive assay for hepatitis B surface antigen. 

She had worked for several years in a live-animal market as the sole poultry butcher. Her stall was located in a corner of the market (red dot in Fig. S1 in the Supplementary Appendix, available with the full text of this letter at NEJM.org). Except for the definite exposure from her working environment, she had had no contact with other animals or febrile patients. All the live poultry she slaughtered came from a neighboring stall (green dot in Fig. S1 in the Supplementary Appendix). The live poultry had been purchased from a secondary wholesale market, where poultry raised on various farms were congregated before being sold to live-animal markets. 

Laboratory investigation by means of various methods — including real-time reverse-transcriptase–polymerase-chain-reaction (RT-PCR) assay, viral isolation, and full-genome sequencing — confirmed that the patient was infected with the novel H7N9 virus. 

To trace the possible source of infection, investigators collected 5 environmental samples from the two stalls in the market and 13 samples from the secondary wholesale market on March 29. One poultry-cage specimen from the neighboring stall was positive for the novel H7N9 virus. 

Furthermore, mixed avian-influenza viral nucleic acids (e.g., subtypes H3, H7, N8, and N9) were detected on subtype-specific real-time RT-PCR from one feces sample collected from the secondary wholesale market. 

Two viral strains, one from the patient (Nanjing/1) and one from poultry-cage specimens obtained in the neighboring stall (Env/Nanjing), were successfully isolated (GenBank numbers, KC896771-KC896778 for the case specimen and KC896763-KC896770 for the environmental specimen). 

Genome comparison showed that the similarity in the nucleic acids found in the two isolates ranged from 98.9% to 100%; this would translate into an amino acid similarity of 98.2% to 100%. Both isolates had potentially functional amino acid sites related to mammal- or human-adapting substitution T189A, Q226L, and G228S (H3 numbering) in the receptor-binding site of hemagglutinin. 

The two isolates showed E rather than K at position 627 of BP2. However, Nanjing/1 showed K rather than Q at position 591 of PB2, which has been shown to cooperate with position 627 of PB2, and the combination of 591K–627E showed higher virulence than that of 591Q–627E in mice with H5N1 viruses4 (Table S1 in the Supplementary Appendix). 

These findings suggest that the novel virus had been evolving and might, with a few amino acid mutations, adapt to humans.

H7N9: Clinical findings in 111 cases

Thanks again to Greg Folkers for sending the link to this NEJM article, published today: Clinical Findings in 111 Cases of Influenza A (H7N9) Virus Infection. The abstract:

BACKGROUND 

During the spring of 2013, a novel avian-origin influenza A (H7N9) virus emerged and spread among humans in China. Data were lacking on the clinical characteristics of the infections caused by this virus. 

METHODS 

Using medical charts, we collected data on 111 patients with laboratory-confirmed avian-origin influenza A (H7N9) infection through May 10, 2013. 

RESULTS 

Of the 111 patients we studied, 76.6% were admitted to an intensive care unit (ICU), and 27.0% died. The median age was 61 years, and 42.3% were 65 years of age or older; 31.5% were female. A total of 61.3% of the patients had at least one underlying medical condition. Fever and cough were the most common presenting symptoms. 

On admission, 108 patients (97.3%) had findings consistent with pneumonia. Bilateral ground-glass opacities and consolidation were the typical radiologic findings. Lymphocytopenia was observed in 88.3% of patients, and thrombocytopenia in 73.0%. Treatment with antiviral drugs was initiated in 108 patients (97.3%) at a median of 7 days after the onset of illness. 

The median times from the onset of illness and from the initiation of antiviral therapy to a negative viral test result on real-time reverse-transcriptase–polymerase-chain-reaction assay were 11 days (interquartile range, 9 to 16) and 6 days (interquartile range, 4 to 7), respectively. 

Multivariate analysis revealed that the presence of a coexisting medical condition was the only independent risk factor for the acute respiratory distress syndrome (ARDS) (odds ratio, 3.42; 95% confidence interval, 1.21 to 9.70; P=0.02). 

CONCLUSIONS 

During the evaluation period, the novel H7N9 virus caused severe illness, including pneumonia and ARDS, with high rates of ICU admission and death.

CIDRAP: Alabama officials probe respiratory illness cluster

Via CIDRAP, Lisa Schnirring writes: Alabama officials probe respiratory illness cluster. Excerpt:

Alabama health officials are investigating a cluster of severe respiratory infections from an unknown origin centered around the Dothan area and have asked the state's health providers to be alert for and report similar cases. 

In a press release yesterday the Alabama Department of Public Health (ADPH) said seven people have been hospitalized with similar symptoms: fever, cough, and shortness of breath. Two of the patients have died. The ADPH said it and the Houston County Health Department are conducting the investigation and have consulted with the US Centers for Disease Control and Prevention. 

Dothan, in Houston County, is in the southeastern corner of Alabama near both Georgia and Florida. A report from local TV news station WSFA said hospitalizations in the cluster began on May 16 at the city's Southeast Alabama Medical Center. 

An ADPH alert to health providers said the first three cases were flagged on May 16 by a pulmonologist who reported that three patients with similar symptoms were on ventilators and had no known cause for their illness. 

Tests on samples sent that day to the ADPH clinical lab revealed on May 17 the 2009 H1N1 influenza virus in one of the patients, who died the following day. Another patient who was transferred to the same facility and placed on a ventilator died on May 19. 

Polymerase chain reaction flu panel testing on three other patients who were admitted yielded one H3 influenza positive. The ADPH said though two patients have tested positive for influenza, it's unclear what role the viruses played in the cluster illnesses. 

So far no epidemiologic links have been found among the patients, the ADPH said.

I've seen one speculation, on a site of doubtful credibility, that the outbreak could be connected to nearby Fort Rucker, which presumably sees some traffic to and from various Middle East countries. But so do many other US military bases, so why would southeast Alabama be the only region to see an outbreak of undiagnosed respiratory disease?

Saudi Arabia: An attack on Ali Zaki over coronavirus

Via Al-Riyadh: Arab physician claims on the discovery of 'corona' lie and mislead public opinion. This appears to be an attack on the Egyptian scientist Dr. Ali M. Zaki. As usual, the Google translation from Arabic leaves much to be desired. An excerpt:

Sources denied medical official familiar with "Riyadh" allegations of doctor of Arab nationality "reserve the name" was running one of the private hospitals in the Kingdom before regarding whom proceedings are regular termination services by the hospital in which it operates against the backdrop of his offenses multi Medical Systems and instructions for laboratories Medical applicable in the Kingdom and beyond to the ethics of the medical profession and published the results of laboratory tests and send sensitive to third parties without permission from the competent health authorities. 

Concealed the information for two months and community risk to achieve his personal interests The doctor was "Arab" works department bacteriological laboratory one private hospitals in the Kingdom has claimed in interviews with Western media being harassed after the discovery of infected patients with HIV "krona" متظلما of actions taken by the hospital with him to end his services and made statements different As confirmed by medical sources of dealing with a sample of the virus has not allowed a system of isolation of the virus and publication of the results of the analysis in the journal "bromide" electronic and send a sample of the virus lab European all without taking permission bodies competent health which is in violation of orders, instructions and medical systems in force in this side and beyond the ethics of the medical profession. 

Infringe on the rights of state ownership to grant the rights of the virus was detected of Arsamos Center And about what he claimed the doctor of his discovery of the virus, "Koruna" lied sources claim and said that involves mislead a large public opinion and a major violation of the regulations Saudi Arabia and the International where he published the magazine "Nature" British scientific in its issue dated 01/15/2013 AD effect that the doctor "Arab" Contact expert Dutch virologist Ron fuchsia  [Fouchier], who works center Arsamos Medical (EMC) in Rotterdam, Netherlands on a sample patient has been suggested by the doctor Dutch examination "Koruna" Indeed, the doctor "Arab" to send the sample without taking permission bodies competent health center in the Netherlands and who discovered the new virus by Ron fuchsia.

It goes on. For a more comprehensible account of the dispute, here is Declan Butler's account in Nature News & Comment, January 13.

Saudi Arabia: New "non-Saudi" MERS death

Via the KSA Health Ministry coronavirus page: Ministry News - MOH: "A Novel Coronavirus Case Passed Away in Al-Qassim". The entire report:

The Ministry of Health has announced  the demise of a new non-Saudi case of novel Coronavirus in al-Qassim region, who has been admitted to hospital a few days ago due to severe acute respiratory syndrome and passed away yesterday on Tuesday, May Allah have mercy upon him. 

Within the same vein, MOH has pointed out that most cases have been recorded so far among elderly patients and people of multiple chronic diseases. 

Furthermore, MOH has underscored that Al-Ahasa governorate did not witness any new cases recorded of this virus in the past five days, May Allah be praised.

Follow the link and you'll see al-Qassim is some distance from al-Ahsa province. The reference to a non-Saudi shouldn't be surprising; the kingdom has millions of non-Saudi workers. I'm surprised the ministry didn't offer more details on this case, because everyone is going to want to know who this unfortunate person was.

Canada: Boil-water advisory widens for Montreal area

Via The Gazette: Boil-water advisory widens for Montreal area. Excerpt:

A boil-water advisory issued Wednesday morning for the southwest sector of Montreal has been extended to many other areas both on and off the island and affects an estimated 1.3 million people. City officials said the warning could be in place for at least 24 hours. 

The city issued the new warning at 10:30 a.m. for all areas south of the Metropolitan Expressway, from LaSalle in the west to Pointe aux Trembles in the east. 

Residents in this area are warned to boil the somewhat brownish water flowing out of their taps or use bottled water until further notice. Some of the affected municipalities include: Verdun, Point-St-Charles, St-Henri, Côte-St-Paul, Ville-Émard, Westmount, Côte-St-Luc, Hampstead, Town of Mount Royal, Anjou, Montreal East and the off-island town of Charlemagne. 

Residents are advised to run the taps until until the water runs clear and then boil their drinking water for at least a minute until further notice. 

The city of Montreal issued the boil-water advisory Wednesday morning. Maintenance work at the Atwater water facility affected the quality of water samples and prompted the advisory. The city is recommending boiling water or using bottled water for drinking, preparing baby formula, washing fruits and vegetables, brushing teeth and making ice cubes.