Saturday, October 6, 2012

Indonesia: Bengkulu Residents Haunted Bird Flu

 October 7, 2012
Hundreds of residents of the village of Lawang Periukan Water District Court yesterday (3/10), made of anxiety. Because they feared the people in the village have spread bird flu (avian influenza). With the discovery of 5 chickens died suddenly.
Five chickens, owned by the Great Suryadi Lawang village residents were found dead suddenly behind his chicken coop. Recognition Suryadi, his new chickens were found dead yesterday (3/10) morning when they wanted to be fed. Suryadi astonishment, as she watched the 5 tails ayamnnya was lying lifeless on the back of the cage.
"I used every morning to feed my chickens this. But this morning when I saw the cage, I have 5 chickens lying dead just behind the cage, "said Suryadi.
Fearing the death of chickens due to bird flu attack, Suryadi immediately took steps to report the incident to the chief. Lawang village chief Agung and its apparatuses, shortly after learning that, immediately report the incident to the Extension Officer (PPL) of the Department of Agriculture, Agriculture and Veterinary Office Seluma.
Officers arriving interval of one hour after it was reported. PPL Officer upon arrival at the location immediately perform surgery and take a sample of one of five chicken carcasses of dead chickens.
One officer PPL, Suhardi confirmed directly not sure whether it was because of the death of five birds due to bird flu virus or not. "Yet we can be sure whether this is bird flu or not, need examination in the laboratory first," he said.
He also added that it deliberately took samples of dead chickens, with the aim to do research in the laboratory. So that could certainly result. "In the meantime, samples of chicken carcasses will be taken to laboratotium for further investigation," he concluded. (Hue)

Eurosurveillance: Severe respiratory illness caused by a novel coronavirus, in a patient transferred to the United Kingdom from the Middle East, September 2012

The excerpt below in red is certainly not good news.   Oseltamivir is Tamiflu, which is currently the drug to fight Avian Influenza H5N1 in humans.  The descriptions of the drugs they gave this case are below: 
Evidence suggests that some antiviral drugs, notably oseltamivir, can reduce the duration of viral replication and improve prospects of survival.
In suspected cases, oseltamivir should be prescribed as soon as possible (ideally, within 48 hours following symptom onset) to maximize its therapeutic benefits.[]
Ceftriaxone injection is used to treat certain infections caused by bacteria such as gonorrhea (a sexually transmitted disease), pelvic inflammatory disease (infection of the female reproductive organs that may cause infertility), meningitis (infection of the membranes that surround the brain and spinal cord), and infections of the lungs, ears, skin, urinary tract, blood, bones, joints, and abdomen. Ceftriaxone injection is also sometimes given before certain types of surgery to prevent infections that may develop after the operation. Ceftriaxone injection is in a class of medications called cephalosporin antibiotics. It works by killing bacteria. Antibiotics will not work for colds, flu, or other viral infections. 
Azithromycin is used to treat certain infections caused by bacteria, such as bronchitis; pneumonia; sexually transmitted diseases (STD); and infections of the ears, lungs, skin, and throat. Azithromycin is in a class of medications called macrolide antibiotics. It works by stopping the growth of bacteria. Antibiotics will not work for colds, flu, or other viral infections. (editing is mine).  

Case history
On 14 September 2012, the United Kingdom Health Protection Agency (HPA) Imported Fever Service was notified of a case of unexplained severe respiratory illness in a London intensive care unit. The patient had recently transferred from Qatar and had a history of travel to Saudi Arabia.
He was a previously well 49 year-old man who developed a mild undiagnosed respiratory illness while visiting Saudi Arabia during August 2012, which fully resolved.  He subsequently presented to a physician in Qatar on 3 September, with cough, myalgia and arthralgia, and was prescribed oral antibioticsFive days later, he was admitted to a Qatari hospital with fever (38.4 °C) and hypoxia, with oxygen saturation of 91% on room air. A chest X-ray showed bilateral lower zone consolidation.  He was treated with ceftriaxone, azithromycin and oseltamivir. After 48 hours, he required intubation and ventilation and was transferred by air ambulance to London. During transfer, he was clinically unstable, requiring manual ventilation.

On admission to intensive care in London, he remained severely hypoxic, achieving an arterial PaO2 of 6.5 kPA (normal range: 11–13 kPA) on 100% oxygen with optimised pressure ventilation, and required low-dose norepinephrine to maintain blood pressure.  His white blood cell count was 9.1 x 109/L (normal range: 4–11 x 109/L), C-reactive protein 350 mg/L (normal range: 0–10 mg/L) and creatinine 353 μmol/L (normal range: 53–97 μmol/L), with normal liver function and coagulation. He was treated with corticosteroids and broad-spectrum antibiotics, initially meropenem, clarithromycin and teicoplanin. Colistin and liposomal amphotericin B were subsequently added.
His condition deteriorated between 11 and 20 September, with progressive hypoxia....


Detection of a novel coronavirus
We used real-time PCR on upper (nose and throat swabs) and lower respiratory tract samples (sputum and tracheal aspirates) to test for a range of coronaviruses: OC43, 229E, NL63 and SARS-CoV. We also used a block-based pan-coronavirus PCR with degenerate primers targeted to the conserved RNA-dependent RNA polymerase (RdRp Pol) gene that detects all coronaviruses known to infect humans and a range of animal coronaviruses [6].
The pan-coronavirus assay yielded a band of the correct size in lower respiratory tract samples, but the assays for OC43, 229E, NL63 and SARS-coronaviruses were negative. Sanger sequencing of the pan-coronavirus PCR product (a 251 base pair fragment encompassing nucleotides 104–354 of the NSP12 gene) yielded a sequence that on BLAST analysis gave genetic identity of 81% to bat coronavirus/133/2005 (GenBank accession number DQ648794.1) and 75% identity to porcine haemagglutinating encephalomyelitis virus strain VW572 (GenBank accession number DQ011855.1)
The sequence identified is available on the HPA website [7].  In response to this identification, a new set of real-time RT PCR assays were developed [8]. The results of these assays tested on novel coronavirus tissue culture material and clinical samples from this confirmed case are shown in Table 2. 

Table 2. Real-time PCR results of coronavirus samples, September 2012
Click on Table below:

On the basis of the sequence obtained, a maximum likelihood tree (Figure) showed that the virus belongs to the genus Betacoronavirus, with closest relationships to bat coronaviruses HKU4 and HKU5.  Viruses that share more than 90% sequence identity in the conserved replicase domain are considered to belong to the same species by the International Committee on Taxonomy of Viruses (ICTV).  Our sequence comparisons suggested that the virus nucleic acid fragment identified is derived from a novel coronavirus that is distinct from all coronaviruses described to date.

The origin for this novel virus is unknown. Epidemiological human and animal investigations in the region of origin are required to distinguish between an animal reservoir that either directly or indirectly transmits the virus occasionally to humans, and a previously unrecognised endemic infection of humans that causes severe outcomes in a few of those infected. Distinguishing between these possibilities will require wider application of more specific and sensitive molecular assays for coronaviruses, and greater awareness of the possible presence of coronaviruses in human acute severe respiratory illness. Extensive serological testing of potentially exposed human populations and contacts will be a key indicator of the extent of disease due to novel coronaviruses.

Complete document:

Recombinomics: Michigan H3N2v Cases With PB1 E618D and H1N1pdm09 M Gene

October 4, 2012  

The CDC has released a large series of H3N2v sequences from August, 2012 cases, increasing the number of July/August sets to 90.  Included were two sets of sequences from two cases in Michigan collected on August 16.  Sequences from one case, A/Michigan/20/2012, cover seven of the eight gene segments (all except NS), while the second set, A/Michigan/19/2012, from an adult (54M), covered PB1 and PA.  The shared sequences were virtually identical suggesting all 8 gene segments match.  Both PB1 sequences had E618D and were closely related to sequences from 2010 human cases, as was seen in recent swine sequences from June collections in Ohio (A/swine/Ohio/1/2012, A/swine/Ohio/6/2012, A/swine/Ohio/7/2012).

As seen in the Ohio swine sequences, the N2 was closely related to sequences from the first 10 cases in 2011 and were from a lineage found in H1N2 swine.  Moreover, these sequences also had an H1N1pdm09 M gene as well as an H3 gene that was related to human H3N2v sequences from US cases (2009-2012).

The presence of PB1 E618D and H1N1pdm09 M genes in the Ohio swine sequences raised concerns of increased human adaptation, although prior to the release of the Michigan sequences, this combination had not been reported in humans.  All 2012 cases had an H1N1pdm09 M gene, but none had PB1 E618D or the N2 lineage seen in early 2011 cases.  Instead, all had an N2 lineage that circulated in H3N2v swine and was first seen in human H3N2v in sequences from the West Virginia day care center (
(A/West Virginia/06/2011 and A/West Virginia/07/2011).

The presence of PB1 E618D in two cases in Michigan raises concerns of increased transmission.  Michigan reported 5 cases in August and sequences from the first case, A/Michigan/14/2012, was similar to other 2012 H3N2v cases.  However, Michigan has announced a sixth case which has been “under investigation” for several weeks (as noted in the past 3 Michigan flu updates for weeks 36-38).  More information on this case and other cases “under investigation” would be useful.

The two cases with PB1 E618D and an N2 gene found in 2011 cases once again highlights the discordance between human and swine cases.  The N2 gene found in the two 2012 Michigan cases are widespread in swine (including the 4 June cases in Ohio), yet all other reported human H3N2v cases in 2012 have the N2 lineage found in the West Virginia outbreak.  Prior to the explosion of cases in July and August, swine with this N2 as well as H3 and MP which matches the human cases was limited to two examples (in North Carolina and Indiana).

The limited number of human cases with the N2 that is widespread in swine suggests that jumps from swine to human are relatively rare, but the two newly released sequences from Michigan raises concerns that the spread of this novel constellation may be increasing.



[In summary: Worldwide influenza activity from 20 May to 22 Sep 2012 was elevated in the temperate Southern Hemisphere and tropical regions compared with their levels outside the usual influenza season.

In the United States, low levels of seasonal influenza activity were detected, and influenza A (H3N2) viruses were most commonly identified. Antigenic characterization of viral isolates from specimens submitted during the summer demonstrated that the majority of influenza A viruses are antigenically similar to the influenza vaccine strains contained in the current Northern Hemisphere 2012-13 vaccine available for us this season.

More than 300 cases of the influenza A (H3N2) variant virus were detected in 10 states but not elsewhere. The majority of these cases were associated with direct contact with swine.

The majority of recent influenza A viruses are well-matched to the influenza vaccine for this season. Annual influenza vaccination remains the best method for preventing influenza and its associated complications, but the 2012-13 seasonal influenza vaccine does not provide protection against the H3N2v virus. Although community transmission of this H3N2v has not been identified, the potential for this virus to develop the ability to transmit efficiently from person-to-person is of concern. Rapid and intensive investigation of each variant case is necessary to evaluate the spread of disease and the possibility of person-to-person transmission.

 Interested readers should consult the original text via the source URL to obtain details of the literature cited. - Mod.CP
A HealthMap/ProMED-mail map can be accessed at:] 


Date: Fri 5 Oct 2012

Source: NBC News, Associated Press (AP) report [edited]

The potential scope of the meningitis outbreak that has killed at least 5 people widened dramatically Thu 4 Oct 2012, as health officials warned that hundreds, perhaps thousands, of patients who got steroid back injections in 23 states could be at risk. Clinics and medical centers rushed to contact patients who may have received the apparently fungus-contaminated shots and the FDA urged doctors not to use any products at all from the Massachusetts pharmacy that supplied the suspect steroid solution. It is not clear how many patients received tainted injections, or even whether everyone who got one will get sick.

So far, 35 people in 6 states -- Tennessee (25), Virginia (4), Maryland (2), Florida (2), North Carolina (1) and Indiana (1) -- have contracted fungal meningitis, and 5 of them have died, according to the CDC. All had received steroid shots for back pain, a highly common treatment.

In an alarming indication the outbreak could get a lot bigger, Massachusetts health officials said the pharmacy involved, the New England Compounding Center [NECC] of Framingham, MA, has recalled 3 lots consisting of a total of 17 676 single-dose vials of the steroid, preservative-free methylprednisolone acetate. An unknown number of those vials reached 75 clinics and other facilities in 23 states between July 2012 and September 2012, federal health officials said. Several hundred of the vials, maybe more, have been returned unused, a Massachusetts official said.

But many other vials were used. At a clinic in Evansville, Indiana, more than 500 patients got injections from the suspect lots, officials said. At 2 clinics in Tennessee, more than 900 patients, perhaps many more, did.

The investigation began about 2 weeks ago after a case was diagnosed in Tennessee. The time from infection to onset of symptoms is anywhere from a few days to a month, so the number of people stricken could rise.

Investigators this week found contamination in a sealed vial of the steroid at the New England company, according to FDA officials. Tests are under way to determine if it is the same fungus blamed in the outbreak. The company has shut down operations and said it is working with regulators to identify the source of the infection.

"Out of an abundance of caution, we advise all health care practitioners not to use any product" from the company, said Ilisa Bernstein, director of compliance for the FDA's Center for Drug Evaluation and Research.

The type of fungal meningitis involved is not contagious like the more common forms. It is caused by a fungus often found in leaf mold and is treated with high-dose antifungal medications, usually given intravenously in a hospital. The common mold _Aspergillus_ was cultured from 5 patients, the CDC said Thursday [4 Oct 2012].

The New England company is what is known as a compounding pharmacy. These pharmacies custom-mix solutions, creams, and other medications in doses or in forms that generally aren't commercially available. Other compounding pharmacies have been blamed in recent years for serious and sometimes deadly outbreaks caused by contaminated medicines. Compounding pharmacies are not regulated as closely as drug manufacturers, and their products are not subject to FDA approval.

A national shortage of many drugs has forced doctors to seek custom-made alternatives from compounding pharmacies. The New England company at the center of the outbreak makes dozens of other medical products, state officials said. But neither the company nor health officials would identify them.

The company said in a statement Thursday [4 Oct 2012] that despite the FDA warning, "there is no indication of any potential issues with other products." It called the deaths and illnesses tragic and added: "The thoughts and prayers of everyone employed by NECC are with those who have been affected."

A 2011 state inspection of the Framingham facility gave the business a clean bill of health.

[Byline: Mike Stobbe]


[editing in red is mine]
In this update:

[1] UK - HPA investigation findings, Eurosurveillance

[2] UK - Clinical and laboratory findings, Eurosurveillance

[3] Saudi Arabia - ongoing investigations, newswire

[4] USA - current recommendations, MMWR


[1] UK - HPA investigation findings, Eurosurveillance

Date: 4 Oct 2012

Source: Eurosurveillance Volume 17, Issue 40, 4 Oct 2012 [edited]

Rapid communications

The United Kingdom Public Health response to an imported laboratory confirmed case of a novel coronavirus in September 2012


On [22 Sep 2012], a novel coronavirus, very closely related to that from a fatal case in Saudi Arabia 3 months previously, was detected in a previously well adult transferred to intensive care in London from Qatar with severe respiratory illness. Strict respiratory isolation was instituted. Ten days after last exposure, none of 64 close contacts had developed severe disease, with 13 of 64 reporting mild respiratory symptoms. The novel coronavirus was not detected in 10 of 10 symptomatic contacts tested.

The outbreak of severe acute respiratory syndrome (SARS) in 2003, which led to 8422 cases and 916 deaths worldwide [1], highlighted the potential for newly emerging zoonotic coronaviruses to transmit from person to person, especially in healthcare settings, and to cause severe human illness.

On [22 Sep 2012], the Health Protection Agency (HPA) in London, United Kingdom (UK), confirmed infection with a novel coronavirus in a patient in a London hospital who had been transferred from Qatar 11 days previously. This patient represents the 2nd confirmed case of severe acute respiratory illness caused by this novel coronavirus. The 1st case was identified in a Saudi Arabian national who died in June 2012 [2,3]. We describe the exposure history, the public health response and follow-up of close contacts of the case in London.

Case exposure history and laboratory investigations

The case is a previously well 49-year-old male who travelled to Saudi Arabia from [31 Jul 2012 to 18 Aug 2012], where he and several of his travelling companions developed rhinorrhoea and fever (Figure 1). On [18 Aug 2012], he travelled to Qatar, where his respiratory symptoms resolved 3 days later. While in Qatar, he spent time on a farm, where he keeps camels and sheep, although no direct contact with these animals was reported.

On [3 Sep 2012], he reported a mild respiratory illness. Six days later, he required hospitalisation due to development of bilateral pneumonia. His condition worsened, and he subsequently required intubation and ventilation. On [12 Sep 2012], he was transferred by air ambulance to an intensive care unit in London, where acute renal impairment was also detected. Due to further deterioration, he was transferred to another London hospital on [20 Sep 2012] [3].

Following the report on ProMED-mail on [20 Sep 2012] [2] of the detection of a novel coronavirus (until further taxonomic denomination, herewith referred to as hCoV-EMC) in a Saudi Arabian patient who had died from severe respiratory illness and renal failure, and as no diagnosis had been established despite investigations for common causes of pneumonia and pathogens endemic to the Middle East, the patient in London was investigated for novel coronavirus infection. On [21 Sep 2012], a coronavirus was detected in respiratory tract samples using a pan-coronavirus PCR assay, and on [22 Sep 2012] sequencing of the PCR amplicon showed a sequence very closely related to the hCoV-EMC detected in the earlier patient from Saudi Arabia [4]. The virus belongs to the genus beta-coronavirus, with closest relationship to bat coronaviruses [4].

Figure 1. Timeline of disease and travel history of novel coronavirus case, London, August to September 2012 [available at above URL link]

Public health management

The identification of a novel coronavirus of the same group as the SARS-CoV, with 2 clinically severe human cases including one fatality, led to a public health response being mounted to isolate the case, identify and test close contacts and to prevent onward transmission. Once the patient was found to have a novel coronavirus infection, he was isolated in a negative-pressure single room, and full personal protective equipment (PPE), including gowns, gloves, eye protection and high filtration masks were worn by staff and other contacts. Interim case and close contact definitions were developed [5].

A possible case was defined as: any person with acute respiratory syndrome which includes fever (greater than or equal to 38 C), or history of fever and cough requiring hospitalisation, or with suspicion of lower airway involvement (clinical or radiological evidence of consolidation) not explained by another infection or aetiology with history of either travel to or residence in Saudi Arabia or Qatar, or close contact with a confirmed case in the 10 days before onset of illness.

A close contact was defined as the following:

- Healthcare and social care workers: workers who provided direct clinical or personal care or examination of a symptomatic confirmed case or within close vicinity of an aerosol generating procedure AND who was not wearing full personal protective equipment (PPE) at the time. Full PPE is defined as a correctly fitted high filtration mask (FFP3), gown, gloves and eye protection.

- Household: any person who had prolonged face-to-face contact with the confirmed case(s) any time during the illness after onset in a household setting.

- Other close contacts: any person who had prolonged face-to-face contact with a confirmed case while symptomatic in any other enclosed setting and who was not wearing a mask, e.g. school, visitor to the hospital to the bed side of a symptomatic confirmed case.

These definitions were used as the basis for identifying further possible cases and contacts. Guidelines were developed on the investigation and public health management of these cases and their close contacts.

Identification and follow-up of individuals who had close contact with the case at any time during his symptomatic period from entry into the UK up until implementation of full isolation on [21 Sep 2012] (including healthcare workers and family), was rapidly initiated by HPA staff and staff from the London hospitals' Infection Control Teams. Close contacts were followed up for a period of 10 days from the date of last exposure to the index case. If contacts developed respiratory illness in this period, they were asked to self-isolate in their homes (or were isolated in hospital if requiring admission).

The hospital in Qatar was informed to allow them to initiate appropriate follow-up for those who had been in contact with the patient.

HPA rapidly developed and published advice to health professionals, the public and travellers [5]. The case was immediately reported under the International Health Regulations to the World Health Organisation and through the European Union Early Warning and Response System (EWRS). Extensive laboratory work was undertaken to characterise the virus and develop new diagnostic tools [3].

Initial epidemiological investigation and preliminary findings

Close contacts of the case were followed up to determine the transmissibility of this novel coronavirus. This included collection of information on clinical illness, virological swabbing of contacts who had respiratory symptoms, and collection of paired sera from all contacts to determine whether there was evidence of recent infection.

It is likely that the patient's infection was acquired in Qatar as he was in Qatar for the 16 days prior to the onset of his most recent respiratory illness in September [2012]. The earlier, mild upper respiratory tract infection, which began during his visit to Saudi Arabia, resolved 2 weeks before onset of the present illness.

By [4 Oct 2012], tracing of contacts had identified 64 persons, among healthcare workers, family and friends, who were reported to have been in close contact with the confirmed case while he was symptomatic in the UK (Figure 2). Ten days after the date of last respective exposure, none of the close contacts had developed severe respiratory disease requiring hospital admission. Interim results have identified 13 close healthcare worker contacts with mild, self-limiting respiratory symptoms. These contacts were self-isolated in their homes until asymptomatic. In addition, one hospitalised patient who had potential contact with the case and subsequently became unwell was identified and subsequently tested negative using a pan-coronavirus assay [4]. The novel coronavirus has not been detected in any of the 10 symptomatic healthcare worker contacts tested by [4 Oct 2012].

Four possible cases with a history of recent travel from Saudi Arabia or Qatar have also been identified and investigated in the UK since active case finding commenced. Although the likelihood of novel coronavirus infection in any of these was considered low, strict infection control measures were taken. For 3 of them, samples were available, and the novel coronavirus was not detected. A 4th case, who died at the beginning of September [2012], remains under investigation.

Figure 2. Outcome of close contact follow-up 10 days or more since last exposure to index case with a novel coronavirus infection, London, September 2012 (n=64) [available at above URL link]

Public health implications

We present a case of severe respiratory illness resulting from a novel coronavirus acquired in the Middle East. The clinical picture is similar to that of a case previously described from Saudi Arabia and caused by a closely related virus. Although cases of SARS, for which the causative agent SARS-CoV is in the same group of coronaviruses, were reported with incubation periods beyond 10 days, 95 percent were reported to have an incubation period of less than 10 days [6]. In the light of this finding, the case of novel coronavirus that we report appears to have been acquired in Qatar based on the known time course of the patient's infection and other available information, unless the illness had an unusual biphasic nature or a very long incubation period.

After 10 days of follow-up, there has been no confirmed evidence of ongoing person-to-person transmission resulting in severe disease or milder laboratory confirmed infection among close contacts, despite extensive active contact tracing. Completion of case-contact investigation, including serological testing when available, will determine whether mild or asymptomatic infection among close contacts has occurred. In addition, serological investigation in the countries of origin of the 2 confirmed cases should be considered to look for evidence of possible previous infection in the general population. Studies in animals are also necessary to determine whether there is an animal reservoir for this infection and what it might be.

Early detection and investigation of cases of severe respiratory illness among travellers returning from countries where infection with novel coronavirus has been reported and their close contacts will support the further elucidation of the epidemiological characteristics of this novel virus. An outbreak of severe respiratory illness of unknown aetiology was reported from the Middle East earlier in 2012 [7]. Work needs to be undertaken to determine whether a novel coronavirus has been circulating more widely in the general population in the Middle East already for some time or whether the virus was more recently introduced from an unknown animal reservoir.


1. World Health Organization (WHO). WHO final summary SARS, 15 August 2003: Summary table of SARS cases by country, 1 November 2002 - 7 August 2003. Geneva; WHO; 2003. Available from:

2. ProMED-mail. Novel coronavirus - Saudi Arabia: human isolate. Archive Number: 20120920.1302733. 20 September 2012. Available from:

3. Corman VM, Eckerle I, Bleicker T, Zaki A, Landt O, Eschbach-Bludau M, et al. Detection of a novel human coronavirus by real-time reverse-transcription polymerase chain reaction. Euro Surveill. 2012;17(39):pii=20285. Available from:

4. Bermingham A, Chand MA, Brown CS, Aarons E, Tong C, Langrish C, et al. Severe respiratory illness caused by a novel coronavirus, in a patient transferred to the United Kingdom from the Middle East, September 2012. Euro Surveill. 2012;17(40):pii=20290. Available from:

5. Health protection Agency (HPA). Algorithm for investigation and management of possible cases of severe acute respiratory illness associated with a novel coronavirus. London; HPA; 2012. Available from:

6. Lessler J, Reich NG, Brookmeyer R, Perl TM, Nelson KE, Cummings DA. Incubation periods of acute respiratory viral infections: a systematic review. Lancet Infect Dis. 2009; 9(5):291-300. [abstract available at:]

7. European Centres for Disease Control (ECDC). Communicable Disease Threats Report (Week 18, 29 April-5 May 2012). Stockholm; ECDC: 2012 Available from:

[Reported by: R G Pebody1, M A Chand1, H L Thomas1,2,3, H K Green1, N L Boddington1, C Carvalho1,3, C S Brown1, S R Anderson1, C Rooney1, E Crawley-Boevey1, D J Irwin1, E Aarons4, C Tong4, W Newsholme4, N Price4, C Langrish4, D Tucker4, H Zhao1, N Phin1, J Crofts1, A Bermingham1, E Gilgunn-Jones1, K E Brown1, B Evans1, M Catchpole1, J M Watson1

1. Health Protection Agency (HPA), London, United Kingdom

2. Field Epidemiology Training Programme (FETP), Health Protection Agency, London, United Kingdom

3. European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control, (ECDC), Stockholm, Sweden

4. Guy's and St Thomas' NHS Foundation Trust and King's Health Partners, London, United Kingdom]

Human SARS Virus Genomic Replikin™ Count Rises to the Level that Preceded the 2003 Lethal SARS Outbreak


    Human SARS Virus Genomic Replikin™ Count Rises to the Level that Preceded the 2003 Lethal SARS Outbreak (via PR Newswire)

       LONDON, Oct. 5, 2012 /PRNewswire/ -- The identification of the virus responsible for a second case of SARS-like respiratory virus, "London1_novel CoV 2012", has raised concerns over the risk of the disease spreading (1). These concerns may be justified given the observed rise in virus's genomic Replikin…



HPA: Epidemiological protocols and forms for comprehensive assessment of early novel coronavirus cases and their close contacts in the United Kingdom

“The First Few Hundred (FF100)” Enhanced Case and Contact Protocol v3.0

The epidemiological and virological investigation of the first cases of acute respiratory infection associated with novel coronavirus and their close contacts is essential in order to inform guidance and policy in directing the United Kingdom’s (UK) public health response.
The epidemiological methods to guide data collection for the comprehensive assessment of the “first few hundred cases and their close contacts” are set out in this document. The protocol outlines the investigation of persons with laboratory confirmed novel coronavirus infection, along with their close contacts.

Swine flu outbreak in Midwest prompts reminders about safety precautions at SC State Fair

[Please see the right side-bar for more information on H3N2v]

Saturday, Oct. 06, 2012
South Carolina health officials are taking advantage of publicity about a new strain of swine flu that sickened hundreds of people in Indiana and Ohio this summer to remind people to take precautions while visiting livestock exhibitions.

Avoid petting pigs in those exhibitions, and wash your hands after touching any livestock or their enclosures.

The S.C. State Fair, which opens Wednesday, includes the largest of the dozens of public livestock shows in the state. The State Fair for years has posted warning signs in livestock enclosures about the danger of disease transmission, and hand-washing stations popped up in the barns a few years ago during the last swine flu scare.

Humans and pigs both have flu viruses, and usually they don’t affect the other species. But every once in a while a variant develops that can jump from pigs to humans or humans to pigs. A H3N2 variant that popped up last year in pigs began moving to humans this year.

Symptoms in people have been mild, and the variant hasn’t jumped easily from person to person. Spread has been limited to people who have had direct contact with infected pigs. About 305 cases have been confirmed in 10 states, none in the Southeast, according to the Centers for Disease Control and Prevention.

 Full article:

Read more here:

Read more here:


Public response to the 2009 influenza A H1N1 pandemic: a polling study in five countries

The Lancet Infectious Diseases, Early Online Publication, 5 October 2012
doi:10.1016/S1473-3099(12)70206-2Cite or Link Using DOI
Dr Gillian K SteelFisher PhD a Corresponding AuthorEmail Address, Robert J Blendon ScD a b, Johanna RM Ward MSc a, Robyn Rapoport MA c, Emily B Kahn PhD d, Katrin S Kohl MD e



Many important strategies to reduce the spread of pandemic influenza need public participation. To assess public receptivity to such strategies, we compared adoption of preventive behaviours in response to the 2009 H1N1 influenza pandemic among the public in five countries and examined whether certain non-pharmaceutical behaviours (such as handwashing) were deterrents to vaccination. We also assessed public support for related public health recommendations.


We used data from simultaneous telephone polls (mobile telephone and landline) in Argentina, Japan, Mexico, the UK, and the USA. In each country, interviews were done in a nationally representative sample of adults, who were selected by the use of random digit dial techniques. The questionnaire asked people whether or not they had adopted each of various preventive behaviours (non-pharmaceutical—such as personal protective and social distancing behaviour—or vaccinations) to protect themselves or their family from H1N1 at any point during the pandemic. Two-tailed t tests were used for statistical analysis.


900 people were surveyed in each country except the USA where 911 people were contacted. There were wide differences in the adoption of preventive behaviours between countries, although certain personal protective behaviours (eg, handwashing) were more commonly adopted than social distancing behaviours (eg, avoiding places where many people gather) across countries (53—89% vs 11—69%). These non-pharmaceutical behaviours did not reduce the likelihood of getting vaccinated in any country. There was also support across all countries for government recommendations related to school closure, avoiding places where many people gather, and wearing masks in public.


There is a need for country-specific approaches in pandemic policy planning that use both non-pharmaceutical approaches and vaccination.


US Centers for Disease Control and Prevention and the National Public Health Information Coalition.

EMPRES-i FAO Listing of Low Pathogenic Avian Influenza H5N1 Domestic & Wild Poultry Outbreaks in the U.S. & Mexico Since 2004

From EMPRES-i FAO (Global Animal Disease Information System) This is a listing of Low Pathogenic Avian Influenza H5N1 Outbreaks in wild and domestic poultry in the United States since 2004.

Click on chart to enlarge:

Friday, October 5, 2012

CDC: Persons with Meningitis Linked to Epidural Steroid Injections, by State

United States map of Persons with meningitis linked to epidural steroid injections.
Persons with meningitis linked to epidural steroid injections:
Florida: 2 cases
Indiana: 3 cases
Maryland: 2 cases, including 1 death
Michigan: 4 cases
North Carolina: 1 case
Tennessee:29 cases, including 3 deaths
Virginia: 6 cases, including 1 death

Multistate Meningitis Outbreak Investigation

October 5, 2012
CDC is coordinating a multistate investigation of meningitis among patients who received epidural steroid injections (medication injected into the spine). Several of these patients have had strokes related to the meningitis. In several patients, the meningitis was found to be caused by a fungus that is common in the environment but rarely causes meningitis. This form of meningitis is not contagious. The source of the fungus has not yet been identified, and the cause of infections in the other patients is still being assessed.

CDC Recommendations for Clinicians:

Meningitis and Stroke Associated with Potentially Contaminated Product: Health Alert Network (HAN) Adobe PDF file [PDF - 207 KB]
Interim Instructions for Clinical Teams Regarding Diagnostic Testing Adobe PDF file [PDF - 76 -KB]
Interim Treatment Options Adobe PDF file [PDF - 80 KB]

 Additional Federal Agencies Involved: FDAExternal Web Site Icon
External Web Site Icon
Patient Information:
Is the source of the outbreak known?
CDC is investigating medications and products that are associated with this outbreak of meningitis. At this point, there is not enough evidence to determine the original source of the outbreak, however there is a link to an injectable steroid medication.  The lots of medication that were given to patients have been recalled by the manufacturer.
What are the states that received the implicated product?
California, Connecticut, Florida, Georgia, Idaho, Illinois, Indiana, Maryland, Michigan, Minnesota, North Carolina, New Hampshire, New Jersey, Nevada, New York, Ohio, Pennsylvania, Rhode Island, South Carolina, Tennessee, Virginia, Texas, and West Virginia
What is meningitis?
Meningitis refers to inflammation of the protective membranes covering the brain and spinal cord known as the meninges. The inflammation is usually caused by an infection frequently with a bacteria or virus, but meningitis can also be caused by less common pathogens such as fungi. The severity of illness and the treatment for meningitis differ depending on the cause. Thus, it is important to know the specific cause of meningitis.
What is fungal meningitis?
Fungal meningitis occurs when the protective membranes that cover the brain and spinal cord are infected with a fungus.  Fungal meningitis can develop after a fungus spreads through the bloodstream from somewhere else in the body, as a result of the fungus being introduced directly into the central nervous system, or by direct extension from an infected body site next to the central nervous system.
Is fungal meningitis common after epidural injections?
Epidural injections are generally very safe procedures, and complications are rare.  Fungal meningitis is an extremely rare cause of meningitis overall, including after epidural injections. The type of epidural medication given to patients affected by this outbreak is not the same type of medication as that given to women during childbirth.
What are the symptoms of fungal meningitis?
Symptoms of fungal meningitis are similar to symptoms of other forms of meningitis, however they often appear more gradually and can be very mild at first.  In addition to typical meningitis symptoms, like headache, fever, nausea, and stiffness of the neck, people with fungal meningitis may also experience confusion, dizziness, and discomfort from bright lights. Patients might just have one or two of these symptoms.

U.S. government names SARS a select agent, restricting labs that work on virus


The Centers for Disease Control has added SARS to the list of select agents in the United States, a move designed to try to ensure the virus stays within the confines of highly regulated laboratories.
The addition, which the CDC first proposed over two years ago, was given legal status this week when the revised select agent list was published in the U.S. Federal Registry.
The timing of the move is both ironic and co-incidental.
SARS has faded from view since its frightening outbreak was contained mid-way through 2003. Before the virus was brought under control, however, 32 countries reported a total of 8,422 cases and 916 deaths, according to the World Health Organization.
But there has been a resurgence of SARS talk in the past 10 days or so triggered by the World Health Organization's announcement that a newly discovered coronavirus has killed a Saudi Arabian man and severely sickened a man from Qatar. The Qatari remains in critical condition in a British hospital.
SARS is a member of the coronavirus family.
"Should SARS CoV" - coronavirus - "be intentionally or accidentally introduced into the population of the United States, as evidenced by the 2002-2003 multi-national outbreaks, the consequences could be significant," CDC spokesperson Jason McDonald explained in an emailed response to questions about the motivation for the move.
Adding the SARS virus to this list means only U.S. laboratories registered with the Federal Select Agent Program can work on the virus.
Laboratories that aren't registered with the program but which have samples of the SARS virus or SARS genetic material must either apply for status with the program, transfer that material to a registered laboratory or provide the program with proof that they have destroyed the material.
One of the key figures behind Canada's SARS fight said the move is a wise one.
"I think there's reason to be concerned and reason to be smart about it. And do you have to go to this length? Well, probably," said Dr. Donald Low, chief microbiologist at Toronto's Mount Sinai Hospital.
Mount Sinai, which treated many SARS patients, for a period had a collection of SARS samples under lock and key in special freezers.
"I don't think we have any left now. I think we got rid of all the tissue and everything," Low said, adding the material was incinerated.
Canada was one of the countries worst hit by SARS, with 375 probable and suspected cases and 44 deaths. Most of the cases occurred in Toronto.
Canada does not have a select agent program. In this country, research with the SARS virus and other disease agents is governed by the Human Pathogens and Toxins Act, which was enacted in 2009. It classifies SARS as a "risk group 3 pathogen". More deadly virus such as Ebola are risk group 4.
During the SARS outbreak, infectious disease experts hoped that if they could halt spread in people, they could stop what was clearly an animal virus from establishing itself in the human population. The idea was to put SARS "back in the box."
The theory proved correct. When scientists learned how the virus spread and hospitals learned how to spot SARS cases, a combination of quarantine for people exposed to the virus and protective gear for health-care workers broke the chains of transmission.
But the virus has reappeared three times since SARS was contained, each time the result of a lab accident. At least 13 people - six infected in labs and seven contacts of those lab workers - contracted SARS in three separate lab accidents in the fall of 2003 and spring of 2004. Two of the accidents were in China and the third was in Singapore.
The report on the revisions to the select agent list in the Federal Registry acknowledges that when it first proposed adding SARS, the CDC received a few complaints from universities, public health laboratories and government and commercial facilities.
The critics claimed it would hinder research on the virus, calling the requirements of registering for and complying with the Select Agent Program "an onerous burden."
But other responses supported the move and in the end the CDC pushed on with the proposal. The lethality of the virus - about 11 per cent of cases died - as well as the fact there are no vaccines to stop it or drugs to treat it are among the reasons the CDC cited to support its decision.
The arrival on the scene of a new coronavirus may awaken interest in SARS research. And the move to restrict which labs can work on the virus and under what circumstances may reignite criticism in some quarters of the U.S. research community.
But Dr. Michael Osterholm of the Center for Infectious Diseases Research and Prevention at the University of Minnesota said the emergence of the new virus underscores why it is important to be careful with SARS.
"It just points out that coronaviruses can and will likely return ... including the SARS virus. So I think the attention paid to the coronavirus in general is appropriate," he said.
"It's important that we just not let this virus get out again."
McDonald said CDC records suggest 123 entities in the United States had SARS viruses at some point in time.
Of those, 66 are already registered with the select agent program. Of the remainder, only four still possess SARS coronaviruses. "And we are working with them to get registered with the select agent program."
Despite the fact SARS is on the select agent list, U.S. government regulations do not require researchers who work with the virus to do so in the highest containment setting, BSL4 laboratories. Most SARS research can be done in BSL2 labs, though some more dangerous experiments must be done in BSL3, McDonald said.

Wednesday, October 3, 2012

When New Diseases Emerge, Experts Are Faster On The Uptake

October 3, 2012
Scientists have recently discovered three new human viruses.

One, from the Arabian Peninsula, causes severe pneumonia and kidney failure. Another sent two Missouri farmers to the hospital with severe fatigue and low blood platelets. The third, in central Africa, causes a new kind of hemorrhagic fever.

The most striking thing about all three new viruses is that they were found on the basis of just two or three human cases. That's a long way from where the world was 10 years ago, when another new virus popped up in Asia and quickly went global.


Tuesday, October 2, 2012

Philippine Airport Officials on Alert After SARS Threat

[We previously reported on the Philippine Health Minister's comments here]

October 2, 2012
Manila: Alarmed by coronavirus, a new strain of virus that causes severe acute respiratory syndrome (SARS), Philippine health department ordered authorities to revive machines that monitor temperatures of people who arrive at air and sea ports nationwide, a senior official said.
“The department of health is watching coronavirus closely because it’s a SARS-like virus,” explained Abigail Valte, deputy presidential spokesperson.
“A team from the Bureau of Quarantine is also on alert for any possible illnesses that may be carried by (Filipino) citizens or tourists who come to the country,” said Valte, adding, “We have dealt with illnesses like that [in the past].”
But the World Health Organization (WHO) has not advised special screening of temperature of people arriving at air and seaports as a measure to contain the spread of coronavirus.


Monday, October 1, 2012

A new rhabdovirus from a patient with hemorrhagic fever

1 October 2012

Viral hemorrhagic fevers in AfricaHemorrhagic fevers are among the most graphic viral diseases, inspiring movies, novels, and a general fear of infection. They are characterized by an abrupt onset and a striking clinical course involving bleeding from the nose and mouth, vomiting with blood, and bloody diarrhea. The most famous hemorrhagic fevers are produced by infection with filoviruses like Ebola virus, but members of three other viral families – Arenaviridae, Bunyaviridae, and Flaviviridae – can also cause this syndrome. The isolation of a novel rhabdovirus from an African with hemorrhagic fever suggests that members of a fifth viral family can also cause this disease.

Three cases of hemorrhagic fever that occurred in the spring of 2009 were noteworthy because none of the typical viral suspects could be detected in one patient. Two were young (13, 15 year old) students in the village of Mangala, Bas-Congo province, Democratic Republic of Congo. They lived near each other and went to the same school. Both arrived at the local health center with typical symptoms of hemorrhagic fever, and both died 2-3 days later. The third case was a 32 year old male nurse at the health center who was involved in the care of the other two patients. He developed symptoms of hemorrhagic fever but recovered within a few days.
Deep sequence analysis of RNA extracted from the serum of patient #3 revealed the presence of a novel rhabdovirus, provisionally named Bas-Congo virus (BASV). Phylogenetic analyses reveal that BASV is substantially diverged from the two main human rhabdoviruses, rabies virus and Chandipura virus (ten of the 160 known species of rhabdoviruses have been isolated from humans). BASV is more related to viruses of the Tibrogargan group and the Ephemerovirus genus, which contain arthropod-borne viruses that infect cattle, but clusters separately in an independent branch of the phylogenetic tree.


Killers on the loose: the deadly viruses that threaten human survival

Could the next big animal-human disease wipe us out?

The Next Big One is a subject that disease scientists around the world often address. The most recent big one is Aids, of which the eventual total bigness cannot even be predicted – about 30 million deaths, 34 million living people infected, and with no end in sight. Fortunately, not every virus goes airborne from one host to another. If HIV-1 could, you and I might already be dead. If the rabies virus could, it would be the most horrific pathogen on the planet. The influenzas are well adapted for airborne transmission, which is why a new strain can circle the world within days. The Sars virus travels this route, too, or anyway by the respiratory droplets of sneezes and coughs – hanging in the air of a hotel corridor, moving through the cabin of an aeroplane – and that capacity, combined with its case fatality rate of almost 10%, is what made it so scary in 2003 to the people who understood it best.
A poultry farm in China A worker disinfects a poultry farm in China after an outbreak of the deadly H5N1 strain of bird flu in 2006. Photograph: China Photos/Getty Images
Human-to-human transmission is the crux. That capacity is what separates a bizarre, awful, localised, intermittent and mysterious disease (such as Ebola) from a global pandemic. Have you noticed the persistent, low-level buzz about avian influenza, the strain known as H5N1, among disease experts over the past 15 years? That's because avian flu worries them deeply, though it hasn't caused many human fatalities. Swine flu comes and goes periodically in the human population (as it came and went during 2009), sometimes causing a bad pandemic and sometimes (as in 2009) not so bad as expected; but avian flu resides in a different category of menacing possibility. It worries the flu scientists because they know that H5N1 influenza is extremely virulent in people, with a high lethality. As yet, there have been a relatively low number of cases, and it is poorly transmissible, so far, from human to human. It'll kill you if you catch it, very likely, but you're unlikely to catch it except by butchering an infected chicken. But if H5N1 mutates or reassembles itself in just the right way, if it adapts for human-to-human transmission, it could become the biggest and fastest killer disease since 1918.

It got to Egypt in 2006 and has been especially problematic for that country. As of August 2011, there were 151 confirmed cases, of which 52 were fatal. That represents more than a quarter of all the world's known human cases of bird flu since H5N1 emerged in 1997. But here's a critical fact: those unfortunate Egyptian patients all seem to have acquired the virus directly from birds. This indicates that the virus hasn't yet found an efficient way to pass from one person to another.

Two aspects of the situation are dangerous, according to biologist Robert Webster. The first is that Egypt, given its recent political upheavals, may be unable to staunch an outbreak of transmissible avian flu, if one occurs. His second concern is shared by influenza researchers and public health officials around the globe: with all that mutating, with all that contact between people and their infected birds, the virus could hit upon a genetic configuration making it highly transmissible among people.
"As long as H5N1 is out there in the world," Webster told me, "there is the possibility of disaster… There is the theoretical possibility that it can acquire the ability to transmit human-to-human." He paused. "And then God help us."

We're unique in the history of mammals. No other primate has ever weighed upon the planet to anything like the degree we do. In ecological terms, we are almost paradoxical: large-bodied and long-lived but grotesquely abundant. We are an outbreak.

And here's the thing about outbreaks: they end. In some cases they end after many years, in others they end rather soon. In some cases they end gradually, in others they end with a crash. In certain cases, they end and recur and end again. Populations of tent caterpillars, for example, seem to rise steeply and fall sharply on a cycle of anywhere from five to 11 years. The crash endings are dramatic, and for a long while they seemed mysterious. What could account for such sudden and recurrent collapses? One possible factor is infectious disease, and viruses in particular.

The dangers presented by zoonoses are real and severe, but the degree of uncertainties is also high. There's not a hope in hell, as Webster told me, of predicting the nature and timing of the next influenza pandemic. Too many factors vary randomly.

I have asked not just Webster, but many other eminent disease scientists the same two-part question: 1) will a new disease emerge, in the near future, sufficiently virulent and transmissible to cause a pandemic on the scale of Aids or the 1918 flu, killing tens of millions of people?; and 2) if so, what does it look like and whence does it come? Their answers to the first part have ranged from maybe to probably. Their answers to the second have focused on various viruses prone to mutation, especially those for which the reservoir host is some kind of primate.
But the difficulty of predicting precisely doesn't oblige us to remain blind, unprepared and fatalistic. We can at least be vigilant; we can be well prepared and quick to respond. The scientists are on alert. They are our sentries. But we, too, should understand in some measure the basic outlines and dynamics of the situation. We should appreciate that these recent outbreaks of new diseases, as well as the recurrence and spread of old ones, are part of a larger pattern, and that humanity is responsible for generating that pattern. We should recognise that they reflect things that we're doing, not just things that are happening to us.

Link to complete article:

Sunday, September 30, 2012

WHO: Revised interim case definition – novel coronavirus

Interim case definition as of 29 September 2012

Case finding and classification scheme for Severe Acute Respiratory Infections associated with novel coronavirus infection:

The following scheme is recommended for identifying cases that should be tested for infection with the novel coronavirus recently described. The goals of this scheme are to ensure a systematic approach to appropriate identification and investigation of patients who may be infected with the virus without overburdening health care systems with unnecessary testing. It should be noted that this information was developed based on data from two confirmed cases and as such some degree of clinical judgment is required where individual cases are concerned.

Patients to be investigated (referred to as “Patient Under Investigation”):

  • A person with an acute respiratory infection, which may include fever (≥ 38°C , 100.4°F) and cough; AND
  • suspicion of pulmonary parenchymal disease (e.g. pneumonia or Acute Respiratory Distress Syndrome (ARDS)) based on clinical or radiological evidence of consolidation; AND
  • travel to or residence in an area where infection with novel coronavirus has recently been reported or where transmission could have occurred;* AND
  • not already explained by any other infection or aetiology, including all clinically indicated tests for community-acquired pneumonia according to local management guidelines.

Management of Patients Under Investigation:

Patients falling into this category should undergo routinely available laboratory tests as clinically indicated according to local management guidelines for Community-Acquired Pneumonia to determine the presence of other potential primary aetiologies of pneumonia. Examples of other aetiologies might include streptococcus pneumoniae, hemophilus influenza type B, legionella pneumophila, other recognized primary bacterial pneumonias, influenza, and respiratory syncytial virus. It is not necessary to wait for all test results for other pathogens to be available before testing for novel coronavirus. In addition, patients with a clear history and clinical presentation consistent with chemical pneumonitis or smoke inhalation should not be considered as a patient under investigation.
If the respiratory disease is unexplained, appropriate clinical specimens should be sent for laboratory investigation. Rapid progress has been made in the characterization of the novel coronavirus, and in the development of sensitive and specific diagnostic assays. WHO is collaborating with partner laboratories to make these available as quickly as possible. It is anticipated that the first batch of reagents, together with information and testing algorithms, will be available for urgent testing within the coming days.
Until then, WHO is able to provide contact information of laboratories willing and able to test for the presence of the novel coronavirus. For further details, national authorities should contact their respective International Health Regulations Contact Point at their WHO Regional Office.
Appropriate infection control measures should be instituted while the patient is under investigation. Should Member States require further guidance on Infection Prevention and Control, please refer to WHO interim guidelines on Infection prevention and control of epidemic- and pandemic-prone acute respiratory diseases in health care (WHO/CDS/EPR/2007.6).

Management of case contacts

Any person who has had close contact** with a probable or confirmed case while the probable or confirmed case was ill should be carefully monitored for the appearance of respiratory symptoms. If symptoms develop with the first 10 days following the contact, the individual should be considered a “Patient Under Investigation” regardless of the severity of illness and investigated accordingly.
If laboratory data, including histopathological examination of fatal cases, cannot be obtained because the patient has died before specimens are taken, clinical specimens cannot otherwise be obtained, or appropriate laboratory testing for other pathogens is not available, then the patient may meet criteria for “Probable Case” as defined below.

Case definitions for reporting

Probable Case

  • A person fitting the definition above of a “Patient Under Investigation” with clinical, radiological, or histopathological evidence of pulmonary parenchyma disease (e.g. pneumonia or ARDS) but no possibility of laboratory confirmation either because the patient or samples are not available or there is no testing available for other respiratory infections, AND
  • close contact** with a laboratory confirmed case, AND
  • not already explained by any other infection or aetiology, including all clinically indicated tests for community-acquired pneumonia according to local management guidelines.

Confirmed Case

A person with laboratory confirmation of infection with the novel coronavirus.


WHO requests that probable and confirmed cases be reported within 24 hours of being classified as such, through the regional focal point for International Health Regulations at the appropriate WHO Regional Office.

* Currently, these areas would include only Qatar and Saudi Arabia (as of 29 September 2012).
** Close contact includes:
  • anyone who provided care for the patient including a health care worker or family member, or had other similarly close physical contact;
  • anyone who stayed at the same place (e.g. lived with, visited) as a probable or confirmed case while the case was symptomatic.

Seasonal Influenza vs. Variant Influenza

This is last weeks chart of the Seasonal Influenza thru the CDC. To view the weekly stats of our seasonal flu (chart below), click on the category in the right side bar entitled:  "Worldwide Update on Influenza Activity".    In the chart below, the 2009 H1N1 is our seasonal H1N1 from the pandemic in 2009.  The A(H3) is part of our seasonal flu, and therefore part of the flu shot that you receive.  I don't know what would be in the A (Subtyping not performed) statistic below, and the B is also part of our normal Seasonal Flu, and covered in our yearly flu shots.

As part of the reorganization of this blog.I have simplified the page.  Specifically,  the right side-bar has been organized to  categorize the influenza strains that post a danger that are not part of our weekly seasonal influenza surveillance.  Note the list of influenza's. They are all found on the right side-bar of this blog. You can read about them and familiarize yourself with them.

  1. Coronavirus - This new coronavirus has been laboratory confirmed in only two cases globally to date: both occurred between July - September 2012.  Tranmission appears to be very limited as, if it were very contagious, we would have expected to have seen more cases in other countries or the people caring for these two cases, the first of which occurred over three months ago.
  2. H1N1 Ontario  -  The H1N1 variant influenza virus (H1N1v) is a non-human influenza virus that normally circulates in animals and rarely infects humans. When these viruses infect humans, they are termed “variant” viruses.
    The H1N1v virus doesn't spread easily from swine to people—and even less easily from person to person. In most cases, the virus causes only mild illness in people.  Currently the human case in Ontario is in critical condition.
  3. H1N1v  -  A recently adopted naming convention for viruses that commonly circulate in swine uses a “v” (for “variant”) when these viruses infect humans, regardless of whether the virus contains the 2009 H1N1 M gene. Following this convention, the Wisconsin virus will be called H1N1v.  The virus identified in Wisconsin has genes from avian, swine and human influenza viruses, making it a so-called “triple reassortant” (tr) virus. Triple reassortant viruses have been circulating in U.S. swine since the 1990s. However the virus detected in Wisconsin is different from earlier triple reassortant influenza A H1N1 viruses in swine (tr-H1N1) in that it has acquired the matrix [M] gene) from the 2009 influenza A (H1N1) virus.
  4. H3N2v  -  This genetic change (acquisition of the 2009 H1N1 virus matrix [M] gene) has been seen in triple reassortant H3N2 viruses that have infected 12 people since August 2011. (These cases occurred in West Virginia (2), Indiana (2), Pennsylvania (3), Maine (2), and Iowa (3).) These variant H3N2 viruses are being called “H3N2v.”
  5. H5N1 - When humans become ill with H5N1 virus infection, severe illness and death may occur. Sporadic human cases mainly occur after contact with infected poultry that were sick or dead, and have been reported in 15 countries.   H5N1 influenza viruses have been circulating among birds for many years, some are highly pathogenic, and infections in humans are uncommon.  There have been no recent changes that pose any additional risk to humans.
  6. H5N1 Clade - Over time, H5N1 viruses have evolved into different groups, called “clades.” Since 2007, 12 different clades of H5N1 viruses have been identified. The FAO report and subsequent media stories focused on an H5N1 virus that has been given a nomenclature (name) of “clade”.  The clade viruses are very active viruses and are spreading more widely in poultry and wild birds. While this increases the possibility of human exposures to infected birds or poultry, it does not increase their ability to infect and transmit between people. However, as part of the U.S. government’s pandemic preparedness activities, a vaccine virus candidate to protect humans against this virus already has been created so that vaccine production could begin rapidly if this virus were to change to infect humans and spread easily from person to person. The vaccine virus candidate is an exact match to currently circulating viruses.
  7. Worldwide Update on Influenza Activity - weekly updates on the World's Influenza Activity are to be found here.  The chart above, in this post, can be found at this link.

Recombinomics: Human Betacoronavirus 2c EMC/12 - Human SARS CoV Match

September 28, 2012  

The Ron Fouchier Viroscience lab at the Erasmus Medical Centef has released the complete sequence (30118 BP) of an isolate, Human betacoronavirus 2c EMC/2012, from the recent fatal case (60M) from Saudi Arabia (at Genbank).  The lab is to be congratulated for its rapid release of this important sequence.

Earlier the Health Protection agency had released a 208 BP fragment from a case from Qatar (47M requiring an ECO machine for breathing), which was 99.5% identical to the above sequence, confirming the emergence of a novel human cornavirus from group 2c, which was most closely related to bat coronavirus sequences from isolates from Guangdong Province.  The full sequence was also most closely related to these group 2c bat isolates, which is incorporated in the name assigned to the isolate by the Fouchier lab.

The group 2c coronaviruses are distinct for the human SARS  CoV, which maps to group 2b.  However, coronavirus rapidly evolve via homologous recombination and portions of genes show regions of identity of high homology with coronavirus segments from other species or phylogenetic groups.

An example of this type of homology is seen for positions 14628-14656 which match to the polymerase gene in pp1a, where 28 of the 29 positions match human SARS CoV (see list here).

Correction:  The above match is with human HKU-1, which is from group 2a.  Example with human SARS Cov (group 2b) here (24/25 matches at positions 15475-15499).

The rapid evolution via recombination with sequence present in human SARS CoV raise concerns of human adaptation and species jumping of a novel coronavirus which produces severe and fatal disease in humans.