How reliable are the H7N9 real-time RT-PCRs for low viral loads?

An interesting document that compares the effectiveness of some different diagnostic PCR methods for use in H7 or N9-based flu diagnosis. It seems to show that in a couple of instances H7-specific or H9-specific molecular methods will fail (1:10,000,000 is a pretty extreme dilution) to detect H7N9 at low levels while some assay fail to amplify the intended target altogether. 

This sort of assay variation is pretty commonplace when you compare different PCR designs for the same target. It's a major reason why everyone prefers to design their own assay; each are convinced there's is the best. From this document, the people behind the OFFLU (FLI-H7) assay happen to be right. 

How these data relate to viral load in the human (and animal) samples these may be/have been used on is unknown. This sort of variance may contribute to negative throat swabs in H7N9-cases subsequently proven positive using lower respiratory tract samples (e.g. sputum) in which the viral load is presumed to be higher.

OFFLU: a network of expertise on animal influenza established jointly in 2005 by the World Organisation for Animal Health (OIE) and the Food and Agriculture Organization of the United Nations (FAO) to support and coordinate global efforts to prevent, detect and control important influenzas in animals.
CNIC: Chinese National Influenza Center

That (don't call me novel) coronavirus is back!

Media reports, FluTrackers and Avian Flu Diary describe five recent deaths and two other critically ill cases under close watch in the Al-Ahasa region of the Kingdom of Saudi Arabia, linked to infection with the newly identified human coronavirus HCoV-EMC. This virus was first isolated in September 2012 from a 60M (60-year-old male) with pneumonia and renal failure in Jeddah, KSA. 

Further evidence for bats as a major source of CoVs came in a recent study in Emerging Infectious Diseases. Yang and colleagues identified a novel CoV from each of 2 bat species. 

The newly identified betacoronaviruses (betaCoVs), Bat Rp-coronavirus/Shaanxi2011 and Bat Cp-coronavirus/Yunnan2011 (rolls of the tongue doesn't it?) were not that closely related to human betaCoVs but resided in the bat verison of the SARS-like COVs.

First weekly H7N9 report from China?

A report from the Ministry of Health describes 19 cases during the period spanning from April 25th to May 1st. 

There are also 2 new deaths (total now at 26)- but no details provided for any of the cases. Stay tuned next Thursday for more.

Four reassortment events led to H7N9 emergence.

With thanks to Prof. Ross Barnard, University of Queensland for helpful contributions.

A new article just published at the Lancet describes a detailed genetic analysis of four H7N9 virus sequences, in the context of all likely contributing influenza virus sequence. The resultant virus' HA and NA genes may have been contributed by migratory birds a year prior to acquisition of internal genes from poultry influenza viruses. 

Since its emergence "several months ago", H7N9 has divided into at least two different groups (lineages). One strain (Shanghai/1) has signs of oseltamivir resistance.

Influenza virus transmission.

An interesting blog post from 2006 by Revere on some aspects of what H5N1 virulence (in terms of disease severity), transmission and preconceptions. 

Do we put too much stock in believing that recently emerged viruses eventually settle in to their new hosts, seeking a perfect balance between virus replication, transmission and host mortality? 

In other words, do viruses adapt over time so that originally severe infection outcomes (like pneumonia) become mild illnesses (like the common cold or just feeling a it crook). 

There may be some parallels to be drawn with H7N9 as we continue down its path. 

Or perhaps H7N9 has been adapting to humans for longer than we think?

A(nother) new real-time PCR-based H7N9 test.

US CDC have made available their CDC H7N9 rRT-PCR for use on suspect cases (see interim guidance for defining cases) and in combination with their existing Flu rRT-PCR Dx Panel ("r"=real-time; "Dx"=Diagnosis/Diagnostic) after FDA support through an Emergency Use Authorization.

Enormous risk described.

A new scientific article in the Chinese Science Bulletin talks of there being a high risk of a continuing and severe outbreak of H7N9 in the future. It extrapolates from the first 91 cases (today's case count is at 128), using a mathematical formula that could be heavily influenced by the appearance of decent numbers of mild cases - should testing find mild cases of course. 

Given the variation seen among many aspects of the different influenza viruses of recent years, I'm inclined to maintain my wait-and-see attitude a little longer before stocking the pantry.

Authorities considering human-to-human spread in Hunan?

crofsblogs reports on a news article quoting the Hunan Provincial Health Department will be setting up isolation wards in medical institutions to cater for fever and H7N9 influenza cases (allowing for interpretation of machine translation). 

This suggests to me that Hunan is expecting more cases and that they might be worried about human-to-human spread.

Son of Shandong's 1st H7N9 case positive for H7N9.

No evidence for human-to-human (h2h) transmission though. No evidence against it being the cause either of course. See my comments from the 18th regarding the first reported H7N9 case and family cluster. They still apply. 

Incubation time being surreptitiously the same as the (presumed) incubation period means nothing. Two people completely geographically isolated could have the the same gap between onsets and the second case would obviously not have been infected by the first. 

Even if the sequences of the two viruses are very similar, that does not prove h2h transmission. Chances are that many of the H7N9s will have very similar sequences reflecting that they have originated form the same animal (or human) source at some point.

What does this mean? 

It doesn't mean the sky is falling - contacts, by their very nature share things. In a family you often share (inhale, have land in your eyes etc) aerosolized (virus-laden) droplets as well as common surfaces contaminated by with those aerosols, when you have an acute virus infection. Coughing and sneezing do that. 

But you also share common tasks. 

There is so far no clear evidence of direct Dad to Son (or Son to Dad) transmission here (there is a timing issue that is intriguing)- the father and son may have simply shared the same airspace (I think its pretty safe to say this is transmitted through the air in some form) with an animal host during contact, handling, butchery, cleaning etc. Despite testing of animals to date finding very few have detectable H7N9 infections.

Guangdong creates a buffer against H7N9 entering Hong Kong.

Destruction of poultry in Guangdong province, the last province between Hong Kong and an inexorable march of H7N9-infected eastern Chinese provinces, has someFluTrackers noting that H7N9 may already be in Guangdong. 

UPDATE: An H7, but not H7N9.