Break out the bug zapper: DENV-5 is the new dengue virus in town!

A report from the Third International Conference on Dengue and Dengue Haemorrhagic Fever describes the discovery, by researchers from the University of Texas Medical Branch, of a new type of dengue virus (DENV). he virus was found during screening of samples from 2007, collected from Malaysia's northern Sarawak state.

Click to enlarge. An alignment of the previously known 4 dengue virus complete genome sequence. 
The GenBank accession number is shown next to the serotype's name.
They share 68% olignucleotide identity. Aligned using Geneious 6.1.6.

Dengue viruses have an ~11 kilobase, positive-sense, RNA genome enveloped in a lipid bilayer membrane (taken from the host cell upon virion exit) resulting in a 50 nanometer particle. 

Dengue viruses belong to the Family Flaviviridae, Genus Flavivirus and belong to the Species Dengue virus. The viral genome produces a single polyprotein that is cut into 10 proteins (called C, M, E, NS1, NS2A, NS2B, NS3, NS4a, NS4b, NS5). M and E are embedded in the viral membrane.

New virions are assembled on the surface of the endoplasmic reticulum. Dengue virus is transmitted to non-human primates and humans via a mosquito vector (primarily of the genus Aedes) and infection can result in dengue haemorrhagic fever.

This virus, DENV-5 (preusmably), was discovered by Dr Nikolaos Vasilakis and colleagues. It is the 5th member of the species and the first addition in 50-years. DENV-1 to DENV-4, called serotypes (because they interact differently with our immune response to them) are approximately 65% identical in sequence.

How this latest discovery will impact on existing efforts to interrupt, treat or prevent infection and disease remain to be seen. As does a full research publication.

Thanks to FluTrackers for their earlier post on this.

Further Reading:

1. http://www.nature.com/scitable/topicpage/dengue-viruses-22400925

Australia on watch for illness among Hajj pilgrims

A report from Radio Australia highlight the ongoing need to be watchful for acute respiratory infections developing among pilgrims returning from Hajj.

Gregory Härtl (spokesperson, World Health Organisation) noted the need to keep an eye out... 

It could well be that a returning pilgrim gets back, starts feeling sick and is found to be diagnosed with MERS, and what we consequently are asking countries to do is to increase their surveillance and to know what symptoms to look for on the one hand, and for pilgrims to be on alert and to tell their doctors they were on Hajj if they start to feel sick.

Professor Charles Watson (Curtin University) noted that disease is most likely to be an issue when pilgrims return to their countries rather than while they were within the Kingdom of  Saudi Arabia.

Thanks to Crawford Kilian for bringing this report to my attention via Twitter and on his blog.

Latest MERS-CoV cases

The 1st of the 3 most recent cases were from Qatar (6 in total) and the other 2 seem to have originated in or around Riyadh in the Kingdom of Saudi Arabia (KSA). 

Some details on each case are below (preceded by the FluTrackers' number):

1. FT#144. 61-year old male (61M) with comorbidities, hospitalized October 11th with influenza-like symptoms, no travel outside Qatar in the preceding 2-weeks. Owner of a farm, he had significant contact with camels, sheep and chickens. Some animals were tested but were not MERS-CoV POS
2. FT#145. 73M with comorbidities and no specific travel history outside of Riyadh. ICU.
3. FT#146. 54? No travel history outside the eastern region of KSA/Riyadh. ICU.

There are now 144 cases - remembering that 2 Italian cases have been moved from confirmed to probable. Their numbers are retained although not counted in the lab confirmed tally. This maintains list integrity for all the cases numbered prior to that change. 

Click to enlarge.

Of the 144, 60 (perhaps 62) have died, a proportion of fatal cases of 42%. Age distribution among fatal MERS-CoV cases is shown in the chart. There are some missing data on sex/age but it shows that the median age of cases is still skewed toward those >55-years of age and that males predominate. The median age of fatal cases lies above that of the total case population (including fatal and surviving cases).

As noted by Helen Branswell today on twitter (@HelenBranswell) and Crawford Kilian on his blog - the English version of the KSA Ministry of Health website has not been updated with its Arabian-language data in 22-days. 

It's becoming very hard to find 2 sources of MERS case information to trust these days. There has been no World Health Organization (WHO) confirmation of the 2 recent KSA cases and there are possibly 2 outstanding fatal cases in the wind. The WHO did pass along the Qatari case details, plus a little more. Communication between the KSA MOH  and WHO (and us) seems to have slowed to a trickle.

MERS-CoV cases begin to tick over again after the Hajj....but not related right?

So by all accounts, Hajj2013 was a very successful event. A lot of lifelong wishes may have been fulfilled and the event went off without any apparent major hitch. A huge undertaking on many fronts.

However, during the Hajj it was hard to avoid seeing  Middle East respiratory syndrome (MERS)-related headlines like...

No cases of MERS virus among pilgrims so far

and my particular favourite...

No infectious disease found

...at all that is. None. Not even bad influenza-like illnesses. No coughs or colds among 2,000,000 people gathered together; 1,300,000 having at some level, shared transportation into the Kingdom of Saudi Arabia (KSA)?

Seriously?

That second quote makes me realise just how important it was for the KSA ministry of health to control this aspect of the Hajj's message; no MERS-CoV disease here. So important, that the message was, to say the least, a little heavy handed.

But now, coinciding with the Hajj ending, we see MERS-CoV detections popping up (3 in 3-days). It's very hard to take seriously the MERS-message. Rest assured we're told, those cases are not at all linked to the Hajj - no travel to that region (now so specific that we are told there is no travel outside of Riaydh) in the previous 14-days. Ironic how that longer incubation period is useful in these happy reports, but not remembered in others, such as when the press note:

Saudi Hajj ends successfully with no reports of MERS virus

Click to enlarge. This graph is from September - highlights a similar case
reporting lull around umrah which then climbed rapidly and steadily
immediately afterwards.

The (longest) 14-day incubation period means we're not out of the woods yet (see my earlier post on timelines). 

Maybe we'll see no new cases among any of the pilgrims. Cool. I doubt that. We have seen 7-day or more breaks in reporting of new MERS-cases before, so this past week is not "out of character". Time will tell, especially from now on for a week or so. Watch that curve closely.

I still wish we could lay off the "everything is fine here right now" message, and instead tell us what's happening to find the host or what testing is being done among those who are not severely ill (take a look at China and H7N9 - include MERS-CoV in your regular respiratory virus testing panel for a little while and see what comes of it). That would be treating us a little less like we are so easily distracted by shiny baubles.

Middle East coronavirus infection control and personal protective equipment...

...are not at all part of the thinking judging by the imagery in this story on alRiyadh.

For a virus that kills 2 in 5 symptomatic people and for which animal hosts or intermediate hosts remain to be excluded or confirmed, there is an alarming and completely irresponsible level of safety being employed by those workers.

Thanks to FluTrackers for bringing it to my attention.

Cute little hedgehogs get CoVs too?

Corman and colleagues from the University of Bonn Medical Centre (clearly not just for human medicine!) have found a proposed new species of coronavirus (CoV) they've assigned to the Genus Betacoronavirus clade C. The new virus is called erinaceus CoV (EriCoV). It inhabits the same clade  that houses the MERS-CoV, but it is not as closely related as are batCoVs and MERS-CoV.

The authors, writing in the Journal of Virology, thought that searching in an order of insectivorous animals, the Order Eulipotyphla, might yield results since most CoV-positive bats (Order Chiroptera) are insectivorous. 

Two of 146 (58.9% of 248 samples were tested  positive sample were targeted for genome sequencing using next generation (454) and conventional PCR sequencing technology, from European hedgehogs (Erinaceus europaeus). Virus was not isolated in cell culture using Vero, pipistrellus bat or shrew (same Order) cells making it less promiscuous in culture than MERS-CoV. Also, it probably uses a different receptor. No sign of disease could be discerned.

With GenBank recovering from being shuttered, it might be a while until the sequences are publicly available.

A summary of Influenza A(H7N9) virus findings in birds and humans [UPDATED, AMENDED FIGURE]

An article from Bloomberg news highlights some interesting studies, how they present opposing conclusions and why we can expect to see more H7N9 activity, perhaps peaking at Chinese New Year.

Click on image to enlarge.
H7N9-positive birds and humans (see MOA report) in 
April 2013. 17x more humans were virus-positive 
than humans were PCR/symptom positive. Based on 
Li et al's April 24th New England Journal of Medicine 
article from a similar time period which uses observation 
for signs of disease among 1,251 followed contacts of 81 cases and
sentinel surveillance PCR data from 5,551 humans to
identify H7N9 cases).

The authors (Khan and Loo) remind us that earlier in the year, China's Ministry of Agriculture reported 46 positive poultry samples among 68,060 tested positive using viral culture, for H7N9 (0.07% or about 1:1,500). 

In a more detailed report from MOA from 30th May 2013, 88 of 899,758 [0.009%] duck, pigeon, chicken (722,380 or 80% of all the samples tested), wild bird, pig, geese, "other" animal or environmental samples were virus [197,389 of the samples tested this way] &/or antibody [702,369 of the samples] positive (chicken, duck and pigeons were the positives; 3 were positive for both). The report presented by Zhang Zhongqiu does not make clear how many swabs and bloods were tested per animal so I'll just talk about sample numbers. The report notes that there were no clinical cases reported from 44 million farming households and no positives from 51,876 samples of 746,212 samples (?chickens) sent to Hong Kong; monitored by the General Administration of Quality Supervision, Inspection and Quarantine, China) nor among the 120/samples being tested per day in Hong Kong. In 1,874 samples collected from Henan and Jiangxi provinces, none were positive. Transmission among chickens was possible but was not efficient among ducks.

• Lam and colleagues (previously reviewed) identified 8 avian H7N9 strains from 1,308 (0.6%) chickens (95% of samples), ducks, pigeon and geese samples collected from live bird markets (LBMs) in Rizhao, Shandong province (about 9 times more than the 1st MOA study above, if they can be compared directly). 
• Yang and colleagues (previously reviewed) found H7N9 antibodies in 25 (6%) of 396 humans poultry workers (none prior to 2013) but only 9 of 1,129 (0.8%) members of the general community showed some weak sign of past exposure (or cross-reaction with another influenza). No viral RNA was found in these poultry workers.
• Wang and colleagues, writing in the Journal of Infectious diseases,  recently traced the source of some cases in the Hangzhou region of Zhejiang, to LBMs. 95 samples from chickens (n=47 samples), ducks (n=9), quails (n=2), pigeons (n=3) and poultry handlers and 4 from water were inoculated into eggs and were tested by real-time RT-PCR, within the first 2-weeks of April 2013. H7N9 RNA was found in 41/85 (48%) of samples. 40% of the chicken samples, 89% of the duck samples and a third of the pigeon samples. No human or environmental samples were positive. The authors concluded that migratory birds would continue the spread of H7N9 viruses and that their findings highlight LBMs as the major source of infection an as such control measures are needed.
• Shi and colleagues reached a similar conclusion in April in the Chinese Science Bulletin. "Strong measures" were needed to control the spread of H7N9 in order to prevent more infections. This followed the testing of 970 samples of drinking water, soil, cloacal and tracheal swabs from LBM poultry in Shanghai and Anhui province using egg inoculation. All 20 (10 from chickens) of the H7N9 isolates came from LBMs in Shanghai, confirming high genetic homology across the H7N9 genome from human H7N9 cases.

Today's Bloomberg article quotes researchers' concerns that the cooler weather will drive the re-appearance of H7N9, since influenza usually reaches epidemic levels during cooler months. In other words they believe this particular strain of H7N9 (the one infecting humans) was never removed from the ecosystem.

Re-opening of the LBMs has been ongoing since June in Shanghai municipality and Zhejiang and Jiangsu provinces, albeit in a more regulated fashion. The cleansing of the markets after culling more than 560,000 poultry from LBMs as of May 2013 combined to precede the precipitous decline in what had been an alarming rate of new cases in those regions. Is testing of these markets an ongoing process?

With the markets refilling from farms located in rural regions with exposure to mobile wild bird populations that may (albeit infrequently) carry H7N9 (and many other influenza viruses including its components), the risk of fresh outbreaks among humans is also growing. 

It's a numbers game. 

Even 1 human case, like the one we saw infected this week could signal an even wider level of circulation of H7N9. Let's hope testing will make sure our number's not up this time around.

Editor's Note - the figure was altered 01.02.14 to correct an error in the proportions and to adjust down the number of contacts since not all had been followed.

Middle East respiratory syndrome coronavirus: how tough is it?

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Influenza A(H7N9) virus case appears in Zhejiang province....

Look I know hypotheses are there to be disproved  but did this one have to be shot down in flames 60-minutes after I said at a talk today, "...perhaps the very quick and large scale bird cullings and the live bird market closures actually eliminated the particular H7N9 that was spreading through humans in South East China earlier in the year. Perhaps even  reaching far enough back to require a whole new random chance mixture of the different H7s and N9s and other genome segments to occur before that virus would ever be seen again."

Brrraaappppp!!!!!

Today we see the first new H7N9 case since early August (which was an onset of July 28th).

A 35-year old male from Shaoxing County, hospitalised on October 8th, tested positive by PCR. He is in serious condition.

Peak daily temperatures are not high in this part of the world currently - below 25'C for the week.

It looks like H7N9 might be well entrenched after all. Where there are severe cases, there may well be less severe ones. 

A scientific article that I reviewed back in August, written by Yang and colleagues, showed that some poultry workers had been exposed to H7N9. These were relatively younger and healthier people than the PCR-positive ill H7N9 cases.

We're in for some interesting times ahead with H7N9; it's not done with us yet.

The Hajj begins

The Kingdom of Saudi Arabia showing the major sites of MERS-CoV
infections and the site of Mecca.

Al Riyadh reports that on Saturday and Sunday 13th the 1,379,000 international pilgrims (94% arriving by air) moved into Mina Valley from the holy city of Mecca (Makkah) located in the Mecca province, the most populated province of the Kingdom of Saudi Arabia (over 5.8 million people). The number includes 752,424 males (55%).

The Hajj starts at sunset (Mahgrib) on Sunday, but many have begun on the Saturday evening.

Pilgrims perform “Tawaf Al-Qudoom” at Mecca (initial round of circumambulation [the act of moving around a sacred object, in this case the cuboidal Kaaba at Mecca]) then move to Mina prior to midday. They sleep there and then move to Arafat after morning prayers. Temperatures were expected to reach 37-41° C yesterday and throughout the week.

Given a 14-day incubation period (most lengthy estimate), if the MERS-CoV is going to show up any differently among hajis this year than it did as a result of last year's Hajj (you may have noticed that no pandemic ensued), we should see those cases having presented with symptoms by 
Sunday the 27th. If we really want to get a feel for how easily transmissible this virus is, then this is the opportunity to observe and test.

Of course, this is an artificial date, given pilgrims have been assembling and mingling for some time during the lead-up to Sunday evening, but I'm using that date as the outer limit for appearance of symptomatic cases using a timepoint in which many people definitely congregated together in large numbers.

We may also see a rise in cases appearing outside the KSA as retuning pilgrims picking up infection just before they depart, become symptomatic on home soil. Or we may not.

Thanks to FluTrackers for posting this link.