MERS-CoV case tally bursts through 100...

1st Source I saw: FluTrackers
FluTrackers has noted that the Kingdom of Saudi Arabia Ministry of Heath site has another batch of cases and a death among people infected with Middle East respiratory syndrome coronavirus (MERS-CoV).

Currently the case tally is at 103 with 48 deaths; the proportion of fatal cases is 46.6%

• 31, Male, underlying conditions, in an intensive care unit, stable, Asir region
• 55, Male, underlying conditions, contact of another case, asymptomatic
• 51, died, Riyadh

FluTrackers MERS case list also notes a discrepancy in the KSA tally which suggests another case is positive - but no details whatsoever exist for that. I've added it to the tally for now.

Do we have a MERS-CoV outbreak in Riyadh? Most of the cases in the past 3 days have come from this region.

There is also noise of a case in a Jordanian hospital - I will be updating this post as these data coalesce and we get some more info on the cases.

Two new MERS-CoV cases and the death of an existing case, all from Riyadh

FluTrackers reports on two new MERS-CoV cases and the death of a previously infected person.

The Kingdom of Saudi Arabia's English and Arabic Ministry of Health (MOH) notes a 50-year old male (50M) and a 70-year old female (70F), both with underlying diseases and without dates of illness onset or hospitalisation. Both are in an intensive care unit.

On the Arabic-language site only, is the announcement of the death of a 54-year old "citizen". No sex or date of illness onset or hospitalisation or anything else that gives a clue as to who this may be. I have no 54-year old people on my list. 

There is still no English-language MOH version of the announcement of the previous 2 MES-CoV cases (50M and 59M) 2-days ago. The last English update, prior to the cases tonight, was August 1st.

A very piecemeal way of disclosing public health information. I can't imagine this gives many prospective visitors a good sense of the situation being under control and carefully managed.

Most hajj pilgrims are elderly...

...this is according to a story in today's Arab News, chair of the national establishment of pilgrims fro Arab countries was quoted:

We noticed, however, that most of the pilgrims who arrive from these countries are elderly

This follows on from yesterday's post about Russian pilgrims whose numbers have been limited by request, using a ballot system. 

Whether they were also restricted by age according to the "rules" is less clear.

It is also worth noting that many pilgrims plan far ahead and spend considerable time saving for the costs of the journey to Saudi Arabia for their hajj pilgrimage. It is perhaps not surprising that many are older people.

Taphozous perforatus - The Egyptian Tomb Bat

Rage of Taphozous perforatus.
Image from the IUCN Red List, via Wikipedia

This furry little fella '(~10cm long, 6cm forearm, 34cm wingspan and weighing in at 28g) occurs  throughout northern and sub-Saharan Africa, the Arabian peninsula and Asia, east to India. 

It's name, "tomb bat" comes from the genus name Taphozous which is derived from the Greek word for tomb/grave (Taphos). Also, males don't have beards like T. hildegardeae males do...apparently...just in case you meet one in a dark alley.

It is an insectivorous bat (moths and beetles) found in small colonies that avoid forest and preferring open woodland along rivers and wooded savanna. It roosts under rocks (e.g. sea caverns, deep caverns, old wells, tunnels,) or in buildings (e.g. old disused structures, castles, forts,mosques) during the day.

This bat is a member of the Order Chiropetera, Family Emballonuridae, Genus Taphozous, Species T.perforatus.

Specific countries where the bat has been found include: Benin, Botswana, Burkina Faso, The Democratic Republic of the Congo, Djibouti, Egypt, Ethiopia, Gambia, Ghana, Guinea-Bissau, India, Iran, Israel, Kenya, Mali, Mauritania, Niger, Nigeria, Oman, Pakistan, Saudi Arabia, Senegal, Somalia, Sudan, Tanzania, Togo, Uganda, Yemen, Zimbabwe

This bat is a threatened species.

Some more information, and the references:

• http://www.iucnredlist.org/details/21463/0
• http://books.google.com.au/books?id=sdY_sa1FPw0C&pg=PA50&lpg=PA50&dq=egyptian+tomb+bat&source=bl&ots=Jm_q9QKssF&sig=0hB56REa0KnXTsZWDhv_MZp8Qlc&hl=en&sa=X&ei=TUcVUvzXCY2jkQW0qIDQCA&ved=0CGwQ6AEwCg#v=onepage&q=egyptian%20tomb%20bat&f=false
• http://www.iucnredlist.org/details/21463/0
• South Asian Mammals,Their Diversity, Distribution, and Status Srinivasulu and Srinivasulu. http://link.springer.com/book/10.1007/978-1-4614-3449-8/page/1
• http://en.wikipedia.org/wiki/Mauritian_tomb_bat
• Dengis, Carol A. (May 17 1996). "Taphozous mauritianus". Mammalian Species (American Society of Mammalogists) 522: 1–5
• Colket and Wilson. Taphozous hildegardeae, Mammalian species, No. 597. p1-3. 

MERS-CoV genetic sequences found in Taphozous perforatus bat

Profs Ziad Memish and Ian Lipkin, and a team of collaborators including researchers from the EcoHelath Alliance, have published, in Emerging Infectious Diseases, their discovery of viral sequences in the faecal pellet of an Egyptian tomb bat.

Photo courtesy of Dr Jonathan H. Epstein.

Copyright EcoHealth Alliance 2013

MERS-CoV was only found in 1 of 29 Taphozous perforatus (Egyptian tomb bat, see some more detail on these in my next post) animals. These and 67 other bats captured in mist nets for this study, were observed nesting in abandoned ruins.

Samples from Bisha, Unaizah and Riyadh (Kingdom of Saudi Arabia) were snap-frozen on site, collected during October 2012 and April 2013. The October shipment was opened and thawed by US customs. Samples included wing biopsy, blood, throat swab, rectal swab and faecal pellets were collected for testing. Apart from RNA virus testing  bats were speciated by DNA analysis (cytochrome B gene). The T. perforatus bat identity could not be confirmed genetically because there was no reference sequence on GenBank - but it was similar to another member of the genus.

Helicase, RNA-dependent RNA polymerase (RdRp) and nucleocapsid or envelope regions were targeted for amplification and sequencing. 227/1003  samples (22.6%) were positive for an alpha or beta-CoV. 

The find, represented by a phylogenetic tree using on a 181nt RNA sequence fragment from the RNA-dependent RNA polymerase gene (100% identical to a sequence from the index case in Bisha, betaCoV 2c EMC/2012 over this region), secures bats as the/a primary animal source. So long as there was no contamination at customs or that the sequence actually came from a food source. Not too likely for either of those. 

Obviously more work will need to be done to find more instances, complete the genome (or at least sequence larger genetic fragments to make everyone happy) and isolate infectious virus - but this finding is a significant step in confirming a starting point for understanding how humans get infected by the MERS-CoV.

It's a shame this new fragment of the RdRp does not overlap with that sequence from the recent South African "nearest match" to MERS-CoV. In adjacent regions of the RdRp though, the South African virus does seems more genetically distant than this T. perforatus find.
  Perhaps we can re-visit the transmission chain issue with a view to how bats might infect a (probable) secondary host - say the camel for now - I'd suggest that palm trees might have a role in this as well as a possible role in direct human infections if sap/dates/drinks were consumed by the most at risk groups; elderly men with underlying conditions. Perhaps this consumption even has a role in them developing a chronic kidney-related disease? I previously wrote a little about this 19th June and on risk in a post 28th July.

2nd French MERS-CoV patient still in serious condition

1st sources: @makoto_au_japon & @HelenBranswell

Nord Pas-de-Calais reports that the patient remains in intensive care in serious condition. He is not in isolation as he is MERS-CoV free.

The 51-year-old male (51M) patient was locally infected, showing signs on May 8th 2013. He was believed to have been infected after sharing a 20m² room and single bathroom, with the MERS-CoV index case, 64M from the United Arab Emirates. 

51M was admitted to hospital in Lille May 9th. He has been there for 104 days or 3-months and 12 days.

The index case died May 28th.

16,000 Russian hajj pilgrims September 6 - October 9

1st source: @makoto_au_japon

Russia and India Report also notes that..

According to the rules, pilgrims should be no older than 65 years of age and no younger than 12 years of age.

According to my list and among those with details available:

• 53% of MERS-CoV cases and 65% of deaths are older than 55-years
• 74% of cases and 57% of deaths are 65-years or younger
• 2 cases and 1 death are under 12-years of age

I'd say the rules miss a large proportion of the populations most at risk of poor clinical outcomes.

New MERS-CoV case, likely imported, reported in Qatar

1st source: @makoto_au_japon

France 24 reported a case of MERS-CoV in a 59-year-old (59M) Qatari man. He is currently stable.

He is reported by the Qatari Supreme Council of Health (SCH) as having arrived from "another country" and of having symptoms while abroad, so this is then an imported case leaving Qatar's local acquisitions at 2, by my count.

This brings the tally to 97 cases with 46 deaths and the proportion of fatal cases (PFC) drops to 47.4%.

Taihu lake & influenza viruses Part II: people, pigs, poultry and migratory birds

Source of H5N1/H7N9 spatial overlap figure: Many thanks to Dr Ricardo J. Soares Magalhaes, The Univeristy of Queensland.

The figure below, from the Letter I talked about yesterday, published by Wang and colleagues in Emerging Infectious Diseases, Vol 19(11) shows the Lake Tai region.

To clarify, the paper talked about an area of high risk of infection. It did not specify whether the risk was due to exposure to poultry or wild birds. The issue of visiting LBMs and exposure to poultry and their excrement was secondary to the finding of overlapping regions of human cases and proposed region of greater risk.

Having said that, it appears (and these are all web sources so take them with a grain of chicken salt) that a domestic breed of pig and poultry may be farmed around this lake, one of China's largest fresh water bodies containing dozens of islands. Water quality and its levels algae and contaminating animal and human waster have also been issue for the lake, which supplies drinking water to approximately 30-million people in cities within Jiangsu and Zhejiang provinces. 

Expansion of poultry farm seems to have been stopped, if not contracted, and better management of aquaculture and livestock and poultry wastes has been recommended.

However, wild waterfowl as well as duck and goose farms seem to remain around the lake according to at China Travel and the maps at the bottom of this post. There seem to be monkeys and caves (bats?) too and as you would expect, this is also a thoroughfare and winter stopover for wild birds. It's also about 380km north-east of Poyang lake, another important wintering ground for wild waterbirds and one that is known to harbour influenza viruses.

• A study by Duan and colleagues  of >11,500 cloacal swabs from migratory ducks and >36,400 swabs from sentinel ducks identified 90 and 1,681 influenza isolates, respectively during 2002-2007. he sentinel duck seasonal influenza peak overlapped with the migratory duck over-wintering period. Major haemagglutinin (HA) types included H3, H4, H6 and H10. H5N1 was detected during 2005. H7 was also found. The major neuraminidase (NA) type was N6. N9 was not identified. These combined to form 27 HA/NA antigenic combinations.

You can see the overlap between areas of human infections with influenza A(H7N9) virus (green circles; area bounded in blue and green) and H5N1 (red triangles; area bounded in pink).

Below, I have excerpted 2 maps from William Wint and Timothy Robinson's document, Gridded Livestock of the World 2007 written for the Food and Agriculture Organization (FAO) of the United Nations¹. They show using livestock data modelling (which is described in the full document) that there were certainly lots of pigs and poultry in that region in 2007. 

So, the 3-Ps are in place: People, Pigs, Poultry probably kept freshly supplied with out-of-town influenza by migratory birds. 

1. FAO. 2007. Gridded livestock of the world 2007, by G.R.W. Wint and T.P. Robinson. Rome, pp 131.

H7N9 and H5N1 may have emerged from birds around Taihu Lake

Wang and colleagues from the Institute of Disease Control and Prevention of People’s Liberation Army, Beijing, China and from The University of Queensland, Australia writing in Emerging Infectious Diseases, note that most (71%) people in China infected with influenza A(H5N1) virus (spanning from 14/10/2004-17/05/2013) had direct contact with poultry or their excrement. That contact includes work-related handling of live and dead birds and their urine and faeces.
However, most of those infected by influenza A(H7N9) virus had indirect exposure to live birds, mainly through visiting live bird markets (LBMs).

Also of interest, most H7N9 cases were more closely clustered  compared to the more widely spread H5N1 cases.

The authors were looking for an overlap between the earliest known cases of infection of both viruses - perhaps to find a common source of the emergence of these zoonoses - and their studies suggested Taihu (Tai Lake) Lake which is near Anhui province and Shanghai municipality and borders Jiangsu and Zhejiang provinces. All place names that were foci of a lot of H7N9 activity earlier in the year.

The authors conclude that this region may be a key hotspot for spillover of avian influenza to humans. This would be a useful place to add to the emerging influenzavirus watch list and bird sampling/genotyping list. They also reaffirmed the role of LBM visits were another key risk factor for acquiring H7N9.