TWiV 247: Today’s weather in virology

On episode #247 of the science show This Week in Virology, Ian Lipkin joins Vincent, Alan, Rich, and Kathy to describe how his laboratory is searching for the origin of MERS-coronavirus.

You can find TWiV #247 at

Part of MERS-CoV nucleotide sequence found in a bat

What is wrong with this paragraph from today’s New York Times that describes the origin of the Middle East Respiratory Syndrome (MERS) coronavirus:

Health officials confirmed Wednesday that bats in Saudi Arabia were the source of the mysterious virus that has sickened 96 people in the Middle East, killing 47 of them.

Here is the science behind that statement, which has been published in Emerging Infectious Diseases. Samples (fecal, fecal swab, throat swab, blood) were collected from bats in an area of Saudi Arabia where human infections with MERS-CoV have been identified. Total nucleic acids were extracted and analyzed for the presence of coronavirus sequences by polymerase chain reaction. Coronavirus sequences were amplified from 220 of 732 fecal samples and 7 of 91 rectal swab samples or fecal pellets. One PCR product obtained from a single bat sample (fecal pellet of a T. perforatus bat captured in October 2012 in Bisha) had 100% nucleotide identity to a human MERS-CoV isolate.

A single PCR product 190 nucleotides in length from one bat was a perfect match with the genome sequence of a MERS-CoV isolate.

No infectious MERS-CoV has yet been isolated from this single bat. Therefore it is not yet possible to say that bats are the source of virus causing the MERS-CoV outbreak. As I have written previously, a virus is very different from a viral sequence.

It is certainly possible that MERS-CoV originated in a bat. Bats are known to harbor many viruses, and of course the SARS coronavirus originated in bats. But there is more than one explanation for the presence of this short viral sequence in bats. Perhaps the virus (or viral sequence) was obtained when the bat ingested a meal. Perhaps the 190 nucleotides are from a recombinant virus that is not MERS-CoV. I can think of other reasons why bats might not be the source of MERS-CoV.

For these reasons I believe that it is inaccurate for ‘health officials’ and the New York Times to confirm that bats are the source of MERS-CoV. Additional work is clearly needed to show that T. perforatus is the source of MERS-CoV, including isolation of infectious virus from bats and demonstrating infection of bats by the presence of antibodies to the virus. The work is in clearly progress; indeed the results might even be known, but they are not included in the Emerging Infectious Diseases article on which the NY Times piece was based.

Update 1: The term ‘frag-virus’ was proposed in 2008 to indicate viruses known only from sequence data. Although the term never caught on, the short article points out the problems that arise when genomic fragments are used to identify new viruses :

Although unintentional, these reports may mislead the readership of scientific journals and the general press. Having no distinction between preliminary genome-based evidence and conclusive proof by biological isolation and characterization of a replication-competent virus blurs the meaning of new virus.

Update 2: A phylogenetic analysis of the DNA fragment amplified from T. perforatus has been carried out. The author writes that “although this fragment means a very close relative of the human MERS-CoV is found in a bat geographically close to the first case, the fact it is identical in this short region doesn’t mean that these bats are the direct source of the human case.”  I would add even more uncertainty because we have no evidence that the virus was replicating in this single bat.

No further evidence of novel coronavirus

disease timelineThere is no evidence for further spread among humans of a novel coronavirus recently isolated from two individuals with severe respiratory illness. This conclusion has been drawn after scrutinizing the travels (figure) and contacts of a Qatari adult who was transferred to intensive care in London.

While in Saudi Arabia the 49 year old male patient developed mild respiratory illness (rhinorrhea and fever). These symptoms resolved several days after his return to Qatar on 18 August. At the beginning of September he developed another respiratory illness which worsened and required his transport to London. Later that month the novel coronavirus was detected in his respiratory tract.

This timeline suggests that the patient acquired the viral infection in Qatar, as he was there for 16 days prior to illness. How he obtained the infection is not known. He did spend time on a Qatari farm where sheep and camels are kept. The SARS coronavirus is believed to have originated in bats and spread to humans either directly or through animals in meat markets, and the new coronavirus is related to bat coronaviruses.

Sixty-four close contacts were identified among the patient’s health care workers, friends, and family during his stay in the United Kingdom. None of these have developed severe disease, while 13 have displayed mild respiratory symptoms, and the new coronavirus was not detected 10 of these individuals.

These results show that no human to human transmission of the novel coronavirus has taken place that resulted in mild or severe disease. Serological testing for anti-viral antibodies must be done to determine if asymptomatic infections have occurred. It will also be important to conduct serological surveys to determine whether there is evidence for infection in the general populations of Qatar and Saudi Arabia. It is also likely that animal surveys will be done to identify potential reservoirs for the virus.

RG Pebody et al. 2012. The United Kingdom public health response to an imported laboratory confirmed case of a novel coronavirus in September 2012. Eurosurveillance, Volume 17, Issue 40.

Update: A third human infection with the novel coronavirus was confirmed on 4 November 2012 in Saudi Arabia.

A new coronavirus isolated from humans

Coronavirus virionA new coronavirus has been isolated from two individuals with severe respiratory illness. It is different from the SARS coronavirus, but health officials are nonetheless preparing for a rapid response should the virus be detected elsewhere.

The novel coronavirus was first reported by Ali Mohamed Zaki on ProMED-mail on 15 September 2012, from a 60 year old male patient in Saudi Arabia with pneumonia and acute renal failure who died in July. The virus was isolated by culturing sputum on Vero and LLC-MK2 cells, and identified as a coronavirus by polymerase chain reaction. Dr. Zaki sent the virus to Ron Fouchier in the Netherlands who sequenced its genome and confirmed that it is a beta-coronavirus closely related to bat coronaviruses.

At the beginning of September 2012 a 49 year old male Qatari national who had previously traveled to Saudi Arabia was admitted to an intensive care unit in Doha with severe respiratory illness. He was moved to the United Kingdom where laboratory tests confirmed the presence of the novel coronavirus. Comparison of a 200 nucleotide genome sequence with that from the Saudi national revealed 99.5% identity (one mismatch). Alignment of this sequence with that of other coronaviruses shows that the new virus is related to bat coronaviruses.

This new virus is not the SARS coronavirus, but because it is related to bat coronaviruses there is concern that it could spread rapidly among humans and cause serious respiratory disease. This is why WHO has placed health officials in its six regions on alert, and has issued a case definition so that the disease may be readily detected. The definition comprises: acute respiratory syndrome which may include fever (≥ 38°C , 100.4°F) and cough requiring hospitalization or with suspicion of lower airway involvement (clinical or radiological evidence of consolidation) not explained by any other infection or any other aetiology; and close contact within the last 10 days before onset of illness with a probable or confirmed case of novel coronavirus infection while the case-contact was ill, or travel to or residence in an area where infection with novel coronavirus has recently been reported or where transmission could have occurred.

Ron Fouchier doesn’t believe that we should become overly worried about these cases:

There are now six known human coronaviruses; one of them is SARS, but four cause the common cold and are quite innocuous. So let’s keep both feet on the ground and not blow this out of proportion.

The fact that the virus has been isolated from individuals with severe respiratory disease does not mean that it is the causative agent. To prove this requires additional work, as Fouchier notes:

 For starters, we’ll find out whether animals get sick from this virus. You can isolate a virus from a patient, but that does not mean they died from it; to show that it causes disease you need to fulfill Koch’s postulates. That’s what we did for SARS, and it’s what we hope to do here; we’ve applied for emergency ethical approval. The most obvious animal species to put this virus in are mice, ferrets, and perhaps monkeys.

Proof that the new coronavirus is an agent of respiratory disease would come from its isolation from additional patients with the disease. An outbreak of severe respiratory disease in Jordan in April of 2012 is now being reviewed for evidence of the novel coronavirus.

Coronaviruses are composed of enveloped virions that contain a positive strand RNA genome. Human coronaviruses may cause the common cold or severe respiratory illness. In 2002 the SARS coronavirus emerged in China and spread globally, infecting over 8000 individuals and killing more than 900. The SARS coronavirus is believed to have originated in bats and spread to humans either directly or through animals in meat markets. Because the new coronavirus isolated from two patients is related to bat coronaviruses, there is concern that a scenario similar to the SARS outbreak is in the making. Whether or not this is true will be revealed in the coming weeks.

Update. Eurosurveillance has published communications on how to detect the novel coronavirus by real-time polymerase chain reaction; and the case definition and public health measures. The authors conclude:

There is strong evidence that a novel virus caused the severe disease in the two patients. Based on this assumption it can be concluded that the virus poses an as yet poorly defined level of threat to people’s health. There may have been other cases in the past that were missed and serological testing of stored sera and other specimens from such cases will be important. […] Our assessment, based on the limited information currently available, is that the risk of wide spread transmission resulting in severe disease is low. However, the emergence of a novel coronavirus requires a thorough assessment which is currently being coordinated at international level.

Update 2. CDC has published a travel advisory:

At this time CDC, does not recommend that travelers change their travel plans.