20 February 2010

Topography of Scientific Inquiry, Part 2

It may be beneficial for some to have a look at the blog entry dated 7th January, 2010, which was a short analysis of the study published in PLoS, and the requirement, within scientific endeavor, to replicate studies.

This blog entry, once again, is an update and discussion around the latest research paper regarding the presence of XMRV in individuals with ME/CFS to come our of the UK. The aim is to provide factual information about the study and the response from the WPI, who first iderntified XMRV in relation to ME/CFS. The purpose is to generate discussions around this disease process, to further educate others and to continue to promote awareness of this disease process.

Please feel free to use any of the referenced information provided here to engage in these discussions in visible forums, as we work together towards ensuring our families, friends, communities, and medical professionals of this disease process and the desperate need for further research.

The study:

The UK study, conducted by Groom, H., et al (Retrovirology, 2010) aimed at looking for evidence of XMRV in two UK cohorts, and comparing them to controls. There were 170 samples collected from individuals with chronic fatigue syndrome, and 395 control samples from individuals without the disease. The research looked for evidence of XMRV in these samples by either identifying the presence of viral nucleic acids of XMRV, using PCR techniques, or by identifying serological responses in the samples, using a virus neutralisation assay (Groom, H., et al 2010).

First of all, the research looked for evidence of the viruses genetic code in the samples using PCR (Polymerase Chain Reaction). PCR is a method of amplifying a sequence of DNA and then looking for the specific genetic code of XMRV. (There's an simplified example of PCR at http://learn.genetics.utah.edu/content/labs/pcr/ which demonstrates this process in terms that even I can understand!) The research then looked for serological responses in the samples, evidence of XMRV antibodies, which would indicate that the immune system had been activated by XMRV, and had rallied up specific antibodies to fight the virus.

The results:

The results of the study undertaken by Groom, H., et al (2010) failed to identify XMRV by PCR methods in any of the samples.

26/565 samples tested positive for serological activity in response to XMRV, however, according to Groom, H., et al (2010), 25 of these samples were from individuals in the control group. This means only one individual who had a diagnosis of CFS demonstrated neutralising activity towards the virus XMRV. In other words, that sample had antibodies which could target XMRV.

I say 'could' because most of the 26 samples which tested positive for these antibodies, also demonstrated the ability to nutralise the virus particle if it was wrapped in an alternative viral protien coat. So, remembering that a virus is a length of viral DNA wrapped in a protien coat, when the researchers changed that usual protien coat on the virus to a protien coat from a different virus, the samples continued to show a neutralising serelogical response. This may indicate that another virus could have elicited these responses, and thus the antibodies residing in these samples were not necessarily responding to the XMRV.

There was detection of a serological response in 4 samples that was not elicited by a psuedotyped virus, meaning there were 4 samples which elicited a serological response to XMRV only


The conclusions drawn by this research was that there may be a danger in getting accrate results from serological surveys, because the antiviral response to XMRV may also be elicited by other viruses.

One reason why this was deflating for many individuals hoping to see positive results, is because of the involvement of Dr Jonathan Kerr. One of the researchers involved in this research paper, is Dr Jonathan R Kerr BSc, MBBCh, MD, PhD, FRCPath. Dr Jonothan Kerr received his medical qualification from Queens University of Balfast in 1987, and in 1995, he completed his qualifications at a microbiologist, has worked as a microbiologist in Balfast, Mnachester, and London, where, in 2001, he became the consultant senior lecturer in Microbiology at the Imperial College, and in 2005 became the Clinical Senior Lecturer in Inflammation at St Gorges University (IACFS/ME, 2010). Dr Jonathan Kerr worked on a study of parvovirus B19 infection, demonstrating a percentage of cases had developed 'CFS' which lasted for several years, and subsequently became interested in 'Chronic Fatigue Syndrome' (IACFS/ME 2020). IACFS/ME (2010) reports that "he is now the principal investigator in a programme of research on CFS", and is is interested in the genetics of "CFS", and potential relationship with microbial infections.

A discussion of the study:

Of the study, Kate Bishop, one of the researchers, stated "We are confident that, although we were unable to replicate the detection, our PCR assay is more sensitive than the earlier method and possessed the necessary sensitivity to detect XMRV had it been present" (Redorbit, 2010). However, this study fails to provide detail to allow interpretation of how many white blood cells were analyzed, and as a result, this may have impacted the results. The Whittemore Peterson Institue, (2010), have stated that "Insufficient number of cells analyzed may result in failure to detect a low copy virus like XMRV, regardless of the sensitivity of the assay'

The Whittemore Peterson Institute (2010) also stated a difference in collection, preparation and storage of DNA. Neither this UK study, or that published in PLoS, had any data on blood harvesting, storage, or quantity of isolated cells, and technologies used. The research paper published in Science had used "PCR on nucleic acids from both un-stimulated and stimulated white blood cells; XMRV protein expression from stimulated white blood cells; they completed virus isolation on the LNCaP cell line; and a specific antibody response to XMRV" (Whittemore Peterson Institute, 2010). Furthermore, the Whittemore Peterson Institue, (2010), 'When using PCR alone, the Science authors found that four samples needed to be taken at different times from the same patient in order for XMRV to be detected by PCR in freshly isolated white blood cells. More importantly, detection methods other than PCR showed that patients whose blood lacks sufficient amount of XMRV detectable by PCR are actually infected'.

In conclusion, this study is not a replication study. Realistically, a replication study requires the same environmental conditions and technologies are used. The Whittemore Peterson Institue, (2010) have stated that they have provided information and reagents to research groups in different areas to assist accurate replication studies to occur, however, neither this study, or the one published bu PLoS, 'requested positive control blood, plasma or nucleic acids'. This demonstrates that there is still a need for direct replication studies to take place before any concrete statements about the corrolation between ME/CFS and XMRV (causative or coexistant) can be made.


The Whittemore Peterson Institue (2010)., WPI is aware of the recent UK study that was unable to detect the presence of XMRV in any CFS patient samples. Retrieved Febuary 2010 from http://www.wpinstitute.org/news/news_current.html

IACFS/ME (2010)., IACFS/ME Board of Directors 2009. Retrieved Febuary 2010 from http://www.iacfsme.org/LeadershipoftheIACFSME/JonathanKerr/tabid/370/Default.aspx

Redorbit (2010)., Further Doubt Cast On Virus Link To Chronic Fatigue. Retrieved Febuary 2010 from http://www.redorbit.com/news/health/1823927/further_doubt_cast_on_virus_link_to_chronic_fatigue/

Groom, H., Boucherit, v., Makinson, K., Randal, E., Baptista, S., Hagan, S., Gow, H., Mattes, F., Breuer, J., Kerr, J., Stoye, J., Bishop, K. (2010) Absence of xenotropic murine leukaemia virus-related virus in UK patients with chronic fatigue syndrome. Retrovirology 7:10. Retrieved Febuary 2010 from http://www.retrovirology.com/content/pdf/1742-4690-7-10.pdf

1 comment:

  1. Nicely done EK! Good to see you writing again.