SUBMITTING A NOVEL HPV TYPE
How do I know if my HPV sequence corresponds to a putative novel type?
According to HPV taxonomy, a novel HPV type has less than 90% nucleotide similarity of the L1 gene to any other type (de Villiers et al.,2004; Bernard et al.,2010).
The L1 sequences from the officially established HPV types are found at the “Human Reference Clones” section, below the Table.
Here is a video example on how to check novelty of your sequence.
I have blasted my HPV sequence and didn’t find another HPV with more than 90% similarity. Does that mean that my sequence corresponds to a putative novel HPV type?
Not always. Genomes of some of putative novel HPV types might be in the International HPV Reference Center awaiting for re-cloning and confirmation. Therefore, the International HPV Reference Center, encourages all submitting authors, to send their sequence first (before proceeding to cloning) to confirm novelty.
Can my “putative novel HPV type” be cloned in several plasmids?
Yes. Authors can use as many plasmids as needed.
Should I provide information about the bacteria and protocols used for cloning?
Not necessarily. The International HPV Reference Center only requires the plasmids containing the putative novel type and the whole DNA sequence for this type.
Should I provide the primers to the International HPV Reference Center for confirming my putative novel sequence?
It is not necessary, but much appreciated.
Should I provide the whole genomic sequence to the International HPV Reference Center?
Yes. The International HPV Reference Center will re-sequence the whole L1 gene for sequence confirmation, as well as some other random fragments.
Should I publish my sequence in GenBank?
In order to have an officially established HPV type, publishing its sequence in GenBank is not mandatory, but highly recommended. The International HPV Reference Center encourages all authors to promote open access.
How do I send the clones to the International Reference Center?
Authors can send plasmids by normal post, to the following address:
Center for Cervical Cancer Elimination
International HPV Reference Center
Carina Eklund
F56 Karolinska Universitetssjukhuset Huddinge
141 86 Stockholm
There is no need for refrigeration.
When will I know if “my putative novel HPV type” is an officially established HPV type?
The submitting author will receive an email as soon as the International HPV Center has confirmed the sequence. At the same time, the novel type is posted as an officially established type in the International HPV Reference Center webpage.
REQUEST A CLONE FOR ACADEMIC RESEARCH
Can I request several clones at a time?
Yes. But the International HPV Reference Center does not have resources to provide large numbers of clones for free. Requests for more than 10 clones will incur a processing charge.
Can I request clones to be used as positive controls in my experiments?
Yes.
What is an MTA?
MTA stands for Material Transfer Agreement. It is an agreement form, needed to be signed by the requesting author. The International HPV Reference Center will send the clones to the requesting laboratory, once this MTA is signed.
Are all HPV types available for request?
In principle, yes. All HPV types whose owner gave permission to distribute, are available.
PROFICIENCY PANELS
What is the HPV proficiency panel?
The HPV proficiency panel consists of coded tubes with HPV DNA plasmids containing genomes of both oncogenic and benign HPV types. The panel composition is blinded to all laboratories participating in the global HPV proficiency study. There are 2 types of panels. Typing and screening panels.
- The global HPV LabNet TYPING proficiency panels are designed for the typing needs (vaccinology). The panel consists of 41 samples containing purified whole genomic plasmids of HPV 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68a and 68b in a background of human cellular DNA. This challenge is intended to evaluate assays that type HPV and is not appropriate for assays that detect HPV in general or grouped as high risk/low risk.
- The global HPV LabNet SCREENING proficiency panels are designed for the screening needs. The panels consist of 12 samples containing purified whole genomic plasmids of HPV 16, 18, 31, 33, 35, 39, 45, 51, 52, 56, 58, 59, 68a and 68b in a background of human cellular DNA. Participant laboratories will be asked to perform HPV screening using one or more of their usual HPV screening assays. The panel will evaluate the detection of the major oncogenic HPV types as well as detection of other oncogenic HPV types in groups.
To register for any of the HPV proficiency panels (typing/screening) and get more information contact EQUALIS: info@equalis.se.
What is the global HPV proficiency study?
The global HPV proficiency study serves to promote the harmonization and standardization of laboratory procedures. After distributing HPV proficiency panels to participating laboratories and receiving the results, the International HPV Reference Center will evaluate their typing/screening results, provide the results back to the participating laboratory and publish an aggregated overview of the status of HPV detection and typing/screening services worldwide.
Please have a look at previous publications in the corresponding section.
Can I be part of the proficiency panel studies?
Yes. To register for the HPV typing/screening proficiency panels, write to: info@equalis.se.
Authors are welcome to write to hpvcenter@ki.se, if there is any question not answered here.