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PubMed Searching techniques

post #1 of 15
Thread Starter 
A long time ago I said I would put together a guide to searching pubmed for information (I'm in library school, studying this stuff). Well, I think I can start putting it together.

I thought a fun way to do it would be to ask people for questions they have about vaccinations. I will do the search, record the whole process and then share it here. I find it easier to learn this stuff if I can follow through an actual process step-by-step and I figure other people might prefer something similar.

So, the reference desk is open. Anyone have a query that might be suitable for a medical journal search?

Some possible examples:

Prevnar AND ear infections

Vaccine clinical tests

vaccines AND autism

and so forth.

I won't be able to do more than two sample searches (this will take a fair amount of time), so I apologize in advance to anyone who ends up having to do their own research!

Nana (formerly Deborah)
post #2 of 15
I'm going to guess that my question can probably be answered off the top of someone's head:

Does the polio vax still have SV-40 contamination?

If that's too easy, then here's another:

What other viruses were found in the polio vax (SV-1 to SV-39), were they all discovered to have contaminated the vax?

Hope they aren't too silly. Just ones that jumped into my head.
post #3 of 15
Thread Starter 
Turqoise those are great questions! Have to travel to Chicago for a meeting this weekend, but I'll be back Sunday night and start doing some searching on Monday.

I think I can combine the two questions into one search process, so if there is anyone else with an "information need" (librarian lingo, ain't it awful?) please go ahead and put it up.

post #4 of 15
Hi Deborah,

I have a question (information need )

I'm looking for information on the hepatitis b vax and subsequent chronic coughs as a result of the shot.

Don't know if that makes any sense. If I need to clarify, let me know.

P.S. I love that you are calling yourself Nana. It makes me smile every time I see it.
post #5 of 15
Thread Starter 

sorry, will be delay

I'm going to have to wait a little before doing the searches. There is something wrong with my left eye and I'm trying to limit computer time. I don't know what it is and neither do the two doctors I saw today.

post #6 of 15
post #7 of 15
I'm sorry to hear about your eye, Deborah. I hope you/someone can figure out what's wrong with it, and feel better soon.

post #8 of 15
Big Hope you feel better soon! Take care of yourself!
post #9 of 15
Thread Starter 
Thanks, Nana
post #10 of 15
Thread Starter 

Reopening the reference desk

This introduction is very basic, so anyone who already knows about PubMed should skip it!

Introduction to PubMed

PubMed is a database consisting of millions of citations. What you get when you search is a listing of bibliographic information about articles, not the articles themselves. Most articles come with abstracts, which can provide a bit of information about the content. You cannot, however, trust an abstract to give you the whole picture since the abstract is written by the authors of the article.

Citations are sometimes supplied electronically by publishers. They will be added to the database before being processed or indexed. These citations are tagged [PubMed - as supplied by publisher]. Once the citations have been partially processed (basic citation info and abstracts in place), they are tagged [PubMed - in process]. After processing is completed the citations will include complete indexing with MeSH headings (more on this below) and will be tagged [PubMed - indexed for MEDLINE]. At any given moment the database will include thousands of records that are not completely processed. This affects the search process.

Let’s say that you are doing a proper search, using the MeSH headings. Under MeSH, vaccination is the correct term and if you search using immunization, you will miss some relevant citations. However, if you search using vaccination only, you will miss some recent articles that use immunization and do not include the term vaccination in their title or abstract. Once these articles have been completely indexed they will turn up for your vaccination only search.

So, if you just want to get a general overview of what is out there on a topic, you can just use the MeSH terminology and you will get all the articles that are correctly indexed. If you need to be exhaustive, : you need to use the “lay” terms, the “medical” terms and the MeSH headings. When you type in a search term the search system automatically translates it, if possible, into MeSH. It also searches on the term in its non-MeSH form. So, if you type in immunization, the system will translate this into [immunization (all fields) AND vaccination (MeSH)]. Isn’t that helpful?

PubMed is currently split into two databases: old PubMed (1950’s through 1965) and current PubMed (1966 through the present). Searching medical literature prior to the 1950’s can be challenging.
post #11 of 15
Deborah, thanks for the info. I have not done a PubMed search yet as I haven't gone thru all the archived and linked stuff here! (Something about having a toddler and three dogs.....)

Anyhow, you say that it links to abstracts and not complete articles. What do you do if you want the complete article? Are they accessible?
post #12 of 15
Thread Starter 

access to articles

Some are accessible: there will be a link or other information on how to get the article. Most can only be obtained through a library. The library would have to go through interlibrary loan and there would probably be a fee.

If you live near a university with a medical school or a hospital that has a medical library you can ask about memberships for the public.

Even at McGill University, which has a medical school, only a relatively small portion of the journals (indexed on PubMed) are currently in the collection. Scholarly journal costs have been increasing by 14 to 17% a year for over 10 years now, and college library budgets have not been increasing. Guess what has happened?


My family is visiting for the next couple of days, so the next part of the search guide will go up Thursday afternoon or Friday morning. I will be baby cuddling and story-telling in the meantime.
post #13 of 15
Thread Starter 

simian viruses

Here is the link to PubMed. I suggest that you print out these notes and then try following through some of the steps on PubMed to get the hang of working with the system.


Start by searching for terms using the MeSH database. You can access MeSH two ways. In the left-hand column, the second item under PubMed Services is MeSH Database. Or, you can use the drop-down list next to the word “search” in the top-left corner.

Type in one of the terms that you need to find.

Does the polio vax still have SV-40 contamination?
If that’s too easy, then here’s another:
What other viruses were found in the polio vax (SV-1 to SV-39), were they all discovered to have contaminated the vax?
I typed in polio vaccine and got:
No items found.
Suggestions: Plague vaccine; Sabin vaccine; Mumps vaccine; Salk vaccine; Rabies vaccine; Dna vaccines; Aids vaccines; Siv vaccines; Pnuimune vaccine; Viral vaccines;
Although I didn’t find what I was looking for, I got some possible leads. I clicked on Sabin vaccine and got:
1: Poliovirus Vaccine, Oral A live vaccine containing attenuated poliovirus, types I, II, and III, grown in monkey kidney cell tissue culture, used for routine immunization of children against polio. This vaccine induces long-lasting intestinal and humoral immunity. Killed vaccine induces only humoral immunity. Oral poliovirus vaccine should not be administered to immunocompromised individuals or their household contacts. (Dorland, 28th ed)
This is not a broad enough term: I want to look at all possible variations of polio vaccine. Click on the term and you get:
1: Poliovirus Vaccine, Oral
A live vaccine containing attenuated poliovirus, types I, II, and III, grown in monkey kidney cell tissue culture, used for routine immunization of children against polio. This vaccine induces long-lasting intestinal and humoral immunity. Killed vaccine induces only humoral immunity. Oral poliovirus vaccine should not be administered to immunocompromised individuals or their ousehold
contacts. (Dorland, 28th ed)
administration and dosage
adverse effects
antagonists and inhibitors
cerebrospinal fluid
chemical synthesis
diagnostic use
isolation and purification
supply and distribution
therapeutic use

Restrict Search to Major Topic headings only
Do Not Explode this term (i.e., do not include MeSH terms found below this term
in the MeSH tree).

Entry Terms: Oral Poliovirus Vaccine
Vaccine, Oral Poliovirus
Sabin Vaccine
Vaccine, Sabin

All MeSH Categories
Chemicals and Drugs Category
Immunologic and Biological Factors
Biological Products
Viral Vaccines
Poliovirus Vaccines
Poliovirus Vaccine, Oral

There is a lot of information here. The subheadings can be used to limit your search to certain aspects of the topic. The subheading we need, “contamination” doesn’t exist. (Surprise!!!) Further down, under All MeSH Categories, is an excerpt of the applicable tree. You can search a term at any level of the tree and everything below will be included in your search unless you click the “do not explode” box. So, we want to search Poliovirus Vaccines, which will include every variation on the vaccine that has been indexed by PubMed.

Do similar searches for the Simian Viruses:

Here is what I found:

1: Simian virus 5 A species of RUBULAVIRUS originally isolated from cultured primary monkey cells. Its natural host is the DOG in which it causes kennel cough, but it can also infect humans. Year introduced: 2004
2: Viral Structural Proteins Viral proteins that do not regulate transcription. They are coded by viral structural genes and include nucleocapsid core proteins (gag proteins), enzymes (pol proteins), and membrane components (env proteins). Transcription of viral structural genes is regulated by viral regulatory proteins. Year introduced: 1990
3: Simian virus 40 A species of POLYOMAVIRUS originally isolated from Rhesus monkey kidney tissue. It produces malignancy in human and newborn hamster kidney cell cultures. Year introduced: 2001

1: Polyomavirus A genus of potentially oncogenic viruses of the family POLYOMAVIRIDAE. These viruses are normally present in their natural hosts as latent infections. The virus is oncogenic in hosts different from the species of origin. Year introduced: 1994
2: Antigens, Polyomavirus Transforming Polyomavirus antigens which cause infection and cellular transformation. The large T antigen is necessary for the initiation of viral DNA synthesis, repression of transcription of the early region and is responsible in conjunction with the middle T antigen for the transformation of primary cells. Small T antigen is necessary for the completion of the productive infection cycle. Year introduced: 1988
3: Leukoencephalopathy, Progressive Multifocal An opportunistic viral infection of the central nervous system associated with conditions that impair cell-mediated immunity (e.g., ACQUIRED IMMUNODEFICIENCY SYNDROME and other IMMUNOLOGIC DEFICIENCY SYNDROMES; HEMATOLOGIC NEOPLASMS; IMMUNOSUPPRESSION; and COLLAGEN DISEASES). The causative organism is JC Polyomavirus (JC VIRUS) which primarily affects oligodendrocytes, resulting in multiple areas of demyelination. Clinical manifestations include DEMENTIA; ATAXIA; visual disturbances; and other focal neurologic deficits, generally progressing to a vegetative state within 6 months. (From Joynt, Clinical Neurology, 1996, Ch26, pp36-7) Year introduced: 1973
4: JC Virus A species of POLYOMAVIRUS, originally isolated from the brain of a patient with progressive multifocal leukoencephalopathy. The patient's initials J.C. gave the virus its name. Infection is not accompanied by any apparent illness but serious demyelinating disease can appear later, probably following reactivation of latent virus. Year introduced: 2002
5: BK Virus A species of POLYOMAVIRUS apparently infecting over 90% of children but not clearly associated with any clinical illness in childhood. The virus remains latent in the body throughout life and can be reactivated under certain circumstances. Year introduced: 2002
6: Polyomavirus Infections Infections with POLYOMAVIRUS, which are often cultured from the urine of kidney transplant patients. Excretion of BK VIRUS is associated with ureteral strictures and CYSTITIS, and that of JC VIRUS with progressive multifocal leukoencephalopathy (LEUKOENCEPHALOPATHY, PROGRESSIVE MULTIFOCAL). Year introduced: 2002
7: Simian virus 40 A species of POLYOMAVIRUS originally isolated from Rhesus monkey kidney tissue. It produces malignancy in human and newborn hamster kidney cell cultures. Year introduced: 2001
1: Polyomaviridae A family of small, non-enveloped DNA viruses, infecting mainly MAMMALS, and containing a single genus: POLYOMAVIRUS. Year introduced: 2002
Only two of the 40 viruses have been indexed. There seem to be at least two different “species” of viruses and there may very well be many more.

I decided to do my searches on SV-40 and POLYOMAVIRUS.

Now you can switch to PubMed. There is a way of doing searches directly from MeSH, but I’d like to keep things simple.

I typed in:
Simian virus 40
If you click on details (top-right) you can see how PubMed reorganizes your terminology.
("simian virus 40"[MeSH Terms] OR Simian virus 40[Text Word])
results 12,145

Then I did a search on my second term:
Poliovirus Vaccines
Results 3,197

Used History (top, middle) to combine the two searches
Results 96
96 articles can be skimmed in a reasonable amount of time.
Selected seven
Displayed as citations
: Dev Biol (Basel). 2001;105:211-7. Evaluation of the new control methods for oral poliomyelitis vaccine. Grachev VP, Karganova GG, Rumyantsev AA, Ivanova OE, Eremeeva TP, Drozdov SG. Chumakov Institute of Poliomyelitis and Viral Encephalitides RAMS, Moscow Region, Russia. In the draft recommendations for production and control of OPV the WHO proposed new control methods: (i) mutant analysis with PCR and restriction enzyme cleavage (MAPREC) assay that allows evaluation of poliovirus population heterogeneity at the molecular level; (ii) neurovirulence (NV) test using transgenic mice susceptible to polioviruses and (iii) control of the seed lots for the presence of the simian virus 40 (SV40) DNA sequence. This paper is focused on our experience in the practical implementation of the new methods at the Institute of Poliomyelitis and Viral Encephalitides (IPVE). Using methods based on PCR we have demonstrated that working seed viruses used by IPVE for OPV production are free from SV40 DNA sequences. Our experience on the conduction of the OPV type 3 control using TgPVR21 mice NV test (seven vaccine lots) and the MAPREC assay (more than 150 samples of single harvests and monovalent bulks) showed that these methods may be used instead of the monkey NV test, because they could not pass the vaccine failed monkey NV test. The necessity for single harvests control is discussed. MeSH Terms: Animals Human Mice Poliomyelitis/prevention & control* Poliovirus/genetics Poliovirus/pathogenicity Poliovirus Vaccine, Oral/immunology* Poliovirus Vaccine, Oral/standards* Simian virus 40/genetics World Health Organization Substances: Poliovirus Vaccine, Oral

2: Biologicals. 2000 Mar;28(1):1-4. Live oral poliovirus vaccines do not contain detectable simian virus 40 (SV40) DNA. Sierra-Honigmann A, Krause PR. Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, MD 20892, USA. Prior to 1962, poliovirus vaccines produced in rhesus monkey kidney cells were contaminated with SV40. Recent studies reporting the detection of SV40 in human tumours raised concern that SV40 may be oncogenic in humans. To provide further assurance that currently used poliovirus vaccines are not contaminated with SV40, we used the polymerase chain reaction (PCR) to search for SV40 DNA in live oral poliovirus vaccines manufactured in the United States between 1972 and 1996. SV40 DNA sequences were not found in any of the vaccine lots tested. MeSH Terms: Consumer Product Safety DNA, Viral/analysis* Drug Contamination* Human Poliovirus Vaccine, Oral* Simian virus 40/genetics Simian virus 40/isolation & purification* Support, U.S. Gov't, Non-P.H.S. Support, U.S. Gov't, P.H.S. Substances: DNA, Viral Poliovirus Vaccine, Oral

3: Biologicals. 1999 Mar;27(1):1-10. Examination of poliovirus vaccine preparations for SV40 sequences. Sangar D, Pipkin PA, Wood DJ, Minor PD. National Institute for Biological Standards and Control Blanche Lane, South Mimms, Potters Bar, Hertfordshire, EN6 3QG. Oral poliovaccines derived from the strains developed by Sabin have been the basis of vaccination against poliomyelitis in the U.K. since 1962. Contamination of earlier materials with the monkey virus SV40, particularly inactivated Salk type poliovaccines, is well documented. Precautions have been in place for more than 30 years to prevent SV40 contamination of oral poliovaccines based on screening of donor animals and tests for SV40 infectivity. PCR was applied to examine all archived samples of oral poliovaccines available to us dating from 1966 to the present, including all vaccines used in the U.K. since 1980, for the presence of SV40 sequences. Of 132 materials examined, 118 were negative on initial testing and fourteen gave reactions which on further examination were attributed either to cross contamination during handling in the laboratory at National Institute for Biological Standards and Control (NIBSC) or to non-specific amplification. It was concluded that none of the samples contained SV40 sequences. The materials included 69 separate monovalent bulks of poliovirus type 1, 2 or 3 grown on monkey kidney cells from four different manufacturers and 74 bulks grown on human diploid cells from two manufacturers.One additional seed material from 1962 contained low levels of unique and characteristic SV40 sequences. The seed had been treated by the manufacturer to inactivate DNA viruses and tests by the manufacturer and at NIBSC failed to demonstrate the presence of infectious SV40 virus. Monovalent bulks prepared by the manufacturer from this seed were negative for SV40 sequences by PCR.The PCR studies provide no evidence of contamination of oral poliovaccines used in the UK with infectious SV40 and suggest that the steps taken to ensure the absence of infectious SV40 are satisfactory. Copyright 1999 The International Association for Biologicals. MeSH Terms: Animals Base Sequence COS Cells Cell Line Cell Survival Cercopithecus aethiops DNA, Viral/genetics Drug Contamination/prevention & control Human Macaca fascicularis Molecular Sequence Data Papovaviridae Infections/virology Poliovirus Vaccine, Oral/analysis* Poliovirus Vaccine, Oral/standards Polymerase Chain Reaction Reference Standards Sequence Homology, Nucleic Acid Simian virus 40/genetics* Tumor Virus Infections/virology Vero Cells Substances: DNA, Viral Poliovirus Vaccine, Oral

4: Dev Biol Stand. 1998;94:221-5. Examination of poliovaccines for the presence of SV40 sequences. Sangar DV, Wood DJ, Minor PD. National Institute for Biological Standards and Control, Potters Bar, Herts, UK. Batches of monovalent oral poliovirus vaccine bulks previously screened for infectious SV40 by cell culture methods and used in the United Kingdom from 1971-96 in trivalent oral poliovirus vaccine have now been examined by a newly developed PCR for the presence of SV40 sequences. Up to April 1997, over 190 batches have been examined. SV40 sequences were not detected in any of the vaccines. This provides additional assurance that oral poliovirus vaccines used in the U.K. from 1971 are free of SV40 contamination. Publication Types: Review Review, Tutorial MeSH Terms: Animals Cells, Cultured/virology DNA, Viral/chemistry
DNA, Viral/chemistry Drug Contamination Haplorhini Human Poliovirus Vaccine, Inactivated/chemistry* Polymerase Chain Reaction/methods Simian virus 40/isolation & purification* Substances: DNA, Viral Poliovirus Vaccine, Inactivated

5: Dev Biol Stand. 1998;94:217-9. Product quality control testing for the oral polio vaccine. Brock B, Kelleher L, Zlotnick B. Wyeth-Lederle Vaccines and Pediatrics, Pearl River, NY 10965-1299, USA. A brief overview regarding the quality control testing of the Sabin oral polio vaccine is provided. Product testing procedures and specifications are established through product license agreements between the vaccine manufacturer and the FDA Center for Biologics Evaluation and Research. The manufacture and testing of ORIMUNE is a multi-stage process that is closely monitored by the FDA following explicit protocols and requires extensive quality control testing at various stages. Publication Types: Review Review, Tutorial MeSH Terms: Animals Cells, Cultured/virology Haplorhini Licensure Poliovirus Vaccine, Oral/standards* Quality Control Simian virus 40/isolation & purification United States United States Food and Drug Administration Virus Cultivation/standards Substances: Poliovirus Vaccine, Oral

6: JAMA. 1998 Jan 28;279(4):292-5. Comment in: JAMA. 1998 May 20;279(19):1527-8. JAMA. 1998 Nov 4;280(17):1481-2. Contamination of poliovirus vaccines with simian virus 40 (1955-1963) and subsequent cancer rates. Strickler HD, Rosenberg PS, Devesa SS, Hertel J, Fraumeni JF Jr, Goedert JJ. Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Md 20852, USA. CONTEXT: Poliovirus vaccine contaminated with live simian virus 40 (SV40), a macaque polyomavirus that is tumorigenic in rodents, was used extensively in the United States between 1955 and 1963. Simian virus 40 DNA has recently been detected in several rare human tumors, including ependymomas, osteosarcomas, and mesotheliomas. OBJECTIVE: To determine the risk of ependymoma, osteosarcoma, and mesothelioma among Americans who as children received SV40-contaminated poliovirus vaccine. DESIGN: Retrospective cohort study using data from the Surveillance, Epidemiology, and End Results program (1973-1993) and the Connecticut Tumor Registry (1950-1969), as well as national mortality statistics (1947-1973). SETTING: United States. PARTICIPANTS: Birth cohorts that were likely to have received SV40-contaminated poliovirus vaccine as infants, born 1956 through 1962 (60 811730 person-years of observation); as children, born 1947 through 1952 (46430953 person-years); or that were unexposed, born 1964 through 1969 (44959979 person-years). MAIN OUTCOME MEASURES: Relative risk (RR) of each cancer among exposed compared with unexposed birth cohorts. RESULTS: Age-specific cancer rates were generally low and were not significantly elevated in birth cohorts exposed to SV40-contaminated vaccine. Specifically, compared with the unexposed, the relative risk of ependymoma was not increased in the cohorts exposed as infants (RR, 1.06; 95% confidence interval [CI], 0.69-1.63), or as children (RR, 0.98; 95% CI, 0.57-1.69) nor did the exposed have an increased risk of all brain cancers. Osteosarcoma incidence also showed no relation to exposure as infants (RR, 0.87; 95% CI, 0.71-1.06) or children (RR, 0.85; 95% CI, 0.59-1.22). Last, mesotheliomas were not significantly associated with exposure, although the cohorts studied have not yet reached the age at which these tumors tend to occur. CONCLUSIONS: After more than 30 years of follow-up, exposure to SV40-contaminated poliovirus vaccine was not associated with significantly increased rates of ependymomas and other brain cancers, osteosarcomas, or mesotheliomas in the United States. MeSH Terms: Adolescent Adult Brain Neoplasms/epidemiology* Brain Neoplasms/etiology Brain Neoplasms/virology Child Child, Preschool Drug Contamination* Ependymoma/epidemiology* Ependymoma/etiology Ependymoma/virology Human Incidence Infant Mesothelioma/epidemiology* Mesothelioma/etiology Mesothelioma/virology Osteosarcoma/epidemiology* Osteosarcoma/etiology Osteosarcoma/virology Papovaviridae Infections/epidemiology Papovaviridae Infections/etiology Poliovirus Vaccine, Inactivated*/adverse effects Retrospective Studies Risk Simian virus 40*/isolation & purification Tumor Virus Infections/epidemiology Tumor Virus Infections/etiology United States/epidemiology Vaccination Substances: Poliovirus Vaccine, Inactivated

7: Dev Biol Stand. 1996;88:5-7. Safety of biopharmaceuticals: a current perspective. Parkman PD. Parkman Associates, Kensington MD, USA. The impetus for this conference comes in large measure from the continuing development of the ICH Viral Safety document concerned with testing and evaluation of the viral safety of biotechnology products derived from characterized cell lines of human or animal origin [1]. My opening remarks for this conference were, I think, suggested by the organizers in the belief that George Santayana's quote, "Those who cannot remember the past are condemned to repeat it" has validity for this effort. In this brief review I have tried to recall some past unfortunate episodes and outline the lessons that they might have for us. I have also attempted to outline a number of issues which I believe are critical to the success of efforts to guarantee, as much as humanly possible, the safety that we seek balanced against our ability to develop and use important new products. Publication Types: Historical Article Review Review, Tutorial MeSH Terms: Animals Chick Embryo Drug Contamination* History of Medicine, 20th Cent. Human Leukosis Virus, Avian Poliovirus Vaccine, Inactivated/adverse effects Poliovirus Vaccine, Oral/adverse effects Simian virus 40 Viral Vaccines/history* Viral Vaccines/standards Yellow fever virus Substances: Poliovirus Vaccine, Inactivated Poliovirus Vaccine, Oral Viral Vaccines
Next search one of the several possible types of simian virus:

Results 775

I decided to search all vaccines to see if I could turn up contamination in any other vaccine with any of this type of virus.

Combine with vaccines
Results 225

Redid search to eliminate all the SV40 stuff I’d already seen

((("polyomavirus"[MeSH Terms] OR POLYOMAVIRUS[Text Word]) AND ("vaccines"[MeSH Terms] OR vaccines[Text Word])) NOT ("simian virus 40"[MeSH Terms] OR SV 40[Text Word]))

results 55
mostly articles about trying to make vaccines (anti-cancer) using polyomaviruses

chose 4 that looked relevant to contamination issues
displayed as citations

There is a drop-down list box on the left labeled “Display.” I usually choose citation because I’ll get the abstract and the list of terms indexed. This terminology can be used to develop further searches. I also find it helpful in deciphering the reason that a particular article was “found” in my search, especially if the search seems to be turning up lots of irrelevant stuff.

On the right is a box labeled “Send to.” If you choose text, you can copy what you find and paste it into a document without getting a lot of irrelevant formatting. This also saves space.

1: Biologicals. 1997 Dec;25(4):381-90.

Risk assessment on the carcinogenic potential of hybridoma cell DNA: implications for residual contaminating cellular DNA in biological products.

Dortant PM, Claassen IJ, van Kreyl CF, van Steenis G, Wester PW.

Laboratory of Pathology and Immunobiology, National Institute for Public Health and the Environment, Bilthoven, The Netherlands.

The aim of this study was to evaluate the possible carcinogenic potential of residual DNA derived from immortalized and possibly tumorigenic cell lines due to activated oncogenic sequences (oncogenes). These cell lines have been used for the production of biologicals, i.e. monoclonal antibodies, lymphokines and vaccines. The authors used hybridoma DNA as a first model. For this reason experiments in two species were performed, namely in 3-4 week-old female Balb/c mice and newborn Riv:TOX rats. Doses of 250 micrograms DNA, derived from Balb/c hybridoma cells, were injected subcutaneously (s.c.) in 200 mice. These mice
also received a s.c. injection of the solvent only (TE buffer) at another site of the back skin (negative control for local tumour development). An additional group of 50 mice was treated intraperitoneally (i.p.) with the solvent only to serve as a negative control group for possible systemic tumorigenic effects.
Doses of 5 micrograms plasmid pPy1 DNA, containing the entire Polyoma virus genome, served as positive control and were injected s.c. and i.p. in 20 and 50 mice, respectively. Doses of 50 micrograms hybridoma DNA or 5 micrograms pPy1 DNA were injected s.c. in rats too, using nine animals per group. During the
experiment, animals were observed weekly, especially for the occurrence of subcutaneous tumours at the injection sites. The mouse study was terminated after more than 2 years, the rat study after 1 year. Gross necropsy was performed on all animals and histopathological examination of grossly suspected neoplastic lesions was performed. In the mouse experiment, tumour development at the s.c. injection site of the DNA was observed in one out of 20 animals in the pPy1-treated positive control group (neurofibrosarcoma) and one out of 200 animals in the hybridoma DNA-treated group (haemangioma-like lesion). Tumour development at or near the s.c. injection site of the solvent only was observed in two out of 200 animals. In the rat study none out of nine hybridoma DNA-treated rats developed tumours at the injection site, while three out of nine rats of the positive control group, injected with the pPy1 DNA, showed local tumour development (benign and malignant soft tissue tumours.) It is concluded that, at the high dose and numbers of animals tested, parenteral administration of hybridoma DNA does not induce local tumour development. Furthermore, no indications were found for systemic carcinogenic potential of the hybridoma DNA used. Based on a worst case approach of our data, the oncogenic risk of 100 pg residual DNA was estimated to be 2 x 10(-9), a value intermediate of the estimations of the WHO (1987) and the Dutch Health Council (1988) 5 x 10(-11) and 2 x 10(-7), respectively. Therefore, it is unlikely that the risk of 100 pg of DNA derived from other immortalized cell lines will exceed the level of generally accepted cancer risk of 10(-6).
MeSH Terms:
Biological Products*
DNA, Neoplasm/toxicity*
DNA, Viral/toxicity*
Drug Contamination*
Mice, Inbred BALB C
Neoplasms, Experimental/etiology
Risk Assessment
Tumor Cells, Cultured

Biological Products
DNA, Neoplasm
DNA, Viral

2: Biologicals. 1996 Jun;24(2):131-5.

Detection of bovine polyomavirus contamination in fetal bovine sera and modified live viral vaccines using polymerase chain reaction.
Kappeler A, Lutz-Wallace C, Sapp T, Sidhu M.

Biologics Evaluation Laboratory, Animal Diseases Research Institute, Agriculture and Agri-Food Canada, Nepean, Ontario, Canada.

A nested polymerase chain reaction (PCR) assay has been developed for the detection of bovine polyomavirus (BPyV) DNA. The assay has been used to screen commercial lots of fetal bovine serum and modified live veterinary vaccines for the presence of the agent. A PCR product of the expected size was detected after the first round of PCR for eight out of 20 serum lots, but in none of the 14 vaccines tested. The subsequent nested assay revealed that four more serum lots were positive for BPyV DNA, as well as two vaccine lots. When hybridized with a
labelled probe, blots of the PCR products from vaccines revealed that in one of the two positive samples a specific product was present after the first PCR at a level not detectable in gel electrophoresis. Nested PCR appears to be a useful tool for the detection of low level contamination with BPyV DNA of products used in, and derived from cell culture.

MeSH Terms:
DNA, Viral/analysis*
Fetal Blood/chemistry*
Polymerase Chain Reaction
Viral Vaccines/chemistry*

DNA, Viral
Viral Vaccines

3: Arch Virol. 1986;87(3-4):287-96.

Human exposure to bovine polyomavirus: a zoonosis?

Parry JV, Gardner SD.

A competitive-type solid phase radioimmunoassay (RIA) was developed for the detection of antibody to bovine polyomavirus. Comparison of RIA and counter-immunoelectrophoresis (CIE) results on 273 cattle sera indicated that both techniques were detecting antibody of like specificity. Human sera from 256
blood donors, 219 people recently vaccinated against polio, rubella or rabies, 50 immunosuppressed patients and 472 people with various occupational exposure to cattle were tested for antibody to bovine polyomavirus, the foetal rhesus monkey kidney strain, (anti-FRKV) by RIA. Apart from one blood donor and one of 108 rabies vaccinees only those in close contact with cattle possessed anti-FRKV. Compared with 62 per cent seropositive in the natural hosts, cattle, 71 per cent of veterinary surgeons, 50 per cent of cattle farmers, 40 per cent of abattoir workers, 16 per cent of veterinary institute technical staff and 10
per cent of veterinary students were anti-FRKV positive. Our findings indicate that the theoretical hazard of FRKV infection from undetected contamination of current tissue culture derived vaccines may, in practice, be remote. Proposed wider use of primate kidney cells as substrates for new vaccines may increase
this risk.

MeSH Terms:
Antibodies, Viral/analysis
Blood Donors
Environmental Exposure
Polyomavirus/growth & development*
Veterinary Medicine
Viral Vaccines/immunology

Antibodies, Viral
Viral Vaccines

4: Prog Clin Biol Res. 1983;105:149-56.

Frequency of antibody to BK antigen in women whose children developed malignancies and women who developed detectable carcinoma in situ of the cervix during this pregnancy.

Madden DL, Iltis J, Tzan N, Sever JL.

Paired sera from 21 women whose children had malignancy and 15 women who were diagnosed as having abnormal pathology in the cervix and matched normal controls were studied for presence of BK antibodies by the ELISA technique. BK antibody
was detected in 74% of the women in the first serum sample obtained. Evidence of BK antibody rises were observed in eight of 72 women (11%) and was distributed equally among women with abnormal children and women with abnormal pathology in the cervix and controls and that the level of antibody was not influenced by vaccination with killed polio vaccine during this pregnancy. Our serological data fails to show an association between infection with BK virus and malignancy in the children or carcinoma in situ of the cervix.

MeSH Terms:
Antibodies, Viral/analysis*
Antigens, Viral
BK Virus/immunology*
Carcinoma in Situ/etiology
Carcinoma in Situ/immunology*
Cervix Neoplasms/etiology
Cervix Neoplasms/immunology*
Child, Preschool
Enzyme-Linked Immunosorbent Assay
Fluorescent Antibody Technique
Infant, Newborn
Maternal-Fetal Exchange
Middle Aged
Poliovirus Vaccine, Inactivated/immunology
Pregnancy Complications, Neoplastic/immunology*

Antibodies, Viral
Antigens, Viral
Poliovirus Vaccine, Inactivated
I have a feeling that PubMed is not the best place to try to track down info on the other 39 simian viruses. The results are not particularly exciting.

There are some other terms that I didn’t search, (see above) so feel free to play around and see what you can find! Have fun.

Coming soon, the search for Hepatitis Vaccine and chronic coughs…

post #14 of 15
Thread Starter 

Sandy Mintz just published a new "Scandals" on vaccine contamination with animal diseases. Look in the upper left-hand corner for the link.

post #15 of 15
Thread Starter 

hep b vax and coughs

I’m looking for information on the hepatitis b vax and subsequent chronic coughs as a result of the shot.
This turned out to be a frustrating and unsatisfactory search. Starting with the MeSH database I found the following terms:

1: Hepatitis B Vaccines Vaccines or candidate vaccines containing inactivated hepatitis B or some of its component antigens and designed to prevent hepatitis B. Some vaccines may be recombinantly produced. Year introduced: 1993
__________________________________________________ _______________________________

1: Cough A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. It is a protective response that serves to clear the trachea, bronchi, and/or lungs of irritants and secretions, or to prevent aspiration of foreign materials into the lungs.
“Chronic cough” is not a MeSH term.

I started my PubMed search by combining Hepatitis B Vaccines and Cough. This brought up (sadly) the fact that a whole bunch of scientists (idiots?) are working on combining heb b vax with whooping cough vax.

Below is the list of searches I tried.

(chronic[All Fields] AND ("cough"[MeSH Terms] OR cough[Text Word])) AND Hepatitis B Vaccines
results 0

"chronic cough"[All Fields]
results 1088

"chronic cough" AND Hepatitis B Vaccines
results 0

"Hepatitis B Vaccines"[MeSH] AND "Hepatitis B Vaccines/adverse effects"[MeSH]
results 459

"Respiratory Tract Diseases/chemically induced"[MeSH]

My final search combined the last two listed above and produced this:

1: Am J Public Health. 2001 Feb;91(2):313-5.

Importance of attributable risk in monitoring adverse events after immunization:
hepatitis B vaccination in children.

De Serres G, Duval B, Boulianne N, Rochette M, Dionne M, Fradet MD, Masse R.

Institut national de sante publique du Quebec, Quebec Canada.

OBJECTIVES: Most vaccine safety data present only the postvaccination incidence of all adverse events rather than an estimate of attributable risk. This study sought to illustrate the difference between the 2 estimates with data from a
hepatitis B immunization program. METHODS: The incidence of health problems occurring before and after each dose of hepatitis B vaccine in a cohort of 1130 children were compared. RESULTS: Although 47.5% of all children reported an adverse event during the 4 weeks following each of the 3 doses, adverse events
attributable to immunization occurred in only 10.6% of children. CONCLUSIONS:
Postimmunization incidence systematically overestimates the risk of adverse events. Estimating actual attributable risk is necessary to avoid false beliefs regarding immunization.

MeSH Terms:
Adverse Drug Reaction Reporting Systems*
Bias (Epidemiology)
Comparative Study
Data Interpretation, Statistical*
Drug Hypersensitivity/epidemiology
Drug Hypersensitivity/etiology
Drug Monitoring/methods*
Fever/chemically induced
Follow-Up Studies
Gastrointestinal Diseases/chemically induced
Gastrointestinal Diseases/epidemiology
Headache/chemically induced
Hepatitis B Vaccines/adverse effects*
Respiratory Tract Diseases/chemically induced
Respiratory Tract Diseases/epidemiology
Risk Factors
Support, Non-U.S. Gov't
Urban Health/statistics & numerical data
Vaccines, Synthetic/adverse effects*

Hepatitis B Vaccines
Vaccines, Synthetic
You see…the real problem is all those silly people incorrectly blaming vaxes for sick babies…side-effects are actually over-reported!

Anyhow, the answer seems to be that chronic coughs have not been published as a side effect of the hepatitis B vaccine in PubMed.

Please feel free to ask for further explanations if anything is unclear. I didn’t want to overload you all with details of how to search, but I’ll be happy to answer any questions.


Do you want to know how to find specific articles? Find articles by specific authors? Use additional features?

These searches have only demonstrated a few of the nifty features of PubMed.

If there is further interest I can do more...
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