PCR methods & point mutations

[Naveed Panjwani]

Francesc Xavier Lopez-Labrador <100647.73 at compuserve.com> wrote:
>
> Looking for information of PCR methods (different that ARMS or COP)to 
> detect viral point mutations.
> 

I would suggest SSCP (Single Stranded Conformation Polymorphism). Hot
PCR products amplified from a (poentially mutable) portion of the 
viral genome are heated to denature, and immediately run on a glycerol
containing polyacrylamide gel, against a known wild type PCR product
amplified with the same primers. Point mutations will show up as 
shifts in mobility compared to the wild type, as well as the 
appearance or disappearance of bands compared to the wild type pattern.
The banding pattern is a reflection of the various stable conformations
of the single strand, and the shifts are based on alternative
conformations assumed by a non wild type fragment, which are brought 
about at the scale of a single base difference.

This technique has been used in the past with Human Papilloma Viruses
and others (see below), and with great success to detect point 
mutations in hypermutable exons (5-8) of p53 gene. Can be used in 
conjunction with RT-PCR for RNA viruses (see below)

Note: Cold PCR should be done first to rule out large scale genomic re-
organisation, as this would complicate interpretation of the SSCP.

See the following two abstracts to get an idea of application in 
viral genotyping:

------------------------------------1--------------------------------

TI: Posttransplantation lymphoproliferative disorders frequently 
contain type A and not type B 
Epstein-Barr virus.
AU: Frank-D; Cesarman-E; Liu-YF; Michler-RE; Knowles-DM
AD: Department of Pathology, College of Physicians and Surgeons of 
Columbia University, New York, NY, 10021.
SO: Blood. 1995 Mar 1; 85(5): 1396-403
  
AB: Two families of Epstein-Barr virus (EBV), type A and type B, have
 been defined on the basis of sequence divergence in the EBNA-2 gene.
 Type A EBV immortalizes B cells more efficiently in vitro and infects
 immunocompetent individuals more commonly than type B EBV. However,
 increased rates of infection by type B EBV are seen in
 immunocompromised hosts and in many lymphoid neoplasms associated 
with immunocompromise. The posttransplantation lymphoproliferative 
disorders (PT-LPDs) are a heterogeneous group of B-cell neoplasms 
that arise in the setting of immunosuppressive therapy, and are 
associated with EBV infection. Whether type A and/or type B EBV 
are associated with PT-LPDs is unknown. Therefore, we investigated 
27 PT-LPD lesions from 22 solid-organ transplant recipients by 
polymerase chain reaction (PCR) at the EBNA-2 and EBNA-3c loci 
to detect sequence deletions that distinguish the two EBV families. 
Another locus, EBER, was examined by single-strand conformation 
polymorphism analysis (SSCP), in conjunction with direct sequencing 
in selected cases. Type A EBV was found in 24 of 27 cases (89%) as 
seen by amplification of the EBNA-2 and EBNA-3c regions. 
Four different EBER polymorphisms were detected, confirming the 
presence of different type A EBV isolates among these cases. 
Three cases were negative for infection by EBV. Surprisingly, 
despite the immunocompromised state of the hosts, none of the 27 
PT-LPD lesions harbored type B EBV. Thus, although type B EBV may 
commonly infect peripheral blood lymphocytes in immunocompromised 
individuals, they do not appear to induce readily PT-LPD formation.


------------------------------- 2 -----------------------------------

TI: Evolution and selection of hepatitis C virus variants in patients 
with chronic hepatitis C.
AU: Kurosaki-M; Enomoto-N; Marumo-F; Sato-C
AD: Second Department of Internal Medicine, Faculty of Medicine, 
Tokyo Medical and Dental University, Japan.
SO: Virology. 1994 Nov 15; 205(1): 161-9

AB: It has been shown that hepatitis C virus (HCV) populations in vivo
 are composed of different but highly homologous HCV genomes 
(quasispecies) as shown in the hypervariable region (HVR) that exists
 in the N-terminal of the envelope 2 gene of HCV, and that the 
predominant sequence of the HVR of HCV genomes changes rapidly over 
time. To further investigate genetic backgrounds of the change in the
 HVR of HCV genomes, 45 plasma samples serially obtained from nine 
patients with chronic hepatitis C were studied using population-based
 analyses. Total RNA was recovered and the envelope gene containing 
the HVR was amplified by the reverse transcription and nested 
polymerase chain reaction. The amplified cDNA was examined by the 
single strand conformation polymorphism (SSCP) analysis. 
Furthermore, 43 HCV sequences, separated by the SSCP analysis from 
three patients were determined by the dideoxy chain termination 
method, and the phylogenetic analysis was performed using the 
neighbor joining method. The SSCP analysis demonstrated that HCV 
population within each individual were composed of 1 to 6 
quasispecies. These quasispecies populations in vivo changed 
sequentially in eight of nine patients. Gradual selections of 
coexisting quasispecies were observed over 6- to 18-month periods in 
three patients, whereas complete replacements of previous 
quasispecies by new quasispecies were repeatedly observed over 
few-month intervals in five patients. The phylogenetic analysis on 
these quasispecies revealed the continuous accumulation of mutations 
in two patients and discontinuous appearance of evolutionarily 
distant quasispecies in one patient. These results indicate that HCV 
genomes in vivo form quasispecies populations, and that these 
quasispecies populations change during the natural course of chronic 
infection. Genetic mechanisms underlining the change of the HVR of 
HCV genome appear to be either continuous accumulation of mutations 
or selective overgrowth of preexisting minor variants from the large 
spectrum of quasispecies populations.