H5N1 i.m. immnization has fairly good amount of antibodies but they don't neutralize influenza virus whereas antibodies by i.n. route do neutralize influenza virus.
Don't know about influenza but in LCMV in mice that's invariably the case it seems. In humans . . . there is at least one case of a - now obviously discontinued - vaccine that did not result in immunity but instead enhancement of the disease.
It could be possible if you have an immunodominant region that is far from the active site, but it is uncommon since mostly sera are directed towards the antigenic sites that are close to the attachment active site.
Absolutely, it is possible to have binding antibodies to influenza virus, that can be detected by ELISA, but these antibodies are not to the neutralizing epitopes, which are primarily on the Haemagglutinin (HA) antigen. In influenza HAI (Haemagglutination inhibition antibodies) are considered surrogate to the clinical efficacy. Have you checked for the HAI antibodies in your sera?
In HAI, I do see HAI titer for the i.m. group but in microneutralization followed by HA to see MN titer, I don't see any microneutralization titer. Is that possible?
For the MN assay, HA was used as the readout. Briefly, two-fold serial dilutions of sera were added to 50TCID50 of the virus and incubated for 2 hours. Later, serum and virus were transferred to MDCK cells and further after 1 hour of incubation, culture supernatants were replaced by medium supplemented with TPCK Trypsin. This was incubated for 72 hours. After 72 hours, HA was done to find out the MN titer. The highest dilution of serum preventing virus infection was recorded as MN titer.
MN assay in WHO Manual was diluted to 100 TCID50/50 ul or 200TCID50/100 ul for the standard virus concentration to compare other research.
Observation should be under inverted microscope for viral CPE (Cytopathogenic effect) and record status. Incubation virus for 3-4 day in first or second passage may be Hemagglutinin in supernatant.
In each assay, you should have Quality control such as virus and cell control. Virus titration check is diluted in 1/2 log10 and add in plate culture for control your work.