We studied this adaptation through passaging in our previous paper (Ramadhany et al. 2012 ; Yasugi et al., 2012), when we cultured human influenza viruses in embryonated eggs, some mutations occurred in HA binding site even only after 1 time passaging. The population of viruses carrying mutation will become dominant through passaging in egg. To lessen these mutations, culturing human influenza viruses in MDCK cell might be better option.

The genetic changes are less if you culture your viruses in MDCK cells. Though, some of the changes are very well known to occur at the receptor binding site on the HA. But if you grow your human viruses in eggs, the virus in order to adapt to the system is prone to get more genetic changes. But also, those occurring at the receptor binding site are also known. You will have to use both turkey and chicken red blood cells to detect viral titer. After sequencing you will be able to identify which changes are by culture and the new ones.

The changes will be insignificant if you do not do too many passages, anyway, cultivation elsewhere always lead to mutations. 

We studied this adaptation through passaging in our previous paper (Ramadhany et al. 2012 ; Yasugi et al., 2012), when we cultured human influenza viruses in embryonated eggs, some mutations occurred in HA binding site even only after 1 time passaging. The population of viruses carrying mutation will become dominant through passaging in egg. To lessen these mutations, culturing human influenza viruses in MDCK cell might be better option.

Thank you all of your replies, I will use cells in one passage prior sequencing and then try to find specific mutations related with culture.

If you have low viral loads, virus isolation may not be very successful. Typically, specimens with a Ct value close to 34 and above are difficult to isolate on cells and on embryonated eggs, but you can manage to sequence at least HA and NA genes by well designed one-step RT-PCRs followed by nested PCRs.

just one or two passages will not effect must on DNA sequence of genes. Otherwise also virus have some variation among them. so 1 or 2 passage will not have harm.

Nice to read the various opinions. Influenza by and large grows well in Embryonated hen's egg 10-11 doe and in TC as suggested. Growing in eggs or in cell culture the adaptability enhances for the host and gradually the affinity for the original host minuses. But not noticed on the initial passage. 

One passage will be Ok not more than one passage on egg

It will depend on the HA titer of the harvested virus after 1st passage. Some specimen(s) need 2-3 passage.

We cultivated H5N1 virus on egg for 20 successive passages,and detect only one amino acid mutation in passage 13

I agree with the observation of Mohamed Ali. I have propaged Influenza virus on routine basis between 1968 to late nineties ( over 30 years), The high yielding HA titre use to  achieve in 4-6 passages. I normally use to dilute the inoculum as per  the HA results but normally this was -3 to-4 tenfold dilution inoculated 0.2 ml/egg. The results were good most of the time. Rare cases the HA use to fall.. These were repeated by getting back to the previous passage harvested material  kept at -80 o C. in small aliquots. After reaching high repeatable titre, large batch of eggs were prepared to harvest 100-200 ml lot of high HA virus and again stored at -80 o C in 10-20 ml aliquots for future work. In rare cases fall in HA for the stored material was observed.

For the adoption of Influenza virus , my suggestion is fist with cell line because you may get more number of passages, within shot period,

in case of Egg it leads to more cross contamination while during the candling, inculating.

it may depends upon the virus stain

Probably the best way is to try it in cells, because the nature of the influenza viruses I´m using is human adapted (endemic viruses like H1N1, H3N2 and B viruses), so I think that cells will elicit less mutations than in eggs. I will try to find later the possible mutations related with this culture and isolate them. Thank you for all of your answers

Ivan, I agree that you will get less adaptation growing them in culture but there still may some mutations according to this article...

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0079252

9-11 days old live embryonated eggs are the best media to grow influenza virus and the route of inoculation is allointoic roiute. within 5 days (if virus is not high pathogenic) you can harvest allotoic fluid with high virus loafd. If high virulance strain , then embryo will die with in 24-48 hours. the use those eggs for virus harvesting.