You're on the right track here. Many people forget how important the elution volume is. The important thing to concentrate on here is that the eluate is equivalent to your total culture of 1.5 ml or pellet of 5E6 cells.

So if your qPCR reads (for example) 100 copies/ul, your eluate will contain 300 x 100 (30 000, 3E4) copies, and this is the same as the number of copies in your pellet, so the viral titer would be 3E4/5E6 per cell or 3E4/1500 per ul.

That, however, assumes that all the virus is in the pellet. My understanding is that the virus stays in the supernatant unless you're using an ultracentrifuge with centrifugal fields of 40 000 G and above.

You're on the right track here. Many people forget how important the elution volume is. The important thing to concentrate on here is that the eluate is equivalent to your total culture of 1.5 ml or pellet of 5E6 cells.

So if your qPCR reads (for example) 100 copies/ul, your eluate will contain 300 x 100 (30 000, 3E4) copies, and this is the same as the number of copies in your pellet, so the viral titer would be 3E4/5E6 per cell or 3E4/1500 per ul.

That, however, assumes that all the virus is in the pellet. My understanding is that the virus stays in the supernatant unless you're using an ultracentrifuge with centrifugal fields of 40 000 G and above.

I'm not totally clear what you are trying to calculate but here's a suggestion:

• Total input cells to the Qiagen extraction is 5E6
• PCR concentration reads X copies/uL
• Multiply PCR concentration by the dilution into PCR. If you diluted 1uL eluent into a 10uL PCR reaction = 10X copies/uL, this is your eluent concentration.
• Mulitply eluent concentration by your eluent volume = Total output copies

You will have some losses during the DNA extraction, but using this method you can find the ratio between cells input to the extraction and copies output