estimate the proportion of cases with either variant

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GoodTaste

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Variants were identified with the use of sequencing and on the basis of the spike (S) gene status. Data on all symptomatic sequenced cases of Covid-19 in England were used to estimate the proportion of cases with either variant according to the patients’ vaccination status.

Source: NEJM Effectiveness of Covid-19 Vaccines against the B.1.617.2 (Delta) Variant

Does "either" here mean "each of the two (variants)"?
 
Your use of "each" in the question is a little unclear, so I can't say yes or no.

It means that the proportion estimate was for the combination of people with the first or the second variant. They did not distinguish between the first and second variants when creating the overall estimate.
 
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Yes, "either" refers to two.
 
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