Is it correct to say, "The specimen was observed using a microscope."

The reason for the use of the passive voice is because the topic of the paragraph is most likely to be the "specimen" here. This concept may often be overlooked in English, but is widely taught in general language classes in many other languages.

It would be unnatural to use the active voice version if the rest the paragraph was written with the specimen as the topic.

"The virus sample had two DNA strands alongside the nucleus. It was green in color. We observed the specimen using a microscope. It was considered a small virus. It's DNA was very unique".

Notice how the active voice sentence doesn't fit in my crude example above.

Hence you should use the passive voice.

Passive is used in such statements to avoid the need to use "I" or "we". In some contexts (such as scholarly articles) it's considered poor form to for the authors to refer to themselves, except when absolutely necessary.