Rekli su da bakterija nije problem, nego je vjerojatnije riječ o virusu.

In the past tense, the participle agrees with the subject in number and gender.

• rekli su = masculine plural
• rekle su = feminine plural

Croatian uses the masculine plural as the default for a mixed group or when the group’s gender is unknown or unimportant. So rekli su can mean they said for men, a mixed group, or an unspecified group.

Da introduces a subordinate clause, like English that.

So:

Rekli su da bakterija nije problem
= They said that the bacterium/bacteria is not the problem

In English, that is often omitted, but in Croatian da is normally used.

Because nego is the usual word in the pattern not X, but rather Y.

Here the sentence says:

nije problem, nego...
= is not the problem, but rather...

So nego is correcting or replacing the first idea.
Ali also means but, but it is more general and does not fit this correction pattern as well.

A simple comparison:

• Nije bakterija, nego virus. = It isn’t a bacterium, but rather a virus.
• Bakterija je mala, ali opasna. = The bacterium is small, but dangerous.

Here problem is nominative. After biti (to be), Croatian often uses a nominative predicate noun:

bakterija nije problem

Both bakterija and problem are nominative here.

Also, Croatian has no articles, so there is no separate word for the or a. Depending on context, problem can mean a problem or the problem.

This is a fixed expression. You should learn riječ je o + locative as a whole unit.

It means things like:

• it is about
• it is a matter of
• it is a case of
• in context, often we are dealing with

So riječ je o virusu means something like it is about a virus or more naturally it is a virus / we are dealing with a virus.

Although riječ literally means word, that literal meaning is not the important thing here.

Because the preposition o takes the locative case when it means about / concerning.

So:

• nominative: virus
• locative: virusu

That is why the sentence has o virusu.

This is also required by the fixed phrase riječ je o + locative.

Vjerojatnije means more likely. It is the comparative form of vjerojatno.

So:

• vjerojatno = probably / likely
• vjerojatnije = more likely

In this sentence, it works as part of an impersonal expression:

nego je vjerojatnije riječ o virusu

The idea is but it is more likely that it is a virus or but it is more likely that we are dealing with a virus.

It is not directly describing riječ as an ordinary adjective would, so you do not need a feminine form to match riječ.

Su and je are clitics: short unstressed forms that have special word-order rules in Croatian.

That is why you get:

• Rekli su...
• nego je...

rather than putting su or je wherever English would place are/is/have.

A useful beginner rule is that clitics usually go near the beginning of their clause. Croatian word order is flexible, but clitics are one of the main things that make some orders sound natural and others unnatural.