The recently emerged variants of concern (VOC) B.1.1.7 in UK, B.1.1.35 in South Africa and P.1 in Brazil have increased transmissibility and are rapidly spreading worldwide. These variants have several substitutions that allow them to bypass the immune responses and are up to 10 times more contagious than the previous circulating SARS-COV-2 lineages. While in some regions P.1 predominates (as several estates in Brazil), in other countries B.1.1.7 or B.1.1.35 are most prevalent. Therefore, real-time surveillance of VOC is the key for rapid public health responses. In this matter, RT-PCR protocols that are capable of detecting VOCs easily and rapidly are needed. We developed and validated a protocol that detect simultaneously the 3 most widespread VOC. Although this protocol does not discriminate among the VOCs, it can reliably detect mixed infection. Importantly, our protocol successfully identified a co-infection by two SARS-COV-2 lineages (P.1 and B.1), confirmed through complete genome sequencing.