The SARS-CoV-2 virus infection led to millions of deaths during the COVID-19 pandemic. Hundreds of workers from several other Brazilian cities, as well as from other countries, arrive daily in Macaé to work in the oil supply chain, making this city a putative hotspot for the introduction of new viral lineages. In this study, we performed a genomic survey of SARS-CoV-2 samples from Macaé during the first outbreak of COVID-19, combined with clinical data and a molecular integrative analysis. First, phylogenomic analyses showed a high occurrence of viral introduction events and the establishment of local transmissions in Macaé, including the ingression and spread of the B.1.1.28 lineage in the municipality from June to August 2020. Second, SARS-CoV-2 mutations were identified in patients with distinct levels of COVID-19 severity. Third, molecular interactions of the mutated spike protein from three B.1.1.33 local samples and human ACE2 showed higher interactions than that of the wild-type spike protein from the ancestral virus. Altogether, these results elucidate the SARS-CoV-2 genomic profile in a strategic Brazilian city and further explore the functional aspects of SARS-CoV-2 with a characterization of emerging viral mutations associated with clinical data and the potential targets for drug development against SARS-CoV-2.

Summary: Chagas disease is estimated to affect 8 million people worldwide and is responsible for circa 10,000 deaths in Latin America every year. Vector control has been developed as the main strategy to control disease spreading. The identification of new targets is essential, and genes containing small open reading frames (smORFs - < 100 amino acids) are present as hundreds of putative new candidate targets in insect genomes. Here, we show that the prototypic smORF containing gene mille-pattes/polished-rice/tarsalless ( mlpt/pri/tal ) is essential for post-embryonic development of the kissing bug Rhodnius prolixus and for the metacyclogenesis of the Trypanosoma cruzi parasite during nymphal stages. Injection of double-stranded RNA against mlpt (Rp-ds mlpt ) during nymphal stages leads to a plethora of phenotypes which impairs post-embryonic development. First, nymphs of fourth or fifth stage injected with Rp-ds mlpt do not moult. Second, vector digestive physiology is largely modified, and haemozoin is significantly increased in the posterior midgut of Rp-ds mlpt nymphs. Third, Rp- mlpt knockdown inhibits the metacyclogenesis of Trypanosoma cruzi , the etiologic agent of Chagas disease. Thus, our study provides the first evidence of a smORF-containing gene regulating vector physiology, parasitic cycle and disease transmission.