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.

Scopalina ruetzleri is one of the most common marine sponges in the Western Tropical Atlantic, where it has been regarded as widely distributed through distinct biogeographic areas and seemingly unaffected by the Amazon River, the world’s largest input of freshwater and continental sediments. Scopalina ruetzleri has a relatively wide morphological variation in habit and spicules’ shape and size, which raises suspicions of it being a species complex. The examination of a comprehensive collection of previously identified S. ruetzleri specimens enabled us to reassess intraspecific variation through an integrative approach, which included genetics, phylogenetics, statistical, and morphological data. Additional material of Scopalina erubescens and Scopalina hispida from the Western Atlantic were included in the analyses. From the previous intraspecific variation of S. ruetzleri we discovered a cryptic species, Scopalina brasiliana sp. nov., differing subtly in spiculation, as in the proportion of styles and styloids. Both species are highly supported by phylogenetic analyses with COX1, 16S, ITS2, and 28S rDNA sequences. A second cryptic species from Bermuda was also revealed, but only with available ITS2 data; it remains undescribed. Scopalina ruetzleri and S. brasiliana sp. nov. were found in sympatry across a large sector of the Tropical Southwest Atlantic Province, with the new species being currently the only Scopalina occurring in areas further south, in the Warm Temperate Southwestern Atlantic Province. Scopalina ruetzleri was also sympatric with S. hispida in the Tropical Northwestern Atlantic Province, in which the latter appears to be restricted, while S. ruetzleri seems capable of advancing southwards, through the provinces of the Northern Brazilian Shelf and the Southwest Tropical Atlantic. Thus, the continuous distribution of S. ruetzleri from the Gulf of Mexico and the Caribbean to the Brazilian areas seems unaffected by freshwater and sediments carried by the Amazon River, with records of the species at the mouth of this river, at 55 m depth. The southern region of Patagonia hosts no Scopalina species yet, while the Magellanic Province houses three, S. erubescens and Scopalina bunkeri, both from the Malvinas/Falkland Islands, with the former also described here from the Magellan Strait (South Patagonia), and Scopalina cribrosa from Northwest Patagonia. Given the apparent regionalization and sympatry of Scopalina species, many of which have been described in recent years, we advocate for a widespread revision of all other lineages through integrative approaches whenever possible in order to solve taxonomic conflicts, reveal cryptic species, and highlight biogeographic boundaries of these relict heteroscleromorph sponges. ZooBank: https://zoobank.org/References/CC8643D9-7F85-424D-A504-A74EB1F09FBA