First sequenced cases of Omicron BA.2 sublineage in Ecuador.

The largest wave of infection with SARS-CoV-2 virus in Ecuador was observed in mid-December 2021 and early January 2022, driven by B.1.1.529/BA (Omicron) variant. During the second half of March, an increase in the number of daily cases was observed and coincided with the emergence of the BA.2 variant, which we describe in the present study. The first sequenced five cases of SARS-CoV-2 21L/BA.2 in Ecuador were identified using variant specific genotyping by qPCR and confirmed by whole genome sequencing (WGS). The first sequenced Ecuadorian BA.2 isolate was obtained from a person with international travel history who became symptomatic 3 days after travelling, whereas in the other cases no travel history was recorded.

First case of within-host co-infection of different SARS-CoV-2 variants in Ecuador.

Background: COVID-19 infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can cause mild symptoms to severe illness and death. Co-infections of SARS-CoV-2 with other respiratory viruses have been described. However, two SARS-CoV-2 lineage co-infection have been rarely reported. Methodology: A genotyping analysis and two different types of whole genome sequencing were performed (Illumina MiniSeq and ONT MinION). When examining the phylogenetic analysis in NextClade and Pangolin webservers, and considering the genotyping findings, conflicting results were obtained. Results: The raw data of the sequencing was analyzed, and nucleotide variants were identified between different reads of the virus genome. B.1 and P.1 lineages were identified within the same sample. Conclusions: We concluded that this is a co-infection case with two SARS-CoV-2 lineages, the first one reported in Ecuador.

Detection of sentinel bacteria in mangrove sediments contaminated with heavy metals.

Mangroves in the Northwest Coast of South America are contaminated with heavy metals due to wastewater discharges from industries, affecting the biota from this environment. However, bacteria proliferate in these harsh environmental conditions becoming possible sentinel of these contaminations. In this study, bacterial community composition was analyzed by throughput sequencing of the 16S rRNA gene from polluted and pristine mangrove sediments affected by marked differences in heavy metal concentrations. Core bacteria were dominated by Proteobacteria, Firmicutes, and Bacteroidetes phyla, with strong differences between sites at class and genus levels, correlated with metal levels. Increment of abundance on specific OTUs were associated with either elevated or decreased concentrations of metals and with the sulfur cycle. The abundance of Sulfurovum lithotrophicum, Leptolinea tardivitalis, Desulfococcus multivorans and Aminobacterium colombiense increases when metals rise. On contrary, Bacillus stamsii, Nioella nitrareducens and Clostridiisalibacter paucivorans abundance increases when metal levels are reduced. We propose these OTUs as bacterial sentinels, whose abundance can help monitor the restoration programs of contaminated mangrove sediments in the future.

Heavy metal concentration in mangrove surface sediments from the north-west coast of South America.

Mangrove ecosystems are coastal estuarine systems confined to the tropical and subtropical regions. The Estero Salado mangrove located in Guayaquil, Ecuador, has suffered constant disturbances during the past 20 years, due to industrial wastewater release. However, there are no published data for heavy metals present in its sediments and the relationship with anthropogenic disturbance. In the present study, metal concentrations were evaluated in surface sediment samples of the mangrove, showing that B, Cd, Cu, Pb, Se, V, and Zn levels exceeded those declared in international environmental quality standards. Moreover, several metals (Pb, Sn, Cd, Ag, Mo, Zn and Ni) could be linked to the industrial wastewater present in the studied area. In addition, heavy metal levels detected in this mangrove are higher than previous reports on mangrove sediments worldwide, indicating that this mangrove ecosystem is one of the most disrupted on earth.