SARS-CoV-2 reinfection rate before and after VOC Omicron emergence: a retrospective study in Brazil.

SARS-COV-2 reinfection has been reported worldwide, although its rate remains unclear. VOC Omicron's emergence and its sub-variants led to an unprecedented number of COVID-19 cases in several countries, raising concerns regarding reinfection rates. 324,979 RT-qPCR-confirmed positive cases (72.57% from Minas Gerais State) diagnosed between April 1, 2020, and August 31, 2022, at the Hermes Pardini, Grupo Fleury (Brazil) were used to estimate the reinfection rate. Instances of reinfection were characterized by two positive tests occurring with a minimum interval of 60 days. We identified 11,669 cases of reinfection. The states of Minas Gerais, São Paulo, Rio de Janeiro and Goiás represented almost 41% of the reinfections. Up until epidemiological week 46 of 2020, only 14 cases of reinfection were recorded. The majority of reinfections, totalling 6,316 cases, were detected during the circulation period of the Omicron and its sublineages BA.1 and BA.2. Another 4,273 reinfections occurred during the circulation period of sublineages BA.4 and BA.5, revealing two distinct groups of observations. The first group comprised cases of reinfection with a shorter time interval (two infections within a period of up to 200 days), while the second group was associated with a longer time interval (two infections within a period of more than 500 days). The reinfection rate during this period was nearly 8%, which is six times higher than the rate observed at the beginning of the study. In conclusion, our study underscores the dynamic nature of SARS-CoV-2 reinfections and their correlation with emerging variants such as Omicron.

Retrospective Analysis of Omicron in Minas Gerais, Brazil: Emergence, Dissemination, and Diversification.

Brazil is one of the countries most affected by COVID-19, with the highest number of deaths recorded. Brazilian Health Institutions have reported four main peaks of positive COVID-19 cases. The last two waves were characterized by the emergence of the VOC Omicron and its sublineages. This study aimed to conduct a retrospective surveillance study illustrating the emergence, dissemination, and diversification of the VOC Omicron in 15 regional health units (RHUs) in MG, the second most populous state in Brazil, by combining epidemiological and genomic data. A total of 5643 confirmed positive COVID-19 samples were genotyped using the panels TaqMan SARS-CoV-2 Mutation and 4Plex SC2/VOC Bio-Manguinhos to define mutations classifying the BA.1, BA.2, BA.4, and BA.5 sublineages. While sublineages BA.1 and BA.2 were more prevalent during the third wave, BA.4 and BA.5 dominated the fourth wave in the state. Epidemiological and viral genome data suggest that age and vaccination with booster doses were the main factors related to clinical outcomes, reducing the number of deaths, irrespective of the Omicron sublineages. Complete genome sequencing of 253 positive samples confirmed the circulation of the BA.1, BA.2, BA.4, and BA.5 subvariants, and phylogenomic analysis demonstrated that the VOC Omicron was introduced through multiple international events, followed by transmission within the state of MG. In addition to the four subvariants, other lineages have been identified at low frequency, including BQ.1.1 and XAG. This integrative study reinforces that the evolution of Omicron sublineages was the most significant factor driving the highest peaks of positive COVID-19 cases without an increase in more severe cases, prevented by vaccination boosters.

Impact assessment of different DNA extraction methods for non-invasive molecular diagnosis of tegumentary leishmaniasis.

The aim of this study was to evaluate two methods of nucleic acid extraction (spin-column-based method - commercial kit and direct boil - DB) from swab sampling compared to biopsy sampling for the diagnosis of tegumentary leishmaniasis (TL), (cutaneous - CL and mucocutaneous - MCL forms). The impact of these nucleic acid extraction protocols on different types of PCR and LAMP techniques were compared regarding nucleic acid quality, molecular assays accuracy, indirect quantitation, and costs. The evaluated patients were 57 TL cases (36 CL and 21 MCL) and 34 non-cases. Swab samples extracted by the DB method showed a higher DNA degradation rate and worse DNA quality in comparison to the commercial kit. Molecular tests performed on biopsy samples showed identical or higher performance in all analysis, as compared to their own performance on swab samples for TL (CL and MCL). However, only the SSU rRNA TaqMan™ RT-PCR test showed a significant difference between the performance of biopsy and swab samples extracted by commercial kit. The kDNA-cPCR coupled with swab extracted by commercial kit showed the highest accuracy (95.6%) for TL diagnosis. The sensitivity of the LAMP-RT 18S method in swab samples extracted with a commercial kit (82.5%) was close to that found in biopsy samples (86%) for TL diagnosis. The DB extraction method presented the lowest cost. The use of swab as a minimally-invasive sampling method, associated with an efficient nucleic acid extraction protocol, may represent a low-cost alternative for the diagnosis of CL and MCL.

Development and Validation of a PCR-ELISA for the Diagnosis of Symptomatic and Asymptomatic Infection by Leishmania (Leishmania) infantum.

A kDNA PCR enzyme-linked immunosorbent assay (kDNA PCR-ELISA) for the diagnosis of human visceral leishmaniasis (HVL) was developed. The detection limit of the reaction, precision measurements, and cut-off of the kDNA PCR-ELISA were defined in a proof-of-concept phase. A reference strain of Leishmania (Leishmania) infantum and a bank of 14 peripheral blood samples from immunocompetent patients with VL were characterized using techniques considered gold standards, and 11 blood samples obtained from healthy individuals of an endemic area were also assessed. Phase II evaluation determined the performance of the assay in peripheral blood samples from 105 patients with VL (adults and children), 25 patients with Leishmania/HIV coinfection, 40 healthy individuals, and 33 asymptomatic individuals living in endemic areas. The kDNA PCR-ELISA exhibited satisfactory precision, with a detection limit of 0.07 fg of DNA from L. (L.) infantum and 1 parasite/mL blood. The overall sensitivity of the assay for all groups studied was 100% (95% confidence interval [CI]: 97.1-100%), and the specificity was 95% (95% CI: 83.5-98.6%). The kDNA PCR-ELISA was shown to be a useful tool for VL symptomatic and asymptomatic individuals diagnosis and its use in endemic countries may help monitor control interventions.