Genomic characterization of invasive meningococcal X isolates from Brazil, 1992-2022.

INTRODUCTION: Invasive meningococcal disease (IMD) is a major health problem. Given the post-COVID-19 pandemic scenario with the loosening of the non-pharmacological measures to control the virus transmission and considering the observed global reduction of meningococcal vaccination coverage, an increase in IMD cases can be expected. METHODOLOGY: Using whole-genome sequencing, we characterized six Neisseria meningitidis serogroup X (MenX) isolates recovered from IMD cases in Brazil in the last 30 years. RESULTS: The predominance (66.6%, 4/6) of ST2888 presenting fHbp 160, NHBA 129, NadA 21, and PorA 19,15 was found on isolates. Two novel STs, 15458 and 15477, were described. CONCLUSION: This study describes the circulation of MenX lineage ST2888 in Brazil, previously reported only in Europe. Continuous universal surveillance is crucial to implement prompt public health measures aiming to prevent and control non-vaccine preventable serogroup X IMD cases.

SARS-CoV-2 variants in severely symptomatic and deceased persons who had been vaccinated against COVID-19 in São Paulo, Brazil.

COVID-19 vaccination began in São Paulo, Brazil in January 2021, first targeting healthcare workers (HCWs) and the elderly, using the CoronaVac vaccine (Sinovac/Butantan) and subsequently the Oxford/AstraZeneca (ChAdOx1) vaccine (AstraZeneca/FIOCRUZ-RJ). Studies on such vaccines have shown efficacy in preventing severe cases and deaths, but there is a lack of information regarding their effectiveness. This manuscript presents data from the Instituto Adolfo Lutz (IAL), a public health laboratory located in São Paulo City that receives samples from 17 Regional Health Departments under the Secretary of Health of São Paulo, for SARS-CoV-2 genomic surveillance. Through May 15, 2021 IAL received 20 samples for analysis from COVID-19 vaccinated individuals who needed hospitalization and/or died from COVID-19. Next-generation sequencing was performed on an Ion Torrent S5 platform using the AmpliSeq™ SARS-CoV-2 kit. Almost all cases were vaccinated with CoronaVac and presented the gamma variant of concern (VOC). Cases of death were observed mostly in the elderly in nursing homes, and severe cases in younger frontline HCWs. This data confirmed that the SARS-CoV-2 gamma variant is highly transmissible, severe, and lethal for COVID-19 in these groups of individuals, thereby highlighting the importance of continuous vaccination and non-pharmacological prevention measures to avoid virus dissemination and the emergence of new VOCs.

La vacunación contra la COVID-19 empezó en São Paulo (Brasil) en enero del 2021 con los trabajadores de atención de salud (personal de salud) y las personas mayores, empleando la vacuna de CoronaVac (Sinovac/Butantan) y posteriormente la vacuna de Oxford/AstraZeneca (ChAdOx1) (AstraZeneca/FIOCRUZ-RJ). Los estudios sobre estas vacunas han mostrado su eficacia en la prevención de los casos graves y las muertes, pero existe falta de información con respecto a su efectividad. En este artículo se presentan datos del Instituto Adolfo Lutz (IAL), un laboratorio de salud pública ubicado en la ciudad de São Paulo que recibe muestras de 17 departamentos regionales de salud bajo la Secretaría de Salud de São Paulo, relativos a la vigilancia genómica del SARS-CoV-2. Hasta el 15 de mayo del 2021, el IAL había recibido 20 muestras para su análisis de personas vacunadas contra la COVID-19 que necesitaron hospitalización o murieron a causa de esta enfermedad. Se realizó una secuenciación de nueva generación en una plataforma Ion Torrent S5 mediante el kit para el SARS-CoV-2 AmpliSeq™. Casi todos los pacientes se habían vacunado con CoronaVac y presentaban la variante de preocupación gamma. Se observaron muertes principalmente de personas mayores en residencias y casos graves en personal de salud más joven de primera línea. Estos datos confirmaron que la variante gamma del SARS-CoV-2 es sumamente transmisible, grave y letal para la COVID-19 entre estos grupos y destacan la importancia de continuar con la vacunación y las medidas preventivas no farmacológicas para evitar la propagación del virus y la aparición de nuevas variantes de preocupación.

A vacinação contra a COVID-19 começou em São Paulo, Brasil, em janeiro de 2021, primeiramente dirigida a profissionais da saúde e idosos, utilizando a vacina CoronaVac (Sinovac/Butantan), e posteriormente a vacina Oxford/AstraZeneca (ChAdOx1) (AstraZeneca/Fiocruz-RJ). Os estudos sobre tais vacinas revelaram eficácia na prevenção de casos graves e mortes, mas há falta de informação em relação à sua efetividade. Este manuscrito apresenta dados do Instituto Adolfo Lutz (IAL), um laboratório de saúde pública localizado no município de São Paulo, que recebe amostras de 17 Departamentos Regionais de Saúde da Secretaria Estadual de Saúde de São Paulo para vigilância genômica do SARS-CoV-2. Até 15 de maio de 2021, o IAL recebeu 20 amostras para análise de indivíduos vacinados contra a COVID-19 que necessitaram de hospitalização e/ou morreram por COVID-19. O sequenciamento de nova geração foi realizado em plataforma Torrente de íon S5, utilizando o kit AmpliSeq™ SARS-CoV-2. Quase todos os casos foram vacinados com CoronaVac e apresentaram a variante de preocupação (VOC) gama. Os óbitos foram observados principalmente nos idosos de casas de repouso, e os casos graves em profissionais de saúde mais jovens da linha de frente. Esses dados confirmaram que a variante SARS-CoV-2 gama é altamente transmissível, grave e letal para COVID-19 nesses grupos de indivíduos, destacando, assim, a importância da vacinação contínua e de medidas preventivas não farmacológicas para evitar a disseminação viral e o surgimento de novas VOC.

SARS-CoV-2 reinfection in a healthcare professional in inner Sao Paulo during the first wave of COVID-19 in Brazil.

Coronavirus Disease 2019 pandemic remains a threat to public health. We report 2 cases of Coronavirus Disease 2019 infection in the same healthcare professional in Brazil. Genomic analysis identified that primoinfection was caused by the endemic lineage B.1.1.33 while reinfection by the lineage B.1.1.44, a lineage with an additional V1176F mutation in S protein.

COVID-19 laboratory diagnosis: comparative analysis of different RNA extraction methods for SARS-CoV-2 detection by two amplification protocols.

The gold standard for the laboratory diagnosis of COVID-19 is the reverse transcription quantitative real-time polymerase chain reaction (RT-qPCR) assay, which searches for SARS-CoV-2 target genes in nasopharyngeal/oropharyngeal (NP/OP) samples, and its performance depends on the quantity and quality of the RNA input. This study compared the performance and cost-effectiveness of three different kits/reagents for RNA extraction used in COVID-19 diagnosis in Sao Paulo, Brazil. A total of 300 NP/OP samples belonging to suspected cases of COVID-19 stored in a biorepository were randomly selected, and RNA was extracted using (i) automated extraction (Loccus, Extracta Kit FAST), (ii) manual extraction (BioGene Kit, Bioclin, Quibasa), and (iii) quick extraction methods (Lucigen, Quick DNA Extract Kit). Next, the samples were tested using RT-qPCR for SARS-CoV-2 with the Allplex 2019-nCoV modified assay and the Charité-Berlin protocol. All assays/kits were used according to the manufacturer's instructions. For the Allplex kit, the sensitivity in detecting SARS-CoV-2 with previously extracted RNA by different procedures was 100.0% for Loccus, 100.0% for BioGene and 91.9% for Quick. Using the Charité-Berlin protocol, the sensitivities were 81.4% for Loccus, 81.2% for BioGene and 60.7% for Quick. The least sensitive target gene and the gene most affected by RNA extraction procedures was the RNA-dependent RNA polymerase gene (Charité-Berlin protocol). No false-positive SARS-CoV-2 results were detected using RNA obtained from any of the different protocols. In conclusion, Loccus and BioGene RNA extractions were efficient for RT-qPCR assays, and although the BioGene procedure is less expensive, Loccus is the best choice because it allows the rapid handling of hundreds or thousands of samples, a desirable feature during pandemics. Although less sensitive, the Quick extraction is useful during outbreaks coupled with the Allplex amplification kit for SARS-CoV-2 diagnosis (κ = 0.925).

Loop-Mediated Isothermal Amplification (LAMP) Assay for Rapid and Accurate Confirmatory Diagnosis of HTLV-1/2 Infection.

Laboratory diagnosis of human T-lymphotropic viruses (HTLV) 1 and 2 infection is performed by serological screening and further confirmation with serological or molecular assays. Thus, we developed a loop-mediated isothermal nucleic acid amplification (LAMP) assay for the detection of HTLV-1/2 in blood samples. The sensitivity and accuracy of HTLV-1/2 LAMP were defined with DNA samples from individuals infected with HTLV-1 (n = 125), HTLV-2 (n = 19), and coinfected with HIV (n = 82), and compared with real-time polymerase chain reaction (qPCR) and PCR-restriction fragment length polymorphism (RFLP). The overall accuracy of HTLV-1/2 LAMP (95% CI 74.8-85.5%) was slightly superior to qPCR (95% CI 69.5-81.1%) and similar to PCR-RFLP (95% CI 79.5-89.3%). The sensitivity of LAMP was greater for HTLV-1 (95% CI 83.2-93.4%) than for HTLV-2 (95% CI 43.2-70.8%). This was also observed in qPCR and PCR-RFLP, which was associated with the commonly lower HTLV-2 proviral load. All molecular assays tested showed better results with samples from HTLV-1/2 mono-infected individuals compared with HIV-coinfected patients, who present lower CD4 T-cell counts. In conclusion, HTLV-1/2 LAMP had similar to superior performance than PCR-based assays, and therefore may represent an attractive alternative for HTLV-1/2 diagnosis due to reduced working time and costs, and the simple infrastructure needed.