Endovascular (stent-graft)-assisted open vascular anastomosis.

Endovascular and open surgical approaches are an integral part of treating patients with complex vascular disease and are often considered separately. In some situations, traditional open surgical techniques can be used to facilitate an endovascular approach, as example: iliac conduit use for EVAR/TEVAR, subclavian or axillary conduits for complex endovascular aortic repairs (chimney, B-FEVAR), and bypass to great vessels or visceral artery (celiac, superior mesenteric and renal arteries) debranching. As devices and techniques evolve, the open and endovascular approaches can be utilized in more complimentary fashion. This paper describes the use of endovascular procedures to assist difficult open surgical situations such as iliofemoral bypass, aortic arch debranching involving the left subclavian artery, and distal right iliac artery management during open thoracoabdominal aortic aneurysm (TAAA) repair.

SARS-CoV-2 transmission in a highly vulnerable population of Brazil: a household cohort study.

Background: Household transmission studies seek to understand the transmission dynamics of a pathogen by estimating the risk of infection from household contacts and community exposures. We estimated within/extra-household SARS-CoV-2 infection risk and associated factors in a household cohort study in one of the most vulnerable neighbourhoods in Rio de Janeiro city. Methods: Individuals ≥1 years-old with suspected or confirmed COVID-19 in the past 30 days (index cases) and household members aged ≥1 year were enrolled and followed at 14 and 28 days (study period November/2020-December/2021). RT-PCR testing, COVID-19 symptoms, and SARS-CoV-2 serologies were ascertained in all visits. Chain binomial household transmission models were fitted using data from 2024 individuals (593 households). Findings: Extra-household infection risk was 74.2% (95% credible interval [CrI] 70.3-77.8), while within-household infection risk was 11.4% (95% CrI 5.7-17.2). Participants reporting having received two doses of a COVID-19 vaccine had lower extra-household (68.9%, 95% CrI 57.3-77.6) and within-household (4.1%, 95% CrI 0.4-16.6) infection risk. Within-household infection risk was higher among participants aged 10-19 years, from overcrowded households, and with low family income. Contrastingly, extra-household infection risk was higher among participants aged 20-29 years, unemployed, and public transportation users. Interpretation: Our study provides important insights into COVID-19 household/community transmission in a vulnerable population that resided in overcrowded households and who struggled to adhere to lockdown policies and social distancing measures. The high extra-household infection risk highlights the extreme social vulnerability of this population. Prioritising vaccination of the most socially vulnerable could protect these individuals and reduce widespread community transmission. Funding: Fundação Oswaldo Cruz, CNPq, FAPERJ, Royal Society, Instituto Serrapilheira, FAPESP.

Effect of fenestration configuration on renal artery outcomes during fenestrated-branched endovascular aortic repair.

OBJECTIVE: The aim of this study was to evaluate the effect of fenestration configuration and fenestration gap on renal artery outcomes during fenestrated-branched endovascular aortic repair (F/BEVAR). METHODS: A retrospective multicenter analysis was performed, including patients with complex aortic aneurysms treated with F/BEVAR that incorporated at least one small fenestration to a renal artery. The renal fenestrations were divided into groups 1 (8 × 6 mm) and 2 (6 × 6 mm). Primary patency, target vessel instability (TVI), freedom from secondary interventions (SIs), occurrence of type IIIc endoleak, all related to the renal arteries, were analyzed at 30-day, 1-year, and 5-year landmarks. The fenestration gap (FG) distance was analyzed as a modifier, and clustering was addressed at the patient level. RESULTS: A total of 796 patients were included in this study, 71.7% male, with a mean age of 73.3 ± 8.1 years. The mean follow-up was 30.0 ± 20.6 months. Of the 1474 small renal fenestrations analyzed, 47.6% were 8 × 6 mm, and 52.4% were 6 × 6 mm. At the 30-day landmark, primary patency (99.9% vs 98.0%; P value < .001 for groups 1 and 2, respectively), freedom from TVI (99.6% vs 97.1%; P value < .001 for groups 1 and 2, respectively), and freedom from SI (99.8% vs 98.4%; P value = .022 for groups 1 and 2, respectively) were higher in 8 × 6 compared with 6 × 6 fenestrations, and the incidence of acute kidney injury was similar across the groups (92.6% vs 92.7%; P value = .953 for groups 1 and 2 respectively). The primary patency at 1 and 5 years was higher in 8 × 6 fenestrations (1-year: 98.8% vs 96.9%; 5-year: 97.8% vs 95.7%, for groups 1 and 2, respectively, P values = .010 and .021 for 1 and 5 year comparisons, respectively). The freedom from SIs was significantly higher among 6 × 6 fenestrations at 5 years (93.1% vs 96.4%, for groups 1 and 2, respectively, P value = .007). The groups were equally as likely to experience a type Ic endoleak (1.3% and 1.6% for 8 × 6 and 6 × 6mm fenestrations, respectively, P = .689). The 6 × 6 fenestrations were associated with higher risk of kidney function deterioration (17.8%) when compared with 8 × 6 fenestrations (7.6%) at 5 years (P < .001). The risk of type IIIc endoleak was significantly higher among 8 × 6 fenestrations at 5 years (4.9% and 2% for 8 × 6 and 6 × 6 mm fenestrations, respectively; P = .005). A FG ≥5 mm negatively impacted the cumulative 5-year freedom from TVI (group 1: FG ≥5 mm = 0.714, FG <5 mm = 0.857; P < .001; group 2: FG ≥5 mm = 0.761, FG <5 mm = 0.929; P < .001) and the cumulative 5-year freedom from type IIIc endoleak (group 1: FG ≥5 mm = 0.759, FG <5 mm = 0.921; P = .034; group 2: FG ≥5 mm = 0.853, FG <5 mm = 0.979; P < .001) in both groups and the cumulative 5-year patency in group 2 (group 1: FG ≥5 mm = 0.963, FG <5 mm = 0.948; P = .572; group 2: FG ≥5 mm = 0.905, FG <5 mm = 0.938; P = .036). CONCLUSIONS: Fenestration configuration for the renal arteries impacts outcomes. The 8 × 6 small fenestrations have better patency at 30 days, 1 year, and 5 years, whereas 6 × 6 small fenestrations are associated with lower rates of SIs, primarily due to a lower incidence of type IIIc endoleaks. FG ≥5 mm at the level of the renal arteries significantly impacts the freedom from TVI, freedom from type IIIc endoleak, and 5-year patency independently of the fenestration size or vessel diameter.

Dispersion patterns of SARS-CoV-2 variants Gamma, Lambda and Mu in Latin America and the Caribbean.

Latin America and Caribbean (LAC) regions were an important epicenter of the COVID-19 pandemic and SARS-CoV-2 evolution. Through the COVID-19 Genomic Surveillance Regional Network (COVIGEN), LAC countries produced an important number of genomic sequencing data that made possible an enhanced SARS-CoV-2 genomic surveillance capacity in the Americas, paving the way for characterization of emerging variants and helping to guide the public health response. In this study we analyzed approximately 300,000 SARS-CoV-2 sequences generated between February 2020 and March 2022 by multiple genomic surveillance efforts in LAC and reconstructed the diffusion patterns of the main variants of concern (VOCs) and of interest (VOIs) possibly originated in the Region. Our phylogenetic analysis revealed that the spread of variants Gamma, Lambda and Mu reflects human mobility patterns due to variations of international air passenger transportation and gradual lifting of social distance measures previously implemented in countries. Our results highlight the potential of genetic data to reconstruct viral spread and unveil preferential routes of viral migrations that are shaped by human mobility patterns.

Comparative analysis of SARS-CoV-2 variants Alpha (B.1.1.7), Gamma (P.1), Zeta (P.2) and Delta (B.1.617.2) in Vero-E6 cells: ultrastructural characterization of cytopathology and replication kinetics.

This study compares the effects of virus-cell interactions among SARS-CoV-2 variants of concern (VOCs) isolated in Brazil in 2021, hypothesizing a correlation between cellular alterations and mortality and between viral load and transmissibility. For this purpose, reference isolates of Alpha, Gamma, Zeta, and Delta variants were inoculated into monolayers of Vero-E6 cells. Viral RNA was quantified in cell supernatants by RT‒PCR, and infected cells were analyzed by Transmission Electron Microscopy (TEM) for qualitative and quantitative evaluation of cellular changes 24, 48, and 72 hours postinfection (hpi). Ultrastructural analyses showed that all variants of SARS-CoV-2 altered the structure and function of mitochondria, nucleus, and rough endoplasmic reticulum of cells. Monolayers infected with the Delta variant showed the highest number of modified cells and the greatest statistically significant differences compared to those of other variants. Viral particles were observed in the cytosol and the cell membrane in 100 % of the cells at 48 hpi. Alpha showed the highest mean particle diameter (79 nm), and Gamma and Delta were the smallest (75 nm). Alpha and Gamma had the highest particle frequency per field at 48 hpi, while the same was observed for Zeta and Delta at 72 hpi and 24 hpi, respectively. The cycle threshold of viral RNA varied among the target protein, VOC, and time of infection. The findings presented here demonstrate that all four VOCs evaluated caused ultrastructural changes in Vero-E6 cells, which were more prominent when infection occured with the Delta variant.

Creating hemodialysis autogenous access in children and adolescents.

OBJECTIVE: End-stage renal disease (ESRD) in childhood and adolescence is rare, with relatively few published reports of pediatric ESRD vascular access. This study analyzes a 10-year experience creating arteriovenous fistulas (AVFs) in children and adolescents. Our goal is to review our strategy for creating functional autogenous vascular access in younger patients and report our results. METHODS: We retrospectively reviewed data and outcomes for consecutive vascular access patients aged ≤19 years during a 10-year period. Each patient had preoperative vascular ultrasound mapping by the operating surgeon in addition to physical examination. A distal forearm radiocephalic AVF was the first access choice when feasible, and a proximal radial artery inflow AVF was the next option. Demographic data, inflow artery, venous outflow target, and required transposition vs direct AVFs were variables included in the analysis. Primary and cumulative patency were calculated by Kaplan-Meier analysis. RESULTS: Thirty-seven AVFs were created in 35 patients. No grafts were used. Ages were 6 to 19 years (mean, 15 years), and 20 were male. Causes of ESRD included glomerular disease (n = 18) and urinary obstruction or reflux (n = 7), among others. Three had previous AVFs, and 10 were obese. The proximal radial artery supplied AVF inflow in 25 patients and the brachial artery in only seven. Eleven individuals required a transposition and one a vein translocation to the contralateral arm. No patients developed hand ischemia, although two later required banding procedures for high flow. Eleven patients had successful transplants. A single patient died, unrelated to the vascular access. Five AVFs failed. Of these, two had new successful AVFs created, two regained renal function, one was transplanted, and one declined other procedures. Primary and cumulative patency rates were 75% and 85% at 12 months, 70% and 85% at 24 months, and 51% and 85% at 36 months, respectively. Median follow-up was 16 months. CONCLUSIONS: Creating an AVF for hemodialysis is a successful vascular access strategy for pediatric and adolescent patients. Proximal radial artery AVFs provided safe and functional access when a distal AVF was not feasible. Cumulative AVF patency was 85% at 36 months.

Rare Case of Abdominal Aortic and Multiple Visceral Aneurysms in a Pediatric Patient With PIK3CA Mutation and Vasculitis.

Abdominal aortic aneurysms (AAA) are most commonly observed in elderly male patients and are particularly rare in children. Among the pediatric population, they are usually diagnosed in the context of connective tissue disorders, genetic mutations, or vasculitis. The same is true of visceral arteries aneurysms. This case report describes the staged management of an 11-year-old patient presenting PIK3CA mutation and a 5.8 cm infrarenal AAA associated with bilateral common iliac arteries and multiple visceral aneurysms, the largest observed in the superior mesenteric artery (SMA = 3.2 cm). After careful evaluation, decision was made to first approach the most life-threatening lesion (the infrarenal AAA due to the large diameter) and the remaining aneurysms in secondary procedures, with special attention to the SMA aneurysm. The patient underwent a staged repair, with the first phase consisting of an aortobi-iliac graft with the distal anastomosis made at the left common iliac artery and right external iliac artery. The right hypogastric artery was ligated. The second procedure consisted of SMA aneurysm repair with a plication technique, as 7 branches were visualized coming off the aneurysm sac. Postoperative pathology analysis of the aortic and SMA aneurysms sac revealed vasculitis with a mixed inflammatory pattern and a COL3A1 gene heterozygote variant. He is currently in his 18th month after the last surgical intervention, receiving immunomodulatory therapy, with a planned follow-up by the interdisciplinary team to monitor the medications' side effects and the diameter of the remaining visceral aneurysms.

Comparative analysis of SARS-CoV-2 variants Alpha (B.1.1.7), Gamma (P.1), Zeta (P.2) and Delta (B.1.617.2) in Vero-E6 cells: ultrastructural characterization of cytopathology and replication kinetics

Abstract This study compares the effects of virus-cell interactions among SARS-CoV-2 variants of concern (VOCs) isolated in Brazil in 2021, hypothesizing a correlation between cellular alterations and mortality and between viral load and transmissibility. For this purpose, reference isolates of Alpha, Gamma, Zeta, and Delta variants were inoculated into monolayers of Vero-E6 cells. Viral RNA was quantified in cell supernatants by RT‒PCR, and infected cells were analyzed by Transmission Electron Microscopy (TEM) for qualitative and quantitative evaluation of cellular changes 24, 48, and 72 hours postinfection (hpi). Ultrastructural analyses showed that all variants of SARS-CoV-2 altered the structure and function of mitochondria, nucleus, and rough endoplasmic reticulum of cells. Monolayers infected with the Delta variant showed the highest number of modified cells and the greatest statistically significant differences compared to those of other variants. Viral particles were observed in the cytosol and the cell membrane in 100 % of the cells at 48 hpi. Alpha showed the highest mean particle diameter (79 nm), and Gamma and Delta were the smallest (75 nm). Alpha and Gamma had the highest particle frequency per field at 48 hpi, while the same was observed for Zeta and Delta at 72 hpi and 24 hpi, respectively. The cycle threshold of viral RNA varied among the target protein, VOC, and time of infection. The findings presented here demonstrate that all four VOCs evaluated caused ultrastructural changes in Vero-E6 cells, which were more prominent when infection occured with the Delta variant.

Differential Type-I Interferon Response in Buffy Coat Transcriptome of Individuals Infected with SARS-CoV-2 Gamma and Delta Variants.

The innate immune system is the first line of defense against pathogens such as the acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The type I-interferon (IFN) response activation during the initial steps of infection is essential to prevent viral replication and tissue damage. SARS-CoV and SARS-CoV-2 can inhibit this activation, and individuals with a dysregulated IFN-I response are more likely to develop severe disease. Several mutations in different variants of SARS-CoV-2 have shown the potential to interfere with the immune system. Here, we evaluated the buffy coat transcriptome of individuals infected with Gamma or Delta variants of SARS-CoV-2. The Delta transcriptome presents more genes enriched in the innate immune response and Gamma in the adaptive immune response. Interactome and enriched promoter analysis showed that Delta could activate the INF-I response more effectively than Gamma. Two mutations in the N protein and one in the nsp6 protein found exclusively in Gamma have already been described as inhibitors of the interferon response pathway. This indicates that the Gamma variant evolved to evade the IFN-I response. Accordingly, in this work, we showed one of the mechanisms that variants of SARS-CoV-2 can use to avoid or interfere with the host Immune system.

Outcome Analysis Comparing Asymptomatic Juxtarenal Aortic Aneurysms Treated with Custom-Manufactured Fenestrated-Branched Devices and the "Off-The-Shelf" Zenith p-Branch Device.

BACKGROUND: Numerous endovascular options have been used for the repair of juxtarenal aortic aneurysms (JRAAs) over the last 15 years. This study aims to compare the performance between the Zenith p-branch device and custom-manufactured fenestrated-branched devices (CMD) for the treatment of asymptomatic JRAA. METHODS: A single-center retrospective analysis of prospectively collected data was performed. Patients with a diagnosis of JRAA submitted to endovascular repair between July 2012 and November 2021 were included in the study, being divided into 2 groups: CMD and Zenith p-branch. The following variables were analyzed: preoperative information: demographics, comorbidities, and maximum aneurysm diameter; procedural data: contrast volume, fluoroscopy time, radiation dose, estimated blood loss, and technical success; and postoperative data: 30-day mortality, duration of intensive care unit and hospital stay, major adverse events, secondary interventions, target vessel instability, and long-term survival. RESULTS: From a total of 373 physician-sponsored investigational device exemption (Cook Medical devices) cases performed at our institution, 102 patients presented the diagnosis of JRAA. Of these, 14 patients were treated with the p-branch device (13.7%) and 88 (86.3%) with a CMD. Both groups presented similar demographic composition and maximum aneurysm diameter. All devices were successfully deployed, with no type I or III endoleaks observed at procedure completion. The contrast volume (P = 0.023) and radiation dose (P = 0.001) were significantly higher in the p-branch group. No significant difference was observed between the groups for the remaining intraoperative data. No paraplegia or ischemic colitis has been observed during the first 30 days after the surgical procedures. There was no 30-day mortality in either group. One major cardiac adverse event was registered in the CMD group. Early outcomes were similar in both groups. No significant difference was found between the groups with respect to the presence of type I or III endoleaks during the follow-up. From a total of 313 target vessels stented in the CMD group (mean of 3.55 per patient) and 56 in the p-branch group (mean of 4 per patient), 4.79% and 5.35% presented instability, respectively, with no difference observed between the groups (P = 0.743). Secondary interventions were required in 36.4% of the CMD cases and 50% of the p-branch group, but this was not statistically different (P = 0.382). In the p-branch cohort, 2 of 7 reinterventions (28.5%) were target vessel-related and in the CMD group, 10 of 32 secondary interventions (31.2%) were target vessel-related. CONCLUSIONS: Comparable perioperative outcomes were obtained when appropriately selected patients were treated with either the off-the-shelf p-branch or CMD for JRAA. The long-term target vessel instability does not appear impacted by the presence of pivot fenestrations in comparison to other target vessel configurations. Given these outcomes, delay in CMD production time should be considered when treating patients with large juxtarenal aneurysms.

A straightforward one-step strategy for SARS-CoV-2 diagnosis and screening of variants of concern: a multicentre study.

BACKGROUND: The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) has changed unevenly over time around the world. Although whole genome sequencing is the gold standard for virus characterisation, the discovery of alpha VOC causing spike gene target failure (SGTF) result, when tested using an reverse transcription real-time polymerase chain reaction (RT-qPCR) assay, has provided a simple tool for tracking the frequencies of variants. OBJECTIVES: The aim of this study was to investigate if a multiplex RT-qPCR assay (BioM 4Plex VOC) could be used to detect SARS-CoV-2 and to perform a VOC screening test in a single reaction tube. Here, we present the multicentre study evaluating this assay. METHODS: Twelve laboratories have participated in the multicentre study. The BioM 4Plex VOC was distributed to them with detailed instructions of how to perform the test. They were asked to test the BioM 4Plex VOC in parallel with their routine Commercial SARS-CoV-2 diagnostic assay. Additionally, they were requested to select SARS-CoV-2-positive samples with genome sequenced and lineage definition according to PANGO lineage classification. FINDINGS: The BioM 4Plex VOC and commercial RT-PCR assay are equally effective in detecting SARS-CoV-2. Results revealed a specificity of 96.5-100% [95% confidence interval (CI)], a sensitivity of 99.8-100% (95% CI), and an accuracy of 99.8-100% (95% CI). A 99% concordance rate was found between results from the BioM 4Plex VOC and that from available genome sequencing data. MAIN CONCLUSIONS: The BioM 4Plex VOC provides an effective solution to detect SARS-CoV-2 infections and screening for VOCs in a single reaction. It is a straightforward method to help us monitor the frequency and distribution of VOCs and develop strategies to better cope with the pandemics.

Trends and Outcomes in Management of Thoracic Aortic Injury in Children, Adolescent, and Mature Pediatric Patients Using Data from the National Trauma Data Bank.

BACKGROUND: Thoracic aortic injury (TAI) is rare in the pediatric population. Thoracic endovascular aortic repair (TEVAR) is the recommended standard of care for treatment in the adult population given its association with lower rates of mortality and morbidity than traditional open repairs for treatment of TAI. However, there are unique anatomic challenges in treating pediatric patients with TEVAR which may impact the outcomes and pediatric guidelines. We aimed to compare current management trends and outcomes between different pediatric age groups using data from the National Trauma Data Bank (NTDB). METHODS: We analyzed the NTDB from 2007 to 2019 using International Classification of Diseases (ICD)-9 and -10 codes to identify patients with a TAI. We excluded patients older than 21 years and any patients who died in the emergency department. The pediatric patients were stratified by age group: children (1-11 years), adolescent (12-17 years), and mature (18-21 years) patients. Patient characteristics compared included injury mechanism and severity, TAI intervention, and outcomes between the 3 groups using bivariate analysis (analysis of variance for parametric and Kruskal-Wallis for nonparametric variables). These characteristics and outcomes were also compared by TAI intervention and injury mechanism. ICD-9 and -10 procedural codes were used to identify patients who underwent TEVAR, open aortic repair (OAR), or both. The modified Poisson regression was performed with relative risk (RR) to evaluate our primary outcome measure-mortality during the trauma admission. RESULTS: A total of 2,431 pediatric TAI were identified in the NTDB that met the inclusion criteria. This included 134 children (5.5%), 733 adolescent (30.2%), and 1,564 mature (64.3%) patients. Children had significantly lower median Injury Severity Scores (34.1) than the adolescent (38) or mature population (36.1) (P = 0.001). The mechanism of injury differed between age groups. Children had higher rates of blunt trauma (90.3% children, 89.6% adolescent, and 86.8% mature patients) and mature patients had higher rates of penetrating trauma (6% children, 10.1% adolescent, and 12.5% mature patients) (P < 0.001). TAI management also differed significantly between pediatric age groups. Mature patients had significantly higher rates of TEVAR (3% children, 25.2% adolescent, and 29.2% mature patients) and children were most likely to be treated with nonoperative management (NOM) (94% children, 67.9% adolescent, and 64.8% mature patients) (P < 0.001). Patients who were treated with TEVAR were discharge home most frequently (31.8% NOM, 54.1% TEVAR, 44.3% OAR, 22.2% both TEVAR and OAR). Upon modified Poisson regression analysis, patient age was not associated with an increased risk of in-hospital mortality. Intervention with TEVAR (RR: 0.22, 95% CI: 0.15-0.33, P < 0.001) and OAR (RR: 0.58, 95% CI: 0.36-0.93, P = 0.024) were associated with a lower risk of mortality than NOM. CONCLUSIONS: TAI is less prevalent in children compared to adults. TEVAR for TAI is associated with lower risk of in-hospital mortality compared to both NOM and OAR without differences between pediatric subgroups. Further studies should be completed to determine the most appropriate management guidelines.

A straightforward one-step strategy for SARS-CoV-2 diagnosis and screening of variants of concern: a multicentre study

BACKGROUND The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) has changed unevenly over time around the world. Although whole genome sequencing is the gold standard for virus characterisation, the discovery of alpha VOC causing spike gene target failure (SGTF) result, when tested using an reverse transcription real-time polymerase chain reaction (RT-qPCR) assay, has provided a simple tool for tracking the frequencies of variants. OBJECTIVES The aim of this study was to investigate if a multiplex RT-qPCR assay (BioM 4Plex VOC) could be used to detect SARS-CoV-2 and to perform a VOC screening test in a single reaction tube. Here, we present the multicentre study evaluating this assay. METHODS Twelve laboratories have participated in the multicentre study. The BioM 4Plex VOC was distributed to them with detailed instructions of how to perform the test. They were asked to test the BioM 4Plex VOC in parallel with their routine Commercial SARS-CoV-2 diagnostic assay. Additionally, they were requested to select SARS-CoV-2-positive samples with genome sequenced and lineage definition according to PANGO lineage classification. FINDINGS The BioM 4Plex VOC and commercial RT-PCR assay are equally effective in detecting SARS-CoV-2. Results revealed a specificity of 96.5-100% [95% confidence interval (CI)], a sensitivity of 99.8-100% (95% CI), and an accuracy of 99.8-100% (95% CI). A 99% concordance rate was found between results from the BioM 4Plex VOC and that from available genome sequencing data. MAIN CONCLUSIONS The BioM 4Plex VOC provides an effective solution to detect SARS-CoV-2 infections and screening for VOCs in a single reaction. It is a straightforward method to help us monitor the frequency and distribution of VOCs and develop strategies to better cope with the pandemics.

A straightforward one-step strategy for SARS-CoV-2 diagnosis and screening of variants of concern: a multicentre study

BACKGROUND The prevalence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) has changed unevenly over time around the world. Although whole genome sequencing is the gold standard for virus characterisation, the discovery of alpha VOC causing spike gene target failure (SGTF) result, when tested using an reverse transcription real-time polymerase chain reaction (RT-qPCR) assay, has provided a simple tool for tracking the frequencies of variants. OBJECTIVES The aim of this study was to investigate if a multiplex RT-qPCR assay (BioM 4Plex VOC) could be used to detect SARS-CoV-2 and to perform a VOC screening test in a single reaction tube. Here, we present the multicentre study evaluating this assay. METHODS Twelve laboratories have participated in the multicentre study. The BioM 4Plex VOC was distributed to them with detailed instructions of how to perform the test. They were asked to test the BioM 4Plex VOC in parallel with their routine Commercial SARS-CoV-2 diagnostic assay. Additionally, they were requested to select SARS-CoV-2-positive samples with genome sequenced and lineage definition according to PANGO lineage classification. FINDINGS The BioM 4Plex VOC and commercial RT-PCR assay are equally effective in detecting SARS-CoV-2. Results revealed a specificity of 96.5-100% [95% confidence interval (CI)], a sensitivity of 99.8-100% (95% CI), and an accuracy of 99.8-100% (95% CI). A 99% concordance rate was found between results from the BioM 4Plex VOC and that from available genome sequencing data. MAIN CONCLUSIONS The BioM 4Plex VOC provides an effective solution to detect SARS-CoV-2 infections and screening for VOCs in a single reaction. It is a straightforward method to help us monitor the frequency and distribution of VOCs and develop strategies to better cope with the pandemics.

Low prevalence of influenza A strains with resistance markers in Brazil during 2017-2019 seasons.

The influenza A virus (IAV) is of a major public health concern as it causes annual epidemics and has the potential to cause pandemics. At present, the neuraminidase inhibitors (NAIs) are the most widely used anti-influenza drugs, but, more recently, the drug baloxavir marboxil (BXM), a polymerase inhibitor, has also been licensed in some countries. Mutations in the viral genes that encode the antiviral targets can lead to treatment resistance. Worldwide, a low prevalence of antiviral resistant strains has been reported. Despite that, this situation can change rapidly, and resistant strain surveillance is a priority. Thus, the aim of this was to evaluate Brazilian IAVs antiviral resistance from 2017 to 2019 through the identification of viral mutations associated with reduced inhibition of the drugs and by testing the susceptibility of IAV isolates to oseltamivir (OST), the most widely used NAI drug in the country. Initially, we analyzed 282 influenza A(H1N1)pdm09 and 455 A(H3N2) genetic sequences available on GISAID. The amino acid substitution (AAS) NA:S247N was detected in one A(H1N1)pdm09 strain. We also identified NA:I222V (n = 6) and NA:N329K (n = 1) in A(H3N2) strains. In addition, we performed a molecular screening for NA:H275Y in 437 A(H1N1)pdm09 samples, by pyrosequencing, which revealed a single virus harboring this mutation. Furthermore, the determination of OST IC50 values for 222 A(H1N1)pdm09 and 83 A(H3N2) isolates revealed that all isolates presented a normal susceptibility profile to the drug. Interestingly, we detected one A(H3N2) virus presenting with PA:E119D AAS. Moreover, the majority of the IAV sequences had the M2:S31N adamantanes resistant marker. In conclusion, we show a low prevalence of Brazilian IAV strains with NAI resistance markers, in accordance with what is reported worldwide, indicating that NAIs still remain an option for the treatment of influenza infections in Brazil. However, surveillance of influenza resistance should be strengthened in the country for improving the representativeness of investigated viruses and the robustness of the analysis.

Sera of patients infected by earlier lineages of SARS-CoV-2 are capable to neutralize later emerged variants of concern.

Serum samples of 20 hospitalized coronavirus disease 2019 (COVID-19) patients from Brazil who were infected by the earlier severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages B.1.1.28 and B.1.1.33, and by the variant of concern (VOC) Gamma (P.1) were tested by plaque reduction neutralization test (PRNT90) with wild isolates of a panel of SARS-CoV-2 lineages, including B.1, Zeta, N.10, and the VOCs Gamma, Alpha, and Delta that emerged in different timeframes of the pandemic. The main objective of this study was to evaluate if the serum of patients infected by earlier lineages was capable to neutralize later emerged VOCs. We also evaluated if the 4-fold difference in PRNT90 titers is a reliable seropositivity criterion to distinguish infections caused by different SARS-CoV-2 lineages. Sera collected between May 2020 and August 2021 from the day of admittance to the hospital to 21 days after diagnostic of patients infected by the two earlier lineages B.1.1.28 and B.1.1.33 presented neutralizing capacity for all challenged VOCs, including Gamma and Delta. Among all variants tested, Delta and N.10 presented the lowest geometric mean of neutralizing antibody titers, and B.1.1.7, presented the highest titers. Four patients infected with Gamma, that emerged in December 2020, presented neutralizing antibodies for B.1, B.1.1.33, and B.1.1.28, its ancestor lineage. All of them had neutralizing antibodies under the level of detection for the VOC Delta. Patients infected by B.1.1.28 presented very similar geometric mean of neutralizing antibody titers for both B.1.1.33 and B.1.1.28. Findings presented here indicate that most patients infected in early stages of COVID-19 pandemic presented neutralizing antibodies capable to neutralize wild types of all later emerged VOCs in Brazil, and that the 4-fold difference in PRNT90 titers is not reliable to distinguish humoral response among different SARS-CoV-2 lineages.

Influenza A(H11N2) Virus Detection in Fecal Samples from Adélie (Pygoscelis adeliae) and Chinstrap (Pygoscelis antarcticus) Penguins, Penguin Island, Antarctica.

Influenza A viruses infect a range of host species, including a large variety of mammals and more than a hundred species of birds. A total of 95 avian fecal samples were collected from penguin colonies in the South Shetland Islands, close to the Antarctic Peninsula, and tested by reverse transcription-PCR (RT-PCR) to detect avian influenza viruses (AIVs). Five out of seven samples collected from Penguin Island were positive for AIVs. Analysis of the genomes recovered from four samples revealed the detection of influenza A(H11N2) virus in fecal samples from Adélie penguins (Pygoscelis adeliae) and from a colony of chinstrap penguins (Pygoscelis antarcticus). Bayesian phylogeographic analysis revealed the clustering of all currently available H11N2 samples from Antarctica's avifauna in a single cluster that emerged at least in the early 2010s, suggesting its continued circulation on the continent. Our results reinforce the need for continuous surveillance of avian influenza on the Antarctic continent. IMPORTANCE Although wild birds play a role in the transmission and ecology of avian influenza viruses (AIVs) across the globe, there are significant gaps in our understanding of the worldwide distribution of these viruses in polar environments. In this study, using molecular analysis and full-genome sequencing, we describe the detection of distinct influenza A(H11N2) viruses in fecal samples of penguins in the Southern Shetland Islands, Antarctica. We emphasize the need for virus monitoring as AIVs may have implications for the health of endemic fauna and the potential risk of the introduction of highly pathogenic AIVs to the continent.

Implementation of a COVID-19 Genomic Surveillance Regional Network for Latin America and Caribbean region.

The timely release of SARS-CoV-2 first genomic sequences allowed the identification of the etiologic agent and development of diagnostic protocols. Genomic sequencing was a crucial step in generating data for driving laboratory response and detections of SARS-CoV-2 since the start of the COVID-19 pandemic. Because of all the progression and achievements that timely release of genetic sequence data represents in the public health response, the Pan American Health Organization (PAHO) in collaboration with countries' public health laboratories, started implementation of a network for strengthening the Latin America and Caribbean (LAC) region on timely generation of SARS-CoV-2 genomic data. Here we describe the implementation of the COVID-19 Genomic Surveillance Regional Network in the Americas region during the beginning of the pandemic. The establishment of this network has strengthened laboratory response capacity at the country level, as well as facilitated timely release of SARS-CoV-2 genomic information to be used to complement the multiple response strategies for COVID-19 pandemic mitigation. As genomic epidemiology is useful for guiding public health decisions on outbreak and response, we also analysed the first SARS-CoV-2 genomic sequence data from countries of the Latin America and Caribbean Region.

SARS-CoV-2: Ultrastructural Characterization of Morphogenesis in an In Vitro System.

The pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has impacted public health and the world economy and fueled a worldwide race to approve therapeutic and prophylactic agents, but so far there are no specific antiviral drugs. Understanding the biology of the virus is the first step in structuring strategies to combat it, and in this context several studies have been conducted with the aim of understanding the replication mechanism of SARS-CoV-2 in vitro systems. In this work, studies using transmission and scanning electron microscopy and 3D electron microscopy modeling were performed with the goal of characterizing the morphogenesis of SARS-CoV-2 in Vero-E6 cells. Several ultrastructural changes were observed-such as syncytia formation, cytoplasmic membrane projections, lipid droplets accumulation, proliferation of double-membrane vesicles derived from the rough endoplasmic reticulum, and alteration of mitochondria. The entry of the virus into cells occurred through endocytosis. Viral particles were observed attached to the cell membrane and in various cellular compartments, and extrusion of viral progeny took place by exocytosis. These findings allow us to infer that Vero-E6 cells are highly susceptible to SARS-CoV-2 infection as described in the literature and their replication cycle is similar to that described with SARS-CoV and MERS-CoV in vitro models.