Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead

Metagenomic next-generation sequencing (mNGS) is the process of sequencing all genetic material in a biological sample. The technique is growing in popularity with myriad applications including outbreak investigation, biosurveillance, and pathogen detection in clinical samples. However, mNGS programs are costly to build and maintain, and additional obstacles faced by low- and middle-income countries (LMICs) may further widen global inequities in mNGS capacity. Over the past two decades, several important infectious disease outbreaks have highlighted the importance of establishing widespread sequencing capacity to support rapid disease detection and containment at the source. Using lessons learned from the COVID-19 pandemic, LMICs can leverage current momentum to design and build sustainable mNGS programs, which would form part of a global surveillance network crucial to the elimination of infectious diseases.

Immunogenicity and safety of a RBD vaccine against SARS-CoV-2 in a murine model.

INTRODUCTION: Although more than half of the world's population is already vaccinated, the appearance of new variants of concern puts public health at risk due to the generation of new immunogens against the virus as a crucial and relevant strategy in the control of these new variants. METHODS: A preclinical study used a potential vaccine candidate (RBD, SARS-CoV-2). Four groups of BALB/c mice were used, a control group, an adjuvant group, a group inoculated with one dose of RBD subunit protein, and the fourth group inoculated with two doses of RBD subunit protein. RESULTS: No inflammatory or cellular changes were shown in the mice's anatomopathological evaluation. Higher kinetics and 75% seroconversion were obtained in the mice inoculated with two doses of RBD (P < 0.0001). CONCLUSIONS: The application of two doses of the RBD vaccine candidate in BALB/c mice proved safe and immunogenic against SARS-CoV-2.

Implementation of rapid and frequent SARS-CoV2 antigen testing and response in congregate homeless shelters.

BACKGROUND: People experiencing homelessness who live in congregate shelters are at high risk of SARS-CoV2 transmission and severe COVID-19. Current screening and response protocols using rRT-PCR in homeless shelters are expensive, require specialized staff and have delays in returning results and implementing responses. METHODS: We piloted a program to offer frequent, rapid antigen-based tests (BinaxNOW) to residents and staff of congregate-living shelters in San Francisco, California, from January 15th to February 19th, 2021. We used the Reach-Effectiveness-Adoption-Implementation-Maintenance (RE-AIM) framework to evaluate the implementation. RESULTS: Reach: We offered testing at ten of twelve eligible shelters. Shelter residents and staff had variable participation across shelters; approximately half of eligible individuals tested at least once; few tested consistently during the study. Effectiveness: 2.2% of participants tested positive. We identified three outbreaks, but none exceeded 5 cases. All BinaxNOW-positive participants were isolated or left the shelters. Adoption: We offered testing to all eligible participants within weeks of the project's initiation. Implementation: Adaptations made to increase reach and improve consistency were promptly implemented. Maintenance: San Francisco Department of Public Health expanded and maintained testing with minimal support after the end of the pilot. CONCLUSION: Rapid and frequent antigen testing for SARS-CoV2 in homeless shelters is a viable alternative to rRT-PCR testing that can lead to immediate isolation of infectious individuals. Using the RE-AIM framework, we evaluated and adapted interventions to enable the expansion and maintenance of protocols.

Evaluation of the humoral response induced by BBIBP-CorV vaccine by determining neutralizing antibodies in peruvian healthcare personnel. / Evaluación de la respuesta humoral inducida por la vacuna BBIBP-CorV mediante la determinación de anticuerpos neutralizantes en personal sanitario peruano.

OBJECTIVE.: To determine the titer of antibodies against the receptor binding domain (RBD) of the spike protein (S) in health personnel between the 4th and 12th week after receiving the BBIBP-CorV vaccine (Sinopharm). MATERIALS AND METHODS.: We included a total of 168 healthcare workers from two hospitals in the region, who complied with the complete Sinopharm vaccine schedule; serum antibodies were measured using the Elecsys® Anti-SARS-CoV-2 test. RESULTS.: All participants developed antibodies to the RBD domain. The lowest antibody titer level was 1.78 U/mL. Levels equal to or above 250 were found in 70 (41.7%) participants. The geometric mean was 82.6 (95% CI: 67.8-100.6). Women had higher antibody levels. Participants whose antibodies were measured between 4- and 7-weeks post-vaccination showed significantly higher antibody levels than patients whose antibody levels were measured between 10- and 12-weeks post-vaccination. Among patients with a history of COVID-19, antibody levels were found to be at or above 250 U/mL in 88% of cases, compared to 6% among those without a history of COVID-19, (p<0.001). CONCLUSION.: All participants immunized with BBIBPCorV vaccine were positive for antibodies against the SARS-CoV-2 spike protein RBD. The correlation between the titer level and protection against COVID-19, as well as the length of the protection provided by the vaccine, needs to be evaluated.

OBJETIVO.: Determinar el título de anticuerpos frente al dominio de unión al receptor (RBD) de la proteína espiga (S) en personal de salud entre la 4.ª y 12.ª semana luego de haber recibido la vacuna BBIBP-CorV (Sinopharm). MATERIALES Y MÉTODOS.: Se incluyeron 168 trabajadores de salud de dos hospitales de la región, quienes cumplían el esquema completo con vacuna de Sinopharm, y se realizó la medición de anticuerpos en suero mediante la prueba Elecsys® Anti-SARS-CoV-2. RESULTADOS.: Todos los participantes desarrollaron anticuerpos frente al dominio RBD. El valor mínimo fue de 1,78 U/mL. En 70 (41,7%) participantes se encontraron niveles iguales o por encima de 250. La media geométrica fue de 82,6 (IC 95% 67,8-100,6). Las mujeres presentaron un mayor nivel de anticuerpos. El grupo de participantes en los que se midieron anticuerpos entre las semanas 4 y 7 posvacunación mostró niveles de anticuerpos significativamente mayores que los pacientes cuyas determinaciones fueron realizadas entre las 10 y 12 semanas posvacunación. Entre los pacientes con antecedente de COVID-19, los niveles de anticuerpos se encontraron en cifras iguales o por encima de 250 U/mL en el 88% de casos, en comparación con 6% entre aquellos sin antecedente de COVID-19, (p<0,001). CONCLUSIÓN.: Todos los participantes inmunizados con la vacuna BBIBP-CorV presentaron positividad a anticuerpos frente al RBD de la proteína S del SARS-CoV-2. Es necesario evaluar la correlación entre la magnitud de los títulos y la protección frente a COVID-19 y el tiempo de protección conferido por la vacuna.

Computational study, synthesis and evaluation of active peptides derived from Parasporin-2 and spike protein from Alphacoronavirus against colorectal cancer cells.

Parasporin-2Aa1 (PS2Aa1) is a toxic protein of 37 KDa (30 kDa, activated form produced by proteolysis) that was shown to be cytotoxic against specific human cancer cells, although its mechanism of action has not been elucidated yet. In order to study the role of some native peptide fragments of proteins on anticancer activity, here we investigated the cytotoxic effect of peptide fragments from domain-1 of PS2Aa1 and one of the loops present in the binding region of the virus spike protein from Alphacoronavirus (HCoV-229E), the latter according to scientific reports, who showed interaction with the human APN (h-APN) receptor, evidence corroborated through computational simulations, and thus being possible active against colon cancer cells. Peptides namely P264-G274, Loop1-PS2Aa, and Loop2-PS2Aa were synthesized using the Fmoc solid-phase synthesis and characterized by mass spectrometry (MS). Additionally, one region from loop 1 of HCoV-229E, Loop1-HCoV-229E, was also synthesized and characterized. The A4W-GGN5 anticancer peptide and 5-fluorouracil (5-FU) were taken as a control in all experiments. Circular dichroism revealed an α-helix structure for the peptides derived from PS2Aa1 (P264-G274, Loop1-PS2Aa, and Loop2-PS2Aa) and ß-laminar structure for the peptide derived from Alphacoronavirus spike protein Loop1-HCoV-229E. Peptides showed a hemolysis percentage of less than 20% at 100 µM concentration. Besides, peptides exhibited stronger anticancer activity against SW480 and SW620 cells after exposure for 48 h. Likewise, these compounds showed significantly lower toxicity against normal cells CHO-K1. The results suggest that native peptide fragments from Ps2Aa1 may be optimized as a novel potential cancer-therapeutic agents.

Characteristics and clinical outcomes of patients hospitalized with laboratory-confirmed COVID-19-Puerto Rico, March-August 2020.

Hispanics are the majority ethnic population in Puerto Rico where we reviewed charts of 109 hospitalized COVID-19 patients to better understand demographic and clinical characteristics of COVID-19 and determine risk factors for poor outcomes. Eligible medical records of hospitalized patients with confirmed COVID-19 illnesses were reviewed at four participating hospitals in population centers across Puerto Rico and data were abstracted that described the clinical course, interventions, and outcomes. We found hospitalized patients had a median of 3 underlying conditions with obesity and diabetes as the most frequently reported conditions. Intensive care unit (ICU) admission occurred among 28% of patients and 18% of patients died during the hospitalization. Patients 65 or older or with immune deficiencies had a higher risk for death. Common symptoms included cough, dyspnea, and fatigue; less than half of patients in the study reported fever which was less frequent than reported elsewhere in the literature. It is important for interventions within Hispanic communities to protect high-risk groups.

Impact of the Gestational Diabetes Diagnostic Criteria during the Pandemic: An Observational Study.

OBJECTIVE: To analyze the effect of applying alternative diagnostic criteria for gestational diabetes mellitus (GDM) during the COVID-19 pandemic on GDM prevalence and obstetrical and perinatal outcomes, in comparison to usual diagnostic approaches. METHODS: Data from women referred to GDM diagnosis from 1 September to 30 November 2019 were retrospectively collected (2019-group). The same data from the same period in 2020 were prospectively collected (2020-group). In both cases, a two-step diagnostic approach was used, the first step being a screening test (1 h 50 goral glucose tolerance test, OGTT). In 2019 it was followed by a 100 gr OGTT for diagnosis. In 2020, this was replaced by a blood test for the measurement of plasma glucose and HbA1c, according to alternative GDM diagnostic criteria during the COVID-19 pandemic. RESULTS: From 237 women in the 2019 group, 40 (16.9%) were diagnosed with GDM, while from 255 women in the 2020 group, 37 (14.5%) had GDM (p = 0.470). More women in the 2020 group, in comparison to the 2019 group, were nulligravid (41.9% vs. 47.2%, p = 0.013), had a personal history of GDM (11.4% vs. 4.6%, p = 0.013) and had macrosomia in previous pregnancies (10.2% vs. 2.1%, p = 0.001). Obstetrical and perinatal outcomes were similar when comparing women with GDM to non-GDM women in the 2019 and 2020 groups and between GDM women and non-GDM women. CONCLUSION: In a Spanish population, GDM prevalence during the COVID-19 pandemic using the alternative diagnostic criteria was similar to that found in 2019 using the usual diagnostic criteria. Despite women referred for GDM diagnosis during the pandemic having more GDM risk factors, obstetrical and perinatal outcomes were comparable to those observed before the pandemic.

Molecular Human Targets of Bioactive Alkaloid-Type Compounds from Tabernaemontana cymose Jacq.

Alkaloids are a group of secondary metabolites that have been widely studied for the discovery of new drugs due to their properties on the central nervous system and their anti-inflammatory, antioxidant and anti-cancer activities. Molecular docking was performed for 10 indole alkaloids identified in the ethanol extract of Tabernaemontana cymosa Jacq. with 951 human targets involved in different diseases. The results were analyzed through the KEGG and STRING databases, finding the most relevant physiological associations for alkaloids. The molecule 5-oxocoronaridine proved to be the most active molecule against human proteins (binding energy affinity average = -9.2 kcal/mol) and the analysis of the interactions between the affected proteins pointed to the PI3K/ Akt/mTOR signaling pathway as the main target. The above indicates that indole alkaloids from T. cymosa constitute a promising source for the search and development of new treatments against different types of cancer.

Several lineages of porcine epidemic diarrhea virus in Colombia during the 2014 and 2016 epidemic.

Porcine epidemic diarrhea virus (PEDV) is a significant global, enteric coronavirus in pigs and was first reported in Colombia in 2014. However, the epidemiology, genetic and antigenic characteristics of the virus have yet to be investigated. In this study, we investigated the dissemination of PEDV by testing 536 samples by RT-PCR over a 33-month period. The 35.8% of positive samples (n = 192) was significantly different (p < .01) between months over time, with a higher number of positives samples occurring at the beginning of the epidemic and during the second epidemic wave within the main pork producing region. The complete PEDV genomes were generated for 21 strains, which shared a high nucleotide and amino acid sequence identity, except for the spike (S) gene. Recombinant regions were identified within the Colombian strains and between Colombian and Asian PEDV strains. Phylogenetic analysis of the 21 Colombian strains demonstrated the presence of 7 lineages that shared common ancestors with PEDV strains from the United States. Moreover, the antigenic analysis demonstrated residue differences in the neutralizing epitopes in the spike and nucleocapsid proteins. Our results illustrated the simultaneous introduction of the two PEDV genotypes (GIIa American pandemic and S-INDEL) into the Colombian swine industry during the 2014 PEDV epidemic and enhanced our understanding of the epidemiology and molecular diversity of PEDV in Colombia.