Dispersion of SARS-CoV-2 lineage BA.5.1.25 and its descendants in Peru during two COVID-19 waves in 2022.

During the third year of the pandemic in Peru, the persistent transmission of SARS-CoV-2 led to the appearance of more transmissible and immune-evasive Omicron sublineages; in that context, the National Genomic Surveillance of SARS-CoV-2 performed by the Peruvian National Institute of Health detected spike mutations in the circulating Omicron BA.5.1.25 sublineage which was later designated as DJ.1 and increased during the fourth COVID-19 wave, this eventually branched into new sublineages. The introduction, emergence, and timing of the most recent common ancestor (tMRCA) of BA.5.1.25 and its descendants (DJ.1, DJ.1.1, DJ.1.2, and DJ.1.3) were investigated in this paper as well as the time lags between their emergence and identification by the Peruvian National Institute of Health. Our findings show that ongoing genomic surveillance of SARS-CoV-2 is critical for understanding its phylogenetic evolution and the emergence of novel variations.

Diagnostic performance of a point-of-care molecular system for the detection of SARS-CoV-2 in Peru. / Rendimiento diagnóstico de un sistema molecular de uso en el punto de atención para la detección de SARS-CoV-2 en Perú.

The present study assessed the diagnostic performance of the Xpert®Xpress SARS-CoV-2 test in comparison with the Charité protocol real-time RT PCR for the detection of SARS-CoV-2 in Peruvian patients. This was a diagnostic test study that included 100 nasal and pharyngeal swab samples. We obtained an overall concordance of 98.70% (95%CI: 92.98-99.97), with a kappa coefficient of 0.97 (95%CI: 0.86-1.00) and sensitivity and relative specificity rates of 100% and 96.15%, respectively. Additionally, the percentage of the area under the ROC curve was 98.08% in both cases, and an analytical specificity rate of 100% was obtained for the different respiratory viruses evaluated. In conclusion, the Xpert®Xpress SARS-CoV-2 test, by using nasal and pharyngeal swab samples, was highly sensitive and specific, and the kappa coefficient showed an excellent correlation when compared to the reference test. Motivation for the study. To describe and evaluate a closed molecular platform, easy to use and of importance in Peru for the management of diseases of public health priority, now implemented for the detection of SARS-CoV-2. Main findings. Highly sensitive and specific molecular test, with excellent correlation compared to the reference test for detecting SARS-CoV-2. Implications. Can be used in point-of-care laboratories for rapid molecular detection of different infectious agents, including SARS-CoV-2. Little expertise and minimal infrastructure are required to implement it.

En el presente estudio se estimó el rendimiento diagnóstico de la prueba Xpert®Xpress SARS-CoV-2 en comparación con la RT PCR en tiempo real-protocolo Charité, para la detección de SARS-CoV-2 en pacientes peruanos. Se trató de un diseño de prueba diagnóstica que incluyó 100 muestras de hisopado nasal y faríngeo. Se obtuvo una concordancia global de 98,70% (IC95%: 92,98-99,97), con un coeficiente kappa de 0,97 (IC95%: 0,86-1.00); se estimó una sensibilidad y especificad relativa de 100% y 96,15%, respectivamente. Adicionalmente, el porcentaje del área bajo la curva ROC fue 98,08% en ambos casos y se obtuvo una especificidad analítica del 100% para los diferentes virus respiratorios evaluados. En conclusión, la prueba Xpert®Xpress SARS-CoV-2 a partir de muestras de hisopado nasal y faríngeo fue altamente sensible y específica, así mismo el coeficiente kappa mostró una excelente correlación, al compararla con la prueba de referencia. Motivación para realizar el estudio. Descripción y evaluación de una plataforma molecular cerrada, de fácil uso y de importancia en el Perú para el manejo de enfermedades de prioridad en salud pública, ahora implementada para la detección de SARS-CoV-2. Principales hallazgos. Prueba molecular altamente sensible y específica, con una correlación excelente con respecto al referente para detectar SARS-CoV-2. Implicancias. Puede ser utilizada en los laboratorios que se encuentran en los puntos de atención del paciente para la detección molecular rápida de diferentes agentes infecciosos, incluido el SARS-CoV-2. Se necesita poca experticia y mínima infraestructura para poder implementarla.

Conformational isomerism in trans-3-methoxycinnamic acid: From solid to gas phase.

The rotational spectrum of laser ablated trans-3-methoxycinnamic acid has been observed in the 2-8 GHz range using chirped-pulse Fourier transform microwave spectroscopy coupled to a supersonic jet and adapted to support a laser ablation vaporization system (LA-CP-FTMW). Eight stable conformers were theoretically predicted to exist at B3LYP-D3BJ/6-311++(2d,p) level, all of which were experimentally detected. The experimental rotational parameters data evidence the essentially planar structures for all the conformers. The relative population distribution of conformers in the supersonic jet was investigated from relative intensity measurements. Cooling in the jet brings rotational temperatures close to 1 K for all the conformers. The theoretical predictions for the rotational constants and electric dipole moments show good agreement with the experimental constants and selection rules observed. The population distribution of conformers in the supersonic jet was found to be close to the equilibrium distribution calculated at temperatures lower than the stagnation temperature. Finally, the correlation of the observed conformers structures with those found in condensed phases was investigated.

Rendimiento diagnóstico de un sistema molecular de uso en el punto de atención para la detección de SARS-CoV-2 en Perú / Diagnostic performance of a point-of-care molecular system for the detection of SARS-CoV-2 in Peru

RESUMEN En el presente estudio se estimó el rendimiento diagnóstico de la prueba Xpert®Xpress SARS-CoV-2 en comparación con la RT PCR en tiempo real-protocolo Charité, para la detección de SARS-CoV-2 en pacientes peruanos. Se trató de un diseño de prueba diagnóstica que incluyó 100 muestras de hisopado nasal y faríngeo. Se obtuvo una concordancia global de 98,70% (IC95%: 92,98-99,97), con un coeficiente kappa de 0,97 (IC95%: 0,86-1.00); se estimó una sensibilidad y especificad relativa de 100% y 96,15%, respectivamente. Adicionalmente, el porcentaje del área bajo la curva ROC fue 98,08% en ambos casos y se obtuvo una especificidad analítica del 100% para los diferentes virus respiratorios evaluados. En conclusión, la prueba Xpert®Xpress SARS-CoV-2 a partir de muestras de hisopado nasal y faríngeo fue altamente sensible y específica, así mismo el coeficiente kappa mostró una excelente correlación, al compararla con la prueba de referencia.

ABSTRACT The present study assessed the diagnostic performance of the Xpert®Xpress SARS-CoV-2 test in comparison with the Charité protocol real-time RT PCR for the detection of SARS-CoV-2 in Peruvian patients. This was a diagnostic test study that included 100 nasal and pharyngeal swab samples. We obtained an overall concordance of 98.70% (95%CI: 92.98-99.97), with a kappa coefficient of 0.97 (95%CI: 0.86-1.00) and sensitivity and relative specificity rates of 100% and 96.15%, respectively. Additionally, the percentage of the area under the ROC curve was 98.08% in both cases, and an analytical specificity rate of 100% was obtained for the different respiratory viruses evaluated. In conclusion, the Xpert®Xpress SARS-CoV-2 test, by using nasal and pharyngeal swab samples, was highly sensitive and specific, and the kappa coefficient showed an excellent correlation when compared to the reference test.

Características clínicas y laboratoriales de los diez primeros pacientes con diagnóstico de Guillain-Barré en Piura, 2023

El síndrome de Guillain Barré es una enfermedad derivada del compromiso en las neuronas del sistema nervioso periférico por una respuesta descontrolada del sistema inmune que conduce daño axonal y/o desmielinización. El objetivo de este reporte fue describir los 10 primeros casos sospechosos de Síndrome de Guillain Barré en Piura. Se logró identificar la presencia de Campylobacter jejuni en las muestras de heces del 80% de los pacientes reportados. Es muy importante reconocer rápida y oportunamente al paciente con diagnóstico sospechoso de Guillain Barré, y realizar los estudios necesarios en un brote para identificar los agentes desencadenantes del cuadro.

Guillain Barré syndrome is a disease derived from compromise in neurons of the peripheral nervous system by an uncontrolled response from the immune system that leads to axonal damage and/or demyelination. The objective of this report was to describe the first 10 suspected cases of Guillain Barre Syndrome in Piura. It was possible to identify the presence of Campylobacter jejuni in the stool samples of 80% of the reported patients. It is very important to quickly and opportunely recognize the patient with a suspected diagnosis of Guillain Barré, and to carry out the necessary studies in an outbreak to identify the triggering agents of the condition.

Use of liposomal amphotericin B in disseminated cutaneous leishmaniasis caused by Leishmania braziliensis in a pediatric patient with Down syndrome. / Uso de anfotericina B liposomal en leishmaniasis cutánea diseminada causada por Leishmania braziliensis en un paciente pediátrico con síndrome de Down.

We present a case of disseminated cutaneous leishmaniasis with extensive manifestation in a pediatric patient with Down syndrome. The case was confirmed by parasitological and immunological tests. The species was identified as Leishmania (Viannia) braziliensis by polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). The immune deficit that occurs as part of Down syndrome may have been the reason for the aggressive and prolonged clinical manifestations as well as the poor response to stibogluconate and deoxycholate amphotericin. The patient was treated with liposomal amphotericin B and at the end of therapy, showed clinical improvement of the lesions. This report highlights the challenges of the diagnosis and treatment of cutaneous leishmaniasis in immunosuppressed pediatric patients, especially under difficult social, economic and geographic conditions. Leishmaniasis should be considered as a differential diagnosis when treating atypical chronic dermatologic ulcers; the use of liposomal amphotericin in immunocompromised patients should also be considered in these cases.

Se presenta un caso de leishmaniasis selvática cutánea diseminada con manifestación extensa en una paciente pediátrica con síndrome de Down. El caso se confirmó a través de estudios parasitológicos e inmunológicos, mientras que la identificación se realizó mediante la técnica de reacción en cadena de la polimerasa-polimorfismos de longitud de fragmentos de restricción (PCR-RFLP, por sus siglas en inglés), determinándose la especie como Leishmania (Viannia) braziliensis. La manifestación clínica agresiva y prolongada con poca respuesta a estibogluconato y anfotericina desoxicolato pueden deberse al déficit inmunológico que se presenta como parte del síndrome de Down. La paciente eventualmente recibió tratamiento con anfotericina B liposomal y al término de la terapia, mostró mejoría clínica de las lesiones. El presente reporte ilustra los desafíos tanto de diagnóstico como tratamiento de leishmaniasis cutánea en pacientes pediátricos inmunosuprimidos, especialmente en un entorno de difícil acceso social, económico y geográfico, a los servicios de salud. Se recomienda considerar a la leishmaniasis en el diagnóstico diferencial cuando se atienda ulceras crónicas dermatológicas atípicas; así como tener en cuenta el uso de anfotericina liposomal en pacientes inmunocomprometidos.

Factores individuales e institucionales asociados a la vacunación contra el virus de la hepatitis B en recién nacidos de hospitales de Lima y Callao

Introducción. La vacunación contra el virus de la hepatitis B (VHB) en recién nacidos es crucial para la prevención de la transmisión perinatal. Objetivo. Determinar factores individuales e institucionales asociados a la vacunación contra el VHB en las 12 y 24 primeras horas de vida. Métodos. Se diseñó un estudio transversal y multicéntrico. Los datos sobre la vacunación fueron recogidos de los padres y de la revisión de reportes. Los datos de los variables individuales de los recién nacidos y madres fueron recogidos de las historias clínicas. Los datos institucionales fueron recogidos de registros de atención inmediata y directamente del personal de inmunizaciones. Resultados. Se incluyó 777 recién nacidos en 10 establecimientos. En el análisis multinivel resultó favorable a la vacunación en las primeras 12 horas, el mayor tiempo de atención en los servicios de inmunizaciones (RP: 1,0; IC95%: 0,99 - 1,01). Para la vacunación dentro de las 24 horas de vida fue favorable la mayor cantidad de personal de enfermería en los servicios de vacunación (RP: 1,02; IC95%: 1,01 - 1,03) y desfavorable la mayor cantidad de partos al día de los establecimientos (RP: 0,99; IC95%: 0,99 - 0,997). No se identificó factores individuales. Conclusión. Factores institucionales, como el tiempo de atención, la cantidad de personal de enfermería y la cantidad de partos, estuvieron asociados con la vacunación contra el VHB en recién nacidos. Se requiere estrategias de mejora como la introducción de la vacunación en la atención inmediata del neonato para la prevención de la transmisión perinatal del VHB.

Introduction. Vaccination against hepatitis B Virus (HBV) in newborns is crucial for the prevention of perinatal transmission. Objective. To determine the individual and institutional factors associated with vaccine for HBV in newborns in the first 12 hours and 24 hours of life. Methods. A cross-sectional, multicenter-design study was conducted in high level public and private hospitals in Lima Metropolitana and Callao. Information on vaccination was obtained through consultations with parents and review of health service reports. Individual variables of the newborns and their mothers were obtained from the medical records of the newborns. Institutional data were collected from immediate care records and from health personnel responsible for the immunization program. Results. The study was conducted in 10 health facilities, including 777 newborns. In the multilevel analysis, the longest care time in the vaccination service was favorable for vaccination within 12 hours of life (PR: 1,0; 95% CI: 0,9995-1,01); while for vaccination within 24 hours of life was favorable the greater number of nursing personnel (RP: 1,02; IC95%: 1,01-1,03) and unfavorable the greater number of deliveries per day in the institution (RP:0,99; IC95%: 0,99-0,997). No individual factors related to vaccination were identified. Conclusions. Institutional factors, such as length of care, number of nursing staff, and number of deliveries, were associated with newborn HBV vaccination. Improvement strategies are required, such as the introduction of vaccination in the immediate care of the newborn for the prevention of perinatal transmission of HBV.

Contenido de sodio en antimicrobianos parenterales: Una fuente extra de sodio a considerarse en pacientes hospitalizados / Sodium content in parenteral antibiotics: An extra source of sodium to be considered in hospitalized patients

Los antimicrobianos parenterales son esenciales en el tratamiento de infecciones intrahospitalarias, sin embargo, es importante considerar la carga de sodio y volumen que pueden aportar, especialmente, en pacientes con restricción sódica. En el presente estudio se identificaron los antimicrobianos parenterales usados en uno de los hospitales más grandes del Perú. Se revisó la cantidad de sodio intrínseco y se calculó la cantidad de sodio total por día de tratamiento según el régimen frecuentemente usado en adultos. Como resultado, se encontró que 22% de las terapias antimicrobianas superaban el requerimiento de sodio diario, lo que podría ser perjudicial para pacientes con insuficiencia cardiaca, enfermedad renal crónica, con cirrosis hepática, entre otros.

Parenteral antibiotics are essential in the treatment of nosocomial infections; however, their sodium load and volume should be considered as an extra source, especially, in patients with sodium restriction. In this study, we identified the parental antibiotics used in one of the largest hospitals in Peru. We reviewed the amount of intrinsic sodium and we calculated the sodium load per day of treatment according to the commonly used regimen in adults. As a result, we found that 22% of the antibiotic treatment regimens exceed the daily sodium requirement, which could be harmful for patients with heart failure, chronic kidney disease, liver cirrhosis, among others.

Uso de anfotericina B liposomal en leishmaniasis cutánea diseminada causada por Leishmania braziliensis en un paciente pediátrico con síndrome de Down / Use of liposomal anfotericin B in diseminated cutaneous leishmaniasis caused by Leishmania braziliensis in a pediatric patient with Down syndrome

Se presenta un caso de leishmaniasis selvática cutánea diseminada con manifestación extensa en una paciente pediátrica con síndrome de Down. El caso se confirmó a través de estudios parasitológicos e inmunológicos, mientras que la identificación se realizó mediante la técnica de reacción en cadena de la polimerasa-polimorfismos de longitud de fragmentos de restricción (PCR-RFLP, por sus siglas en inglés), determinándose la especie como Leishmania (Viannia) braziliensis. La manifestación clínica agresiva y prolongada con poca respuesta a estibogluconato y anfotericina desoxicolato pueden deberse al déficit inmunológico que se presenta como parte del síndrome de Down. La paciente eventualmente recibió tratamiento con anfotericina B liposomal y al término de la terapia, mostró mejoría clínica de las lesiones. El presente reporte ilustra los desafíos tanto de diagnóstico como tratamiento de leishmaniasis cutánea en pacientes pediátricos inmunosuprimidos, especialmente en un entorno de difícil acceso social, económico y geográfico, a los servicios de salud. Se recomienda considerar a la leishmaniasis en el diagnóstico diferencial cuando se atienda ulceras crónicas dermatológicas atípicas; así como tener en cuenta el uso de anfotericina liposomal en pacientes inmunocomprometidos.

We present a case of disseminated cutaneous leishmaniasis with extensive manifestation in a pediatric patient with Down syndrome. The case was confirmed by parasitological and immunological tests. The species was identified as Leishmania (Viannia) braziliensis by polymerase chain reaction-restriction fragment length polymorphisms (PCR-RFLP). The immune deficit that occurs as part of Down syndrome may have been the reason for the aggressive and prolonged clinical manifestations as well as the poor response to stibogluconate and deoxycholate amphotericin. The patient was treated with liposomal amphotericin B and at the end of therapy, showed clinical improvement of the lesions. This report highlights the challenges of the diagnosis and treatment of cutaneous leishmaniasis in immunosuppressed pediatric patients, especially under difficult social, economic and geographic conditions. Leishmaniasis should be considered as a differential diagnosis when treating atypical chronic dermatologic ulcers; the use of liposomal amphotericin in immunocompromised patients should also be considered in these cases.

Immunogenicity and reactogenicity of a third dose of BNT162b2 vaccine for COVID-19 after a primary regimen with BBIBP-CorV or BNT162b2 vaccines in Lima, Peru.

BACKGROUND: The administration of a third (booster) dose of COVID-19 vaccines in Peru initially employed the BNT162b2 (Pfizer) mRNA vaccine. The national vaccination program started with healthcare workers (HCW) who received BBIBP-CorV (Sinopharm) vaccine as primary regimen and elderly people previously immunized with BNT162b2. This study evaluated the reactogenicity and immunogenicity of the "booster" dose in these two groups in Lima, Peru. METHODS: We conducted a prospective cohort study, recruiting participants from November to December of 2021 in Lima, Peru. We evaluated immunogenicity and reactogenicity in HCW and elderly patients previously vaccinated with either two doses of BBIBP-CorV (heterologous regimen) or BTN162b2 (homologous regimen). Immunogenicity was measured by anti-SARS-CoV-2 IgG antibody levels immediately before boosting dose and 14 days later. IgG geometric means (GM) and medians were obtained, and modeled using ANCOVA and quantile regressions. RESULTS: The GM of IgG levels increased significantly after boosting: from 28.5±5.0 AU/mL up to 486.6±1.2 AU/mL (p<0.001) which corresponds to a 17-fold increase. The heterologous vaccine regimen produced higher GM of post-booster anti-SARS-CoV-2 IgG levels, eliciting a 13% increase in the geometric mean ratio (95%CI: 1.02-1.27) and a median difference of 92.3 AU/ml (95%CI: 24.9-159.7). Both vaccine regimens were safe and well tolerated. Previous COVID-19 infection was also associated with higher pre and post-booster IgG GM levels. CONCLUSION: Although both boosting regimens were highly immunogenic, two doses of BBIBP-CorV boosted with BTN162b2 produced a stronger IgG antibody response than the homologous BNT162b2 regimen in the Peruvian population. Additionally, both regimens were mildly reactogenic and well-tolerated.

Narrativas del donante de plasma convaleciente en EsSalud: motivaciones, miedos, expectativas y experiencias

Objetivos: Explorar, desde las narrativas de la población de donantes de plasma convaleciente en un ensayo clínico, las experiencias en el proceso de donación de sangre. Métodos: Se realizó un estudio cualitativo con diseño fenomenológico. La investigación se llevó a cabo en un hospital de la seguridad social del Perú aplicándose entrevistas semiestructuradas a profundidad. Resultados: Se entrevistó a once donantes de plasma convaleciente. Se identificó que las principales motivaciones de los donantes fueron tanto el poder contribuir a la investigación nacional como, apoyar a pacientes afectados por la COVID-19. Los principales miedos se centran en el posible riesgo de contagio dentro del hospital. Por otro lado, los donantes resaltaron la atención y acompañamiento del personal de salud en el proceso. Las principales expectativas y sugerencias apuntan hacia una mayor difusión de las campañas de donación de sangre en general, con especial énfasis en el tema de seguridad, la mejora en el tiempo del procedimiento de donación (en el caso de la donación de plasma convaleciente, desde el enrolamiento hasta la extracción de plasma convaleciente) y, la implementación de espacios amigables para incentivar las futuras campañas de donación de sangre en general. Conclusiones: Las experiencias de los donantes de plasma convaleciente fueron positivas. Sin embargo, aún hay mejoras que realizar a nivel de procesos e infraestructuras para asegurar campañas exitosas de donación de sangre futuras.

Objectives: To know and explore from convalescent plasma donators' voices the experience in the blood donation process at a social security hospital. Methods: Qualitative study with a phenomenological design. The investigation was carried out in 01 hospitals of the social security of Peru. Semi-structured interviews were carried out. Results: Eleven donors of convalescent plasma were interviewed. The main motivations for donating were being able to contribute to national research and supporting patients affected by COVID-19. Fears focus on the possible risk of contagion within the hospital. Donors emphasised the attention and support of health personnel alongside the donation procedure. The main expectations and suggestions point towards greater dissemination of donation campaigns with special emphasis on safety. Likewise, an improvement in the time of the donation procedure (from enrolment to the extraction of convalescent plasma), and the implementation of friendly spaces to encourage future blood donation campaigns were highlighted. Conclusions: The experience of the convalescent plasma donors was positive. However, improvements must be made in terms of processes and infrastructure to ensure future successful blood donation campaigns.

Viruela del mono (MPOX) en paciente varón heterosexual VIH negativo

Se presenta el caso de un paciente varón de 28 años, heterosexual, con VIH negativo que desarrolló erupción cutánea intensa caracterizada por la presencia de vesículas, pústulas y pápulas umbilicadas confluentes en el pene y región púbica con escasa diseminación en el resto del cuerpo, sin adenopatía ni manifestaciones sistémicas, cuatro días después de haber tenido relaciones sexuales con una prostituta aparentemente sana. El hisopado de las lesiones dérmicas revelaron la presencia de ADN del virus MPOX por PCR en tiempo real. Las pruebas inmunológicas fueron las siguientes: ELISA cuarta generación para VIH y Western Blot negativas, anticuerpos IgM para herpes simplex1=1.2 U/ml, anticuerpos IgM para herpes simplex2=1.9 U/ml, anticuerpos IgM para varicela zóster=0.5 S/CO, FTA-ABS (IgM)=negativo. Se resalta la intensidad de las lesiones cutáneas en el pene y la necesidad de realizar pruebas para descarte de MPOX en prostitutas.

We present the case of a 28-year-old male patient, heterosexual, with negative HIV who developed an intense skin rash characterized by the presence of confluent vesicles, pustules, and umbilicated papules on the penis and pubic region with little spread to the rest of the body, without lymphadenopathy or systemic manifestations, four days after having sexual relations with an apparently healthy prostitute. The swabbing of the dermal lesions revealed the presence of MPOX virus DNA by real-time PCR. The immunological tests were the following: negative fourth-generation ELISA and Western Blot for HIV, IgM antibodies to herpes simplex1=1.2 U/ ml, IgM antibodies to herpes simplex2=1.9 U/ml, IgM antibodies to varicella zoster=0.5 S/CO and negative FTA-ABS (IgM) for syphilis. The intensity of skin lesions on the penis and the need to perform tests to rule out MPOX in prostitutes are highlighted.

Selected Domains within a Comprehensive Geriatric Assessment in Older Patients with Non-Hodgkin Lymphoma are Highly Associated with Frailty.

Background: The incidence of Non-Hodgkin Lymphoma (NHL) is increasing, particularly among older patients who tend to have worse outcomes and can be predisposed to increased toxicities and less treatment tolerance. Therefore, a thorough pre-treatment assessment is essential. A comprehensive geriatric assessment (CGA) can be used to evaluate the older patient considering chemotherapy and is the preferred evaluation tool. However, a formal CGA is laborious, complex and time-consuming. Objectives: To characterize older adults with NHL and determine the CGA variables with the greatest association to frailty in order to propose a more simplified assessment. Methods: We performed a cross-sectional study using data collected from CGAs in NHL patients > 65 years admitted to our oncology service, from September 2015 to August 2017. Our evaluation parameters included: polypharmacy, a screening tool of older people's prescriptions (STOPP), the Lawton scale, Barthel index, Katz index, gait speed, a Timed Up and Go (TUG) test, a Mini-Mental state examination (MMSE), the Yesavage and Gijon scales, a Mini-nutritional assessment (MNA), a Geriatric Syndromes assessment, and a Cumulative Illness Rating Scale-Geriatric (CIRS-G). The formal CGA was comprised of nine domains; frailty was defined as an impairment in > 2 domains. Each parameter was individually compared with frailty, and the results were used to build different multivariate models using logistic regression analyses to obtain the variables with the highest frailty association. Results: A total of 253 patients were included. Their median age was 75.4 years (range 65-92), and 62.1% had > 1 impaired domain, with 39.9% considered frail. Bivariate analysis showed strong associations with age > 85 and all the geriatric parameters except for STOPP. Our final multivariate analysis resulted in 5 domains (the use of > 5 medications, a Lawton < 7, TUG > 20, Yesavage > 5, and the presence of at least one geriatric syndrome) being significantly associated with frailty and performing similarly to a CGA. Conclusion: In our population of older NHL patients, an abbreviated evaluation based of only five domains, polypharmacy, TUG, Lawton scale, Yesavage scale and the presence of at least one geriatric syndrome, had similar performance to a formal CGA in determining frailty.

Genomic surveillance of the Lambda SARS-CoV-2 variant in a global phylogenetic context.

The massive sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and global genomic surveillance strategies allowed the detection of many variants of concern and interest. The variant of interest Lambda (C.37), which originated in South America, has been the most prevalent in Peru and Chile, but its dispersion in other continents still remains unknown. The current study aims to determine the phylogenetic relationship among C.37 isolates worldwide, focusing on spike mutations to understand the spread of Lambda in pandemics. A total of 7441 sequences identified as C.37 were downloaded from the GISAID database; local analysis was carried out to identify spike mutations and phylogenetic analysis was carried out to determine the rate of spread of the virus. Our results showed some spike mutations of Lambda that allowed us to detect small local outbreaks in different countries that occurred in the past and identify several clades that have not yet been designated. Although the lineage C.37 is not epidemiologically relevant in Europe or North America, the endemic behavior of this variant in Peru had a major impact on the second SARS-CoV-2 wave.

High anti-SARS-CoV-2 antibody seroconversion rates before the second wave in Manaus, Brazil, and the protective effect of social behaviour measures: results from the prospective DETECTCoV-19 cohort.

BACKGROUND: The city of Manaus, Brazil, has seen two collapses of the health system due to the COVID-19 pandemic. We report anti-SARS-CoV-2 nucleocapsid IgG antibody seroconversion rates and associated risk factors in Manaus residents before the second wave of the epidemic in Brazil. METHODS: A convenience sample of adult (aged ≥18 years) residents of Manaus was recruited through online and university website advertising into the DETECTCoV-19 study cohort. The current analysis of seroconversion included a subgroup of DETECTCoV-19 participants who had at least two serum sample collections separated by at least 4 weeks between Aug 19 and Oct 2, 2020 (visit 1), and Oct 19 and Nov 27, 2020 (visit 2). Those who reported (or had no data on) having a COVID-19 diagnosis before visit 1, and who were positive for anti-SARS-CoV-2 nucleocapsid IgG antibodies at visit 1 were excluded. Using an in-house ELISA, the reactivity index (RI; calculated as the optical density ratio of the sample to the negative control) for serum anti-SARS-CoV-2 nucleocapsid IgG antibodies was measured at both visits. We calculated the incidence of seroconversion (defined as RI values ≤1·5 at visit 1 and ≥1·5 at visit 2, and a ratio >2 between the visit 2 and visit 1 RI values) during the study period, as well as incidence rate ratios (IRRs) through cluster-corrected and adjusted Poisson regression models to analyse associations between seroconversion and variables related to sociodemographic characteristics, health access, comorbidities, COVID-19 exposure, protective behaviours, and symptoms. FINDINGS: 2496 DETECTCoV-19 cohort participants returned for a follow-up visit between Oct 19 and Nov 27, 2020, of whom 204 reported having COVID-19 before the first visit and 24 had no data regarding previous disease status. 559 participants were seropositive for anti-SARS-CoV-2 nucleocapsid IgG antibodies at baseline. Of the remaining 1709 participants who were seronegative at baseline, 71 did not meet the criteria for seroconversion and were excluded from the analyses. Among the remaining 1638 participants who were seronegative at baseline, 214 showed seroconversion at visit 2. The seroconversion incidence was 13·06% (95% CI 11·52-14·79) overall and 6·78% (5·61-8·10) for symptomatic seroconversion, over a median follow-up period of 57 days (IQR 54-61). 48·1% of seroconversion events were estimated to be asymptomatic. The sample had higher proportions of affluent and higher-educated people than those reported for the Manaus city population. In the fully adjusted and corrected model, risk factors for seroconversion before visit 2 were having a COVID-19 case in the household (IRR 1·49 [95% CI 1·21-1·83]), not wearing a mask during contact with a person with COVID-19 (1·25 [1·09-1·45]), relaxation of physical distancing (1·31 [1·05-1·64]), and having flu-like symptoms (1·79 [1·23-2·59]) or a COVID-19 diagnosis (3·57 [2·27-5·63]) between the first and second visits, whereas working remotely was associated with lower incidence (0·74 [0·56-0·97]). INTERPRETATION: An intense infection transmission period preceded the second wave of COVID-19 in Manaus. Several modifiable behaviours increased the risk of seroconversion, including non-compliance with non-pharmaceutical interventions measures such as not wearing a mask during contact, relaxation of protective measures, and non-remote working. Increased testing in high-transmission areas is needed to provide timely information about ongoing transmission and aid appropriate implementation of transmission mitigation measures. FUNDING: Ministry of Education, Brazil; Fundação de Amparo à Pesquisa do Estado do Amazonas; Pan American Health Organization (PAHO)/WHO.

SARS-CoV-2 seroprevalence and associated factors in Manaus, Brazil: baseline results from the DETECTCoV-19 cohort study.

BACKGROUND: Manaus, located in the Brazilian rainforest, has experienced two health system collapses due to the coronavirus disease 2019 (COVID-19) pandemic. However, little is known about which groups among the general population have been most affected. METHODS: A convenience sampling strategy via online advertising recruited 3046 adults between 19 August 2020 and 2 October 2020. Sociodemographic characteristics, COVID-19-related symptoms, COVID-19 testing, self-medication and prescribed medications were recorded. Serum anti-severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) nucleocapsid immunoglobulin G antibodies were measured with an enzyme-linked immunosorbent assay. Prevalence ratios (PR) were obtained using cluster-corrected and adjusted Poisson's regression models. RESULTS: A crude positivity rate among asymptomatic and symptomatic individuals was estimated at 29.10%, with maximum possible seroprevalence of 44.82% corrected by test characteristics and an antibody decay rate of 32.31%. Regression models demonstrated a strong association towards marginalized low-income and vulnerable residents with limited access to health care. The presence of a COVID-19 case [PR 1.39, 95% confidence interval (CI) 1.24-1.57] or death (PR 2.14, 95% CI 1.74-2.62) in a household greatly increased the risk of other household members acquiring infection. The seroprevalence of SARS-CoV-2 was higher among those who self-medicated to prevent infection (PR 1.36, 95% CI 1.27-1.46). CONCLUSIONS: Disproportionate socio-economic disparity was observed among the study participants. The syndemic nature of COVID-19 in the Amazon region needs differential policies and urgent solutions to control the ongoing pandemic.

Ancient DNA analysis of archaeological specimens extends Chinook salmon's known historic range to San Francisco Bay's tributaries and southernmost watershed.

Understanding a species' historic range guides contemporary management and habitat restoration. Chinook salmon (Oncorhynchus tshawytscha) are an important commercial and recreational gamefish, but nine Chinook subspecies are federally threatened or endangered due to anthropogenic impacts. Several San Francisco Bay Area streams and rivers currently host spawning Chinook populations, but government agencies consider these non-native hatchery strays. Through the morphology-based analysis of 17,288 fish specimens excavated from Native American middens at Mission Santa Clara (CA-SCL-30H), Santa Clara County, circa 1781-1834 CE, 88 salmonid vertebrae were identified. Ancient DNA sequencing identified three separate individuals as Chinook salmon and the remainder as steelhead/rainbow trout (Oncorhynchus mykiss). These findings comprise the first physical evidence of the nativity of salmon to the Guadalupe River in San Jose, California, extending their documented historic range to include San Francisco Bay's southernmost tributary watershed.