ABSTRACT
INTRODUCTION: In November 2021, omicron-a new SARS-CoV-2 variant-was identified in South Africa and almost immediately, WHO declared it a 'variant of concern'. In view of its rapid worldwide spread and its imminent introduction in Cuba, genomic surveillance was strengthened. OBJECTIVE: Describe cases during the first eight epidemiological weeks (epiweeks) of SARS-CoV-2 infection attributable to omicron variant in Cuba by clinical and epidemiological variables. METHODS: From epiweek 48, 2021 to epiweek 4, 2022, 288 nasopharyngeal swabs were processed for sequencing of a 1836 bp fragment of the S gene. Variants were identified according to GISAID database and confirmed by phylogenetic analysis. Variants' association with clinical and epidemiological outcomes was assessed. RESULTS: The first cases of omicron variant were imported, mostly from African countries and the United States. During the period studied, omicron was detected in 83.0% (239/288) of cases processed, while the delta variant was found in 17.0% (49/288). Most persons infected with omicron were symptomatic (63.2%; 151/239) and fully vaccinated (65.3%; 156/239); severe cases and deaths occurred mainly among patients aged ≥65 years (92.9%; 13/14), and 12 of these deaths occurred in fully vaccinated persons (92.3%; 12/13). Omicron spread rapidly throughout the country (from 10% of cases in epiweek 48, 2021, to 100% by epiweek 4, 2022), displacing the formerly predominant delta variant. CONCLUSIONS: Omicron's rapid expansion in Cuba was associated with increased incidence but not with a higher case fatality rate. The relatively milder disease in those infected with this variant could be influenced by the high vaccination coverage, along with the natural immunity acquired as a consequence of previous virus infection.
Subject(s)
COVID-19 , SARS-CoV-2 , Humans , SARS-CoV-2/genetics , Phylogeny , Cuba/epidemiology , COVID-19/epidemiologyABSTRACT
RESUMEN Introducción: Los medios de colecta de muestras clínicas con capacidad de desnaturalizar virus reducen los riesgos de contagio durante el transporte y procesamiento. Objetivo: Emplear el medio de transporte de ácidos nucleicos (TAN) en muestras de exudado nasofaríngeo colectadas para el diagnóstico de SARS-CoV-2. Métodos: Se realizó un estudio experimental para demostrar la capacidad del medio de inactivar la infectividad viral. Se tomó como modelo de virus envuelto el virus Zika (VZk), cuyo nivel de bioseguridad es 2. Se evaluó el desempeño clínico del medio TAN para el diagnóstico de SARS-CoV-2. Se empleó una cepa del VZk propagada en la línea celular Vero y, previo a la infección de las células, el VZk se puso en contacto a intervalos de tiempo diferentes (2; 15 y 30 min) con el medio TAN puro; y luego se realizaron diluciones seriadas (10-1-10-4). La inactivación viral se evaluó por RT-PCR, en el sobrenadante y células colectadas, al culminar el periodo de propagación. El desempeño clínico del medio TAN se estimó tomando como referencia el CITOSWAB® VTM, en 30 exudados nasofaríngeos colectados para diagnóstico de la infección por SARS-CoV-2. Resultados: El VZk preservó su infectividad a diluciones del inóculo ≥ 10-2, independientemente del tiempo de contacto. La sensibilidad y especificidad clínica del medio TAN para el diagnóstico de SARS-CoV-2 fueron del 100 %, respectivamente. Conclusiones: Los resultados sugieren que muestras clínicas positivas a VZk en diluciones ≤ 10-1 del medio TAN pueden ser manipuladas de forma segura, lo que pudiera aplicarse potencialmente al diagnóstico molecular del SARS-CoV-2.
ABSTRACT Introduction: Collection media of clinical samples with the capacity to denature viruses reduce the risk of contagion during transportation and processing. Objective: To use the nucleic acids transport media (NATM) in nasopharyngeal swab samples collected for the diagnosis of SARS-CoV-2. Methods: An experimental study was conducted to demonstrate the medium capacity to inactivate viral infectivity. Zika virus (ZIKV), of biosafety level 2, was used as an enveloped virus model. The clinical performance of the NATM for the diagnosis of SARS-CoV-2 was evaluated. A ZIKV strain propagated in the Vero cell line was used and, prior to cells infection, ZIKV was in contact at different intervals (2; 15, and 30 min) with pure NATM; subsequently, serial dilutions (10-1-10-4) were performed. Viral inactivation was evaluated by RT-PCR in the supernatant and the collected cells when the propagation period was completed. CITOSWAB® VTM was used as reference to estimate the clinical performance of the NATM in 30 nasopharyngeal swabs collected for the diagnosis of SARS-CoV-2 infection. Results: ZIKV remained infectious at inoculum dilutions of ≥ 10-2, regardless of contact time. Clinical specificity and sensitivity of the NATM for the diagnosis of SARS-CoV-2 were 100%, respectively. Conclusions: Results suggest that ZIKV positive clinical samples at dilutions ≤ 10-1 of the NATM can be safely handled, which could potentially be applied to the molecular diagnosis of SARS-CoV-2.
Subject(s)
HumansABSTRACT
RESUMEN Introducción: Se presenta la evaluación preliminar de la actividad antiviral de extractos de Ageratina havanensis (etanólico de tallo, AH-T-EtOH; butanólico de hoja, AH-H-ButOH y acetato de etilo de hoja, AH-H-AcEtO) utilizando dos sistemas inmunoenzimáticos, un ELISA celular (ELISAc) y la técnica de inmunoperoxidasa. Objetivo: Evaluar la actividad antiviral de los extractos de Ageratina havanensis utilizando dos sistemas inmunoenzimáticos. Métodos: Se normalizó y empleó un ELISAc y la técnica de inmunoperoxidasa en evaluar de forma preliminar la actividad antiviral de tres extractos de Ageratina havanensis a diferentes concentraciones y tiempos de adición mediante la detección de la expresión de la proteína E del virus dengue. Resultados: El ELISAc logró como parámetros óptimos: línea celular Vero, antígeno viral en cultivo de células, tiempo de expresión de la proteína E de 96 h, compuesto fijador metanol-acetona y bloqueador leche descremada al 1 %. La menor expresión de la proteína E (mayor inhibición sobre la replicación viral), fue al adicionar el extracto AH-T-EtOH a su mayor concentración y 1 h antes de inocular el virus dengue-2 cepa A15 (VDEN-2 A15). El extracto AH-H-ButOH a concentraciones de 125 µg/mL y 250 µg/mL presentó una ligera limitación de expresión de E 1 h después de la inoculación viral. El extracto AH-H-AcEtO a las concentraciones empleadas, no mostró difererencia añadido antes y después de la inoculación. El ensayo de inmunoperoxidasa exhibió resultados análogos para los extractos. Conclusiones: La mayor inhibición de la replicación viral fue obtenida con el extracto AH-H-ButOH, a su mayor concentración y ambos tiempos de adición. Los ensayos inmunoenzimáticos aplicados son herramientas útiles para evaluar extractos de Ageratina havanensis con posible actividad antiviral.
ABSTRACT Introduction: A preliminary evaluation is presented of the antiviral activity of Ageratina havanensis extracts (stem ethanolic, AH-T-EtOH; leaf butanolic, AH-H-ButOH; and leaf ethyl acetate, AH-H-AcEtO) using two enzyme immunoassays, cellular ELISA (C-ELISA) and immunoperoxidase technique. Objective: Evaluate the antiviral activity of Ageratine havanensis extracts using two enzyme immunoassays. Methods: C-ELISA and immunoperoxidase technique were standardized for use in the preliminary evaluation of the antiviral activity of three Ageratina havanensis extracts at different concentrations and addition times through detection of the expression of the E protein of dengue virus. Results: C-ELISA achieved the following optimal parameters: Vero cell line, viral antigen in cell culture, protein E expression time 96 h, methanol-acetone fixation compound and 1% skimmed milk blocker. The smallest expression of protein E (greatest inhibition over viral replication) was achieved at addition of extract AH-T-EtOH at its highest concentration and 1 h before inoculating dengue-2 virus strain A15 (VDEN-2 A15). Extract AH-H-ButOH at concentrations of 125 µg/ml and 250 µg/ml presented a slight limitation in the expression of E 1 h after viral inoculation. Extract AH-H-AcEtO at the concentrations used did not show any difference when added before and after inoculation. The immunoperoxidase assay exhibited similar results for the extracts. Conclusions: The greatest inhibition of viral replication was obtained with extract AH-H-ButOH at its highest concentration and at both addition times. The enzyme immunoassays applied are useful tools to evaluate Ageratine havanensis extracts with potential antiviral activity.
