COVID-19 mortality in two waves of the pandemic in Cali, Colombia, before and during vaccination roll-out.

Objective: To describe the variation in COVID-19 mortality among residents of Cali, Colombia, in the second wave of the pandemic, before vaccines, and in the fourth wave, with vaccination roll-out in process, taking into account variables of sex, age group, comorbidities, and interval between onset of symptoms and death, and to estimate the number of deaths averted by vaccination. Methods: A cross-sectional study of second wave and fourth wave deaths and vaccination coverage. The frequencies of attributes of deceased population in the two waves were compared, including comorbidities. Machado's method was used to calculate an estimate of the number of deaths averted in the fourth wave. Results: There were 1 133 deaths in the second wave and 754 deaths in the fourth wave. It was calculated that approximately 3 763 deaths were averted in the fourth wave in Cali in the context of vaccination roll-out. Conclusions: The decline in COVID-19-associated mortality observed supports the continuation of the vaccination program. Given the lack of data to explain other possible reasons for this decline, such as on the severity of novel viral variants, the limitations of the study are discussed.

COVID-19 mortality in two waves of the pandemic in Cali, Colombia, before and during vaccination roll-out

[ABSTRACT]. Objective. To describe the variation in COVID-19 mortality among residents of Cali, Colombia, in the second wave of the pandemic, before vaccines, and in the fourth wave, with vaccination roll-out in process, taking into account variables of sex, age group, comorbidities, and interval between onset of symptoms and death, and to estimate the number of deaths averted by vaccination. Methods. A cross-sectional study of second wave and fourth wave deaths and vaccination coverage. The frequencies of attributes of deceased population in the two waves were compared, including comorbidities. Machado’s method was used to calculate an estimate of the number of deaths averted in the fourth wave. Results. There were 1 133 deaths in the second wave and 754 deaths in the fourth wave. It was calculated that approximately 3 763 deaths were averted in the fourth wave in Cali in the context of vaccination roll-out. Conclusions. The decline in COVID-19-associated mortality observed supports the continuation of the vac- cination program. Given the lack of data to explain other possible reasons for this decline, such as on the severity of novel viral variants, the limitations of the study are discussed.

[RESUMEN]. Objetivo. Describir la variación en la mortalidad por COVID-19 en los residentes de Cali, Colombia, en la segunda ola de la pandemia (antes de las vacunas) y en la cuarta ola (durante el despliegue de las vacunas). Se tomaron en cuenta las variables referidas al sexo, grupo de edad, comorbilidades e intervalo entre el inicio de los síntomas y la muerte y se estimó el número de muertes evitadas por la vacunación. Métodos. Estudio transversal sobre las muertes en la segunda y cuarta olas de la pandemia de COVID-19 y la cobertura de vacunación. Se compararon las frecuencias de los atributos correspondientes a la población fallecida durante las dos olas, incluidas las comorbilidades. Se utilizó el método de Machado para estimar el número de muertes evitadas en la cuarta ola. Resultados. Se registraron 1 133 muertes en la segunda ola y 754 en la cuarta. Se calculó que, en el contexto del despliegue de las vacunas, en la cuarta ola se evitaron aproximadamente 3 763 muertes en Cali. Conclusiones. La disminución observada en la mortalidad asociada a la COVID-19 respalda la continuación del programa de vacunación. Dada la falta de datos para explicar otras posibles causas de esta disminución, como puede ser la gravedad causada por las nuevas variantes virales, se analizan las limitaciones del estudio.

[RESUMO]. Objetivo. Descrever a variação da mortalidade por COVID-19 entre residentes de Cali, Colômbia, na segunda onda da pandemia (antes das vacinas) e na quarta onda (com a implantação da vacinação já em anda- mento), considerando as variáveis sexo, faixa etária, comorbidades e intervalo entre início dos sintomas e óbito, bem como estimar o número de óbitos evitados pela vacinação. Métodos. Estudo transversal de mortes e cobertura vacinal na segunda e quarta ondas da pandemia. Foram comparadas as frequências dos atributos da população que foi a óbito durante as duas ondas, incluindo comorbidades. Foi utilizado o método de Machado para estimar o número de mortes evitadas na quarta onda. Resultados. Houve 1.133 mortes na segunda onda e 754 mortes na quarta onda. Calcula-se que cerca de 3.763 mortes foram evitadas na quarta onda em Cali, no contexto da disponibilização das vacinas. Conclusões. A queda observada na mortalidade associada à COVID-19 apoia a continuidade do programa de vacinação. Considerando a falta de dados para explicar outros possíveis motivos para esta queda, como a gravidade das novas variantes do vírus, discutem-se as limitações do estudo.

Spatial modeling and socioeconomic inequities of COVID-19 in the urban area of the city of Cali, Colombia.

COVID-19 has spread worldwide with a high variability in cases and mortality between populations. This research aims to assess socioeconomic inequities of COVID-19 in the city of Cali, Colombia, during the first and second peaks of the pandemic in this city. An ecological study by neighborhoods was carried out, were COVID-19 cases were analyzed using a Bayesian hierarchical spatial model that includes potential risk factors such as the index of unsatisfied basic needs and socioeconomic variables as well as random effects to account for residual variation. Maps showing the geographic patterns of the estimated relative risks as well as exceedance probabilities were created. The results indicate that in the first wave, the neighborhoods with the greatest unsatisfied basic needs and low socioeconomic strata, were more likely to report positive cases for COVID-19. For the second wave, the disease begins to spread through different neighborhoods of the city and middle socioeconomic strata presents the highest risk followed by the lower strata. These findings indicate the importance of measuring social determinants in the study of the distribution of cases due to COVID-19 for its inclusion in the interventions and measures implemented to contain contagions and reduce impacts on the most vulnerable populations.

COVID-19 mortality in two waves of the pandemic in Cali, Colombia, before and during vaccination roll-out / Mortalidad por COVID-19 en dos olas de la pandemia en Cali, Colombia, antes y durante el despliegue de las vacunas / Mortalidade por COVID-19 em duas ondas da pandemia em Cali, Colômbia, antes e durante a disponibilização das vacinas

ABSTRACT Objective. To describe the variation in COVID-19 mortality among residents of Cali, Colombia, in the second wave of the pandemic, before vaccines, and in the fourth wave, with vaccination roll-out in process, taking into account variables of sex, age group, comorbidities, and interval between onset of symptoms and death, and to estimate the number of deaths averted by vaccination. Methods. A cross-sectional study of second wave and fourth wave deaths and vaccination coverage. The frequencies of attributes of deceased population in the two waves were compared, including comorbidities. Machado's method was used to calculate an estimate of the number of deaths averted in the fourth wave. Results. There were 1 133 deaths in the second wave and 754 deaths in the fourth wave. It was calculated that approximately 3 763 deaths were averted in the fourth wave in Cali in the context of vaccination roll-out. Conclusions. The decline in COVID-19-associated mortality observed supports the continuation of the vaccination program. Given the lack of data to explain other possible reasons for this decline, such as on the severity of novel viral variants, the limitations of the study are discussed.

RESUMEN Objetivo. Describir la variación en la mortalidad por COVID-19 en los residentes de Cali, Colombia, en la segunda ola de la pandemia (antes de las vacunas) y en la cuarta ola (durante el despliegue de las vacunas). Se tomaron en cuenta las variables referidas al sexo, grupo de edad, comorbilidades e intervalo entre el inicio de los síntomas y la muerte y se estimó el número de muertes evitadas por la vacunación. Métodos. Estudio transversal sobre las muertes en la segunda y cuarta olas de la pandemia de COVID-19 y la cobertura de vacunación. Se compararon las frecuencias de los atributos correspondientes a la población fallecida durante las dos olas, incluidas las comorbilidades. Se utilizó el método de Machado para estimar el número de muertes evitadas en la cuarta ola. Resultados. Se registraron 1 133 muertes en la segunda ola y 754 en la cuarta. Se calculó que, en el contexto del despliegue de las vacunas, en la cuarta ola se evitaron aproximadamente 3 763 muertes en Cali. Conclusiones. La disminución observada en la mortalidad asociada a la COVID-19 respalda la continuación del programa de vacunación. Dada la falta de datos para explicar otras posibles causas de esta disminución, como puede ser la gravedad causada por las nuevas variantes virales, se analizan las limitaciones del estudio.

RESUMO Objetivo. Descrever a variação da mortalidade por COVID-19 entre residentes de Cali, Colômbia, na segunda onda da pandemia (antes das vacinas) e na quarta onda (com a implantação da vacinação já em andamento), considerando as variáveis sexo, faixa etária, comorbidades e intervalo entre início dos sintomas e óbito, bem como estimar o número de óbitos evitados pela vacinação. Métodos. Estudo transversal de mortes e cobertura vacinal na segunda e quarta ondas da pandemia. Foram comparadas as frequências dos atributos da população que foi a óbito durante as duas ondas, incluindo comorbidades. Foi utilizado o método de Machado para estimar o número de mortes evitadas na quarta onda. Resultados. Houve 1.133 mortes na segunda onda e 754 mortes na quarta onda. Calcula-se que cerca de 3.763 mortes foram evitadas na quarta onda em Cali, no contexto da disponibilização das vacinas. Conclusões. A queda observada na mortalidade associada à COVID-19 apoia a continuidade do programa de vacinação. Considerando a falta de dados para explicar outros possíveis motivos para esta queda, como a gravidade das novas variantes do vírus, discutem-se as limitações do estudo.

Effect of Ivermectin on Time to Resolution of Symptoms Among Adults With Mild COVID-19: A Randomized Clinical Trial.

Importance: Ivermectin is widely prescribed as a potential treatment for COVID-19 despite uncertainty about its clinical benefit. Objective: To determine whether ivermectin is an efficacious treatment for mild COVID-19. Design, Setting, and Participants: Double-blind, randomized trial conducted at a single site in Cali, Colombia. Potential study participants were identified by simple random sampling from the state's health department electronic database of patients with symptomatic, laboratory-confirmed COVID-19 during the study period. A total of 476 adult patients with mild disease and symptoms for 7 days or fewer (at home or hospitalized) were enrolled between July 15 and November 30, 2020, and followed up through December 21, 2020. Intervention: Patients were randomized to receive ivermectin, 300 µg/kg of body weight per day for 5 days (n = 200) or placebo (n = 200). Main Outcomes and Measures: Primary outcome was time to resolution of symptoms within a 21-day follow-up period. Solicited adverse events and serious adverse events were also collected. Results: Among 400 patients who were randomized in the primary analysis population (median age, 37 years [interquartile range {IQR}, 29-48]; 231 women [58%]), 398 (99.5%) completed the trial. The median time to resolution of symptoms was 10 days (IQR, 9-13) in the ivermectin group compared with 12 days (IQR, 9-13) in the placebo group (hazard ratio for resolution of symptoms, 1.07 [95% CI, 0.87 to 1.32]; P = .53 by log-rank test). By day 21, 82% in the ivermectin group and 79% in the placebo group had resolved symptoms. The most common solicited adverse event was headache, reported by 104 patients (52%) given ivermectin and 111 (56%) who received placebo. The most common serious adverse event was multiorgan failure, occurring in 4 patients (2 in each group). Conclusion and Relevance: Among adults with mild COVID-19, a 5-day course of ivermectin, compared with placebo, did not significantly improve the time to resolution of symptoms. The findings do not support the use of ivermectin for treatment of mild COVID-19, although larger trials may be needed to understand the effects of ivermectin on other clinically relevant outcomes. Trial Registration: ClinicalTrials.gov Identifier: NCT04405843.

Predicciones de un modelo SEIR para casos de COVID-19 en Cali, Colombia / Predictions of a SEIR model for COVID-19 cases in Cali-Colombia

RESUMEN Objetivo Predecir el número de casos de COVID-19 en la ciudad de Cali-Colombia mediante el desarrollo de un modelo SEIR. Métodos Se utilizó un modelo determinista compartimental SEIR considerando los estados: susceptibles (S), expuestos (E), infectados (I) y recuperados (R). Los parámetros del modelo fueron seleccionados de acuerdo a la revisión de literatura. En el caso de la tasa de letalidad, se usaron los datos de la Secretaría de Salud Municipal de Cali. Se plantearon varios escenarios teniendo en cuenta variaciones en el número básico de reproducción (R0) y en la tasa de letalidad; además, se comparó la predicción hasta el 9 de abril con los datos observados. Resultados A través del modelo SEIR se encontró que, con el número básico de reproducción más alto (2,6) y utilizando la letalidad calculada para la ciudad de 2,0%, el número máximo de casos se alcanzaría el primero de junio con 195 666 (prevalencia); sin embargo, al comparar los casos observados con los esperados, al inicio la ocurrencia observada estaba por encima de la proyectada; pero luego cambia la tendencia con una disminución marcada de la pendiente. Conclusiones Los modelos epidemiológicos SEIR son métodos muy utilizados para la proyección de casos en enfermedades infecciosas; sin embargo, se debe tener en cuenta que son modelos deterministas que pueden utilizar parámetros supuestos y podrían generar resultados imprecisos.(AU)

ABSTRACT Objective To predict the number of cases of COVID-19 in the city of Cali-Colombia through the development of a SEIR model. Methods A SEIR compartmental deterministic model was used considering the states: susceptible (S), exposed (E), infected (I) and recovered (R). The model parameters were selected according to the literature review, in the case of the case fatality rate data from the Municipal Secretary of Health were used. Several scenarios were considered taking into account variations in the basic number of reproduction (R0), and the prediction until april 9 was compared with the observed data. Results Through the SEIR model it was found that with the highest basic number of reproduction [2,6] and using the case fatality rate for the city of 2,0%, the maximum number of cases would be reached on June 1 with 195 666 (prevalence). However, when comparing the observed with the expected cases, at the beginning the observed occurrence was above the projected, but then the trend changes decreasing the slope. Conclusions SEIR epidemiological models are widely used methods for projecting cases in infectious diseases, however it must be taken into account that they are deterministic models that can use assumed parameters and could generate imprecise results.(AU)

Análisis espacio-temporal del SARS-COV-2 en Cali, Colombia / SARS-coV-2 spatio - temporal analysis in Cali, Colombia

RESUMEN Objetivo Describir la distribución espacio-temporal del COVID-19 en la ciudad de Cali durante el primer mes de epidemia. Métodos Se realizó un análisis exploratorio de datos espaciales, compuesto por un análisis de densidad de Kernel y se verificó la presencia de patrones espaciales por medio de la función K de Ripley. Resultados La distribución espacial de los casos tiende a concentrarse inicialmente en el norte y sur de la ciudad, con una dinámica cambiante hacia el oriente y occidente. Conclusiones El patrón espacial identificado puede estar influenciado por las medidas de aislamiento tomadas a nivel local y nivel nacional, además no se puede descartar el efecto del poco acceso que tiene la población general a las pruebas diagnósticas, los retrasos y represamientos para conocer los resultados de las mismas y aun los posibles sesgos por dificultades en la técnica de toma de la muestra o su conservación.(AU)

ABSTRACT Objective To describe the spatio-temporal distribution of the COVID-19 in the city of Cali during the first month of the epidemic. Methods An exploratory analysis of spatial data was carried out, consisting of a kernel density analysis and the presence of spatial patterns was verified by the K-Ripley function. Results The spatial distribution of the cases tends to initially concentrate in the north and south of the city, with a changing dynamic towards the east and west. Conclusions The identified spatial pattern may be influenced by the isolation measures taken at the local and national level, but the effect of the low access of the general population to diagnostic tests, delays and restraints to know the results cannot be ruled out and even possible biases due to difficulties in the technique of taking the sample or its conservation.(AU)

Objetivo: Descrever a distribuição espaço-temporal do COVID-19 na cidade de Cali durante o primeiro mês da epidemia. Métodos: Foi realizada uma análise exploratória de dados espaciais, consistindo em uma análise de densidade de kernel e a presença de padrões espaciais foi verificada pela função K-Ripley. Resultados: A distribuição espacial dos casos tende a se concentrar inicialmente no norte e no sul da cidade, com uma dinâmica mutante para o leste e oeste. Conclusões: O padrão espacial identificado pode ser influenciado pelas medidas de isolamento tomadas a nível local e nacional, mas não se pode descartar o efeito do baixo acesso da população em geral aos exames diagnósticos, atrasos e limitações para conhecer os resultados e mesmo possíveis vieses devido às dificuldades na técnica de coleta da amostra ou na sua conservação.(AU)

[Predictions of a SEIR model for COVID-19 cases in Cali-Colombia]. / Predicciones de un modelo SEIR para casos de COVID-19 en Cali, Colombia.

OBJECTIVE: To predict the number of cases of COVID-19 in the city of Cali-Colombia through the development of a SEIR model. METHODS: A SEIR compartmental deterministic model was used considering the states: susceptible (S), exposed (E), infected (I) and recovered (R). The model parameters were selected according to the literature review, in the case of the case fatality rate data from the Municipal Secretary of Health were used. Several scenarios were considered taking into account variations in the basic number of reproduction (R0), and the prediction until april 9 was compared with the observed data. RESULTS: Through the SEIR model it was found that with the highest basic number of reproduction [2,6] and using the case fatality rate for the city of 2,0%, the maximum number of cases would be reached on June 1 with 195 666 (prevalence). However, when comparing the observed with the expected cases, at the beginning the observed occurrence was above the projected, but then the trend changes decreasing the slope. CONCLUSIONS: SEIR epidemiological models are widely used methods for projecting cases in infectious diseases, however it must be taken into account that they are deterministic models that can use assumed parameters and could generate imprecise results.

[SARS-coV-2 spatio - temporal analysis in Cali, Colombia]. / Análisis espacio-temporal del SARS-COV-2 en Cali, Colombia.

OBJECTIVE: To describe the spatio-temporal distribution of the COVID-19 in the city of Cali during the first month of the epidemic. METHODS: An exploratory analysis of spatial data was carried out, consisting of a kernel density analysis and the presence of spatial patterns was verified by the K-Ripley function. RESULTS: The spatial distribution of the cases tends to initially concentrate in the north and south of the city, with a changing dynamic towards the east and west. CONCLUSIONS: The identified spatial pattern may be influenced by the isolation measures taken at the local and national level, but the effect of the low access of the general population to diagnostic tests, delays and restraints to know the results cannot be ruled out and even possible biases due to difficulties in the technique of taking the sample or its conservation.

Sindrome autoinmune en la paraparesia tropical espastica/ mielopatia asociada a la infeccion por el virus linfotropico / Autoimmune syndrome in the tropical spastic paraparesis/myelopathy associated with human T-lymphotropic virus infections

Introduccion. Trabajos previos han aportado evidencias de que en la paraparesia espastica tropical/mielopatia asociada con el virus linfotropico humano tipo I, existe un componente autoinmune asociado a su patogenesis. Objetivo. Evaluar el estado autoinmune y la existencia de mimetismo molecular en pacientes con paraparesia espastica tropical del pacifico colombiano. Materiales y metodos. A partir de muestras de plasma de 37 pacientes con paraparesia espastica tropical/mielopatia asociada al HTLV-I, 10 con leucemia de celulas T del adulto, 22 individuos portadores asintomáticos y 20 seronegativos para el HTLV-I, se determinaron niveles plasmaticos de anticuerpos antinucleares y anticardiolipina-2 y de interferon e interleucina- 4. Se evaluo, por Western blot, la reactividad cruzada de plasmas contra proteinas obtenidas de varias fuentes celulares normales del sistema nervioso. Ademas, se estudio la reactividad cruzada de plasmas de seropositivos y del anticuerpo monoclonal LT4 anti-taxp40 en secciones de medula espinal de ratas Wistar no infectadas. Resultados. El 70,2 por ciento y el 83,8 por ciento de los pacientes con paraparesia espastica tropical fueron reactivos para anticuerpos ANA y ACL-2, respectivamente, en contraste con los de leucemia de celulas T del adulto y los seropositivos asintom¨¢ticos (P<0,001). Ademas, el 70,3 por ciento y el 43,2 por ciento de los pacientes con paraparesia espastica tropical tuvieron niveles detectables de IFN-¦Ã e IL-4, respectivamente. El anticuerpo LT4 anti tax-p40 y los plasmas de paraparesia espastica tropical/mielopatia asociada al HTLV-I mostraron una reaccion cruzada con una proteina de PMr 33-35 kDa, obtenida del nucleo de neuronas de la medula espinal de ratas Wistar no infectadas. Conclusion. Se obtuvieron evidencias que apoyan la existencia de un sindrome autoinmune mediado por mimetismo molecular como parte de la etiopatogenesis de la degeneracion axonal observada en la paraparesia espastica tropical en pacientes colombianos de la costa pacifica.

[Autoimmune syndrome in the tropical spastic paraparesis/myelopathy associated with human T-lymphotropic virus infections]. / Síndrome autoinmune en la paraparesia tropical espástica/mielopatía asociada a la infección por el virus linfotrópico humano tipo I de la costa pacífica colombiana.

INTRODUCTION: Previous reports have given evidence that in tropical spastic paraparesis (TSP)/human T-lymphotrophic virus (HTLV-I)-associated myelopathy (HAM), an autoimmune process occurs as part of its pathogenesis. OBJECTIVE: The roles of autoimmunity and the molecular mimicry was evaluated in TSP/HAM patients. MATERIALS AND METHODS: Plasma samples were characterized from patients in the Pacific coastal region of Colombia. Thirty-seven were identified as TSP/HAM, 10 were diagnosed with adult T-cell leukemia virus, 22 were asymptomatic carriers but seropositive for HTLV-I and 20 were seronegative and served as negative controls. Plasmatic levels of the following were determined: antinuclear antibody (ANA) levels, anticardiolipine-2 (ACL-2), interferon- (IFN-gamma) and interleukin-4 (IL-4). Using Western blot, the crossreactivity of the seropositive and seronegative samples was evaluated against proteins extracted from several central nervous system components of non infected Wistar rats. The HTLV-I seropositive plasmas were crossreacted with a monoclonal tax (LT4 anti-taxp40) from spinal cord neurons of non infected Wistar rats. RESULTS: Of the TSP/HAM patients, 70.2% were reactive against ANA and 83.8% against ACL-2, in contrast with those ATL and asymptomatic seropositives subjects that were not reactive (P<0.001). Moreover, 70.3% had detectable levels of IFN and 43.2% had detectable IL-4. LT4 anti-taxp40 and plasma of TSP/HAM exhibited cross reactivity with a MW 33-35 kDa protein from the rat spinal cord nuclei. CONCLUSION: Support was provided for the existence of an autoimmune syndrome mediated by molecular mimicry; the syndrome was responsible for some of the axonal degeneration observed in TSP/HAM patients.

Human papillomavirus in esophageal squamous cell carcinoma in Colombia and Chile.

AIM: To examine the presence of human papillomavirus (HPV) in esophageal squamous cell carcinoma (ESCC) specimens collected from Colombia and Chile located in the northern and southern ends of the continent, respectively. METHODS: We examined 47 and 26 formalin-fixed and paraffin-embedded ESCC specimens from Colombia and Chile, respectively. HPV was detected using GP5+/GP6+ primer pair for PCR, and confirmed by Southern blot analysis. Sequencing analysis of L1 region fragment was used to identify HPV genotype. In addition, P16(INK4A) protein immunostaining of all the specimens was conducted. RESULTS: HPV was detected in 21 ESCC specimens (29%). Sequencing analysis of L1 region fragment identified HPV-16 genome in 6 Colombian cases (13%) and in 5 Chilean cases (19%). HPV-18 was detected in 10 cases (21%) in Colombia but not in any Chilean case. Since Chilean ESCC cases had a higher prevalence of HPV-16 (without statistical significance), but a significantly lower prevalence of HPV-18 than in Colombian cases (P = 0.011) even though the two countries have similar ESCC incidence rates, the frequency of HPV-related ESCC may not be strongly affected by risk factors affecting the incidence of ESCC. HPV-16 genome was more frequently detected in p16 positive carcinomas, although the difference was not statistically significant. HPV-18 detection rate did not show any association with p16 expression. Well-differentiated tumors tended to have either HPV-16 or HPV-18 but the association was not statistically significant. HPV genotypes other than HPV-16 or 18 were not detected in either country. CONCLUSION: HPV-16 and HPV-18 genotypes can be found in ESCC specimens collected from two South American countries. Further studies on the relationship between HPV-16 presence and p16 expression in ESCC would aid understanding of the mechanism underlying the presence of HPV in ESCC.