Enhanced Spike-specific, but attenuated Nucleocapsid-specific T cell responses upon SARS-CoV-2 breakthrough versus non-breakthrough infections

SARS-CoV-2 vaccine breakthrough infections frequently occurred even before the emergence of Omicron variants. Yet, relatively little is known about the impact of vaccination on SARS-CoV-2-specific T cell and antibody response dynamics upon breakthrough infection. We have therefore studied the dynamics of CD4 and CD8 T cells targeting the vaccine-encoded Spike and the non-encoded Nucleocapsid antigens during breakthrough infections (BTI, n=24) and in unvaccinated control infections (non-BTI, n=30). Subjects with vaccine breakthrough infection had significantly higher CD4 and CD8 T cell responses targeting the vaccine-encoded Spike during the first and third/fourth week after PCR diagnosis compared to non-vaccinated controls, respectively. In contrast, CD4 T cells targeting the non-vaccine encoded Nucleocapsid antigen were of significantly lower magnitude in BTI as compared to non-BTI. Hence, previous vaccination was linked to enhanced T cell responses targeting the vaccine-encoded Spike antigen, while responses against the non-vaccine encoded Nucleocapsid antigen were significantly attenuated

Community SARS-CoV-2 seroprevalence before and after the second wave of SARS-CoV-2 infection in Harare, Zimbabwe.

BACKGROUND: By the end of July 2021 Zimbabwe, has reported over 100,000 SARS-CoV-2 infections. The true number of SARS-CoV-2 infections is likely to be much higher. We conducted a seroprevalence survey to estimate the prevalence of past SARS-CoV-2 in three high-density communities in Harare, Zimbabwe before and after the second wave of SARS-CoV-2. METHODS: Between November 2020 and April 2021 we conducted a cross-sectional study of randomly selected households in three high-density communities (Budiriro, Highfield and Mbare) in Harare. Consenting participants answered a questionnaire and a dried blood spot sample was taken. Samples were tested for anti-SARS-CoV-2 nucleocapsid antibodies using the Roche e801 platform. FINDINGS: A total of 2340 individuals participated in the study. SARS-CoV-2 antibody results were available for 70·1% (620/885) and 73·1% (1530/2093) of eligible participants in 2020 and 2021. The median age was 22 (IQR 10-37) years and 978 (45·5%) were men. SARS-CoV-2 seroprevalence was 19·0% (95% CI 15·1-23·5%) in 2020 and 53·0% (95% CI 49·6-56·4) in 2021. The prevalence ratio was 2·47 (95% CI 1·94-3·15) comparing 2020 with 2021 after adjusting for age, sex, and community. Almost half of all participants who tested positive reported no symptoms in the preceding six months. INTERPRETATION: Following the second wave, one in two people had been infected with SARS-CoV-2 suggesting high levels of community transmission. Our results suggest that 184,800 (172,900-196,700) SARS-CoV-2 infections occurred in these three communities alone, greatly exceeding the reported number of cases for the whole city. Further seroprevalence surveys are needed to understand transmission during the current third wave despite high prevalence of past infections. FUNDING: GCRF, Government of Canada, Wellcome Trust, Bavarian State Ministry of Sciences, Research, and the Arts

Protective immune trajectories in early viral containment of non-pneumonic SARS-CoV-2 infection

The antiviral immune response to SARS-CoV-2 infection can limit viral spread and prevent development of pneumonic COVID-19. However, the protective immunological response associated with successful viral containment in the upper airways remains unclear. Here, we combine a multi-omics approach with longitudinal sampling to reveal temporally resolved protective immune signatures in non-pneumonic and ambulatory SARS-CoV-2 infected patients and associate specific immune trajectories with upper airway viral containment. We see a distinct systemic rather than local immune state associated with viral containment, characterized by interferon stimulated gene (ISG) upregulation across circulating immune cell subsets in non-pneumonic SARS-CoV2 infection. We report reduced cytotoxic potential of Natural Killer (NK) and T cells, and an immune-modulatory monocyte phenotype associated with protective immunity in COVID-19. Together, we show protective immune trajectories in SARS-CoV2 infection, which have important implications for patient prognosis and the development of immunomodulatory therapies

Nucleocapsid-specific T cell responses associate with control of SARS-CoV-2 in the upper airways before seroconversion

Despite intensive research since the emergence of SARS-CoV-2, it has remained unclear precisely which components of the early immune response protect against the development of severe COVID-19. Here, we perform a comprehensive immunogenetic and virologic analysis of nasopharyngeal and peripheral blood samples obtained during the acute phase of infection with SARS-CoV-2. We find that soluble and transcriptional markers of systemic inflammation peak during the first week after symptom onset and correlate directly with upper airways viral loads (UA-VLs), whereas the contemporaneous frequencies of circulating viral nucleocapsid (NC)-specific CD4+ and CD8+ T cells correlate inversely with various inflammatory markers and UA-VLs. In addition, we show that high frequencies of activated CD4+ and CD8+ T cells are present in acutely infected nasopharyngeal tissue, many of which express genes encoding various effector molecules, such as cytotoxic proteins and IFN-γ. The presence of IFNG mRNA-expressing CD4+ and CD8+ T cells in the infected epithelium is further linked with common patterns of gene expression among virus-susceptible target cells and better local control of SARS-CoV-2. Collectively, these results identify an immune correlate of protection against SARS-CoV-2, which could inform the development of more effective vaccines to combat the acute and chronic illnesses attributable to COVID-19

Enhanced Spike-specific, but attenuated Nucleocapsid-specific T cell responses upon SARS-CoV-2 breakthrough versus non-breakthrough infections

SARS-CoV-2 vaccine breakthrough infections frequently occurred even before the emergence of Omicron variants. Yet, relatively little is known about the impact of vaccination on SARS-CoV-2-specific T cell and antibody response dynamics upon breakthrough infection. We have therefore studied the dynamics of CD4 and CD8 T cells targeting the vaccine-encoded Spike and the non-encoded Nucleocapsid antigens during breakthrough infections (BTI, n=24) and in unvaccinated control infections (non-BTI, n=30). Subjects with vaccine breakthrough infection had significantly higher CD4 and CD8 T cell responses targeting the vaccine-encoded Spike during the first and third/fourth week after PCR diagnosis compared to non-vaccinated controls, respectively. In contrast, CD4 T cells targeting the non-vaccine encoded Nucleocapsid antigen were of significantly lower magnitude in BTI as compared to non-BTI. Hence, previous vaccination was linked to enhanced T cell responses targeting the vaccine-encoded Spike antigen, while responses against the non-vaccine encoded Nucleocapsid antigen were significantly attenuated

Molecular analysis of the mechanisms involved in THBS4 differential geneexpression in the human brain

Durante las últimas décadas ha crecido el interés en cuestiones como qué nos hace humanos o cómo difiere a nivel molecular el cerebro humano del de nuestros parientes más cercanos. Se han podido identificar cientos de genes con diferencias de expresión entre el ser humano y otros primates no humanos. Sin embargo, es importante estudiar más en detalle estos genes para comprobar si realmente están involucrados en las características específicas de nuestro cerebro. Las trombospondinas son glicoproteínas extracelulares multiméricas que modulan las interacciones entre células y con la matriz extracelular y que se han implicado en la sinaptogénesis. Dentro de la familia de las trombospondinas, los genes de la trombospondina-2 (THBS2) y trombospondina-4 (THBS4) se expresan, respectivamente, alrededor de 2 y 6 veces más en la corteza cerebral humana en comparación con la de chimpancés o macacos. Para conocer las causas de estas diferencias de expresión, hemos llevado a cabo un análisis comparativo y funcional de la región promotora de THBS4 en humanos y en chimpancés. Hemos identificado y validado un sitio de inicio de transcripción (TSS) alternativo para THBS4 que se encuentra 44 kb aguas arriba del TSS de referencia y que genera una nueva isoforma de ARNm que podría haber aparecido más tarde durante la evolución. Para comparar los niveles de expresión de ambos transcritos se realizó RT-PCR cuantitativa en diferentes tejidos humanos y en muestras de corteza cerebral de 11 humanos, 11 chimpancés y 8 macacos. Curiosamente, la nueva isoforma de THBS4 se expresa principalmente en los tejidos cerebrales. Por otra parte, la diferencia de expresión entre humanos y primates no humanos para la isoforma alternativa son consistentes con la encontrada al analizar la expresión total de THBS4. Por tanto, el aumento de la expresión de THBS4 en el cerebro humano parece estar relacionado con una mayor transcripción a partir del promotor alternativo. Para evaluar la actividad de ambas secuencias promotoras en humanos y en chimpancés, hemos llevado a cabo ensayos con un gen indicador en diferentes líneas celulares humanas. Se han encontrado diferencias significativas entre los dos promotores, aunque en las líneas de neuroblastoma que utilizamos no existen diferencias significativas entre especies. Este resultado es consistente con la búsqueda de sitios de unión de factores de transcripción en la región del promotor alternativo, ya que sólo se detectaron tres posibles sitios de unión diferentes entre ambas especies. Se ha comparado también la metilación del ADN en una isla CpG situada aguas arriba de la nueva isoforma de THBS4 en 5 humanos y en 5 chimpancés, detectando niveles bajos de metilación en ambas especies. Basándonos en las predicciones informáticas disponibles y en experimentos piloto de ChIP-Seq, hemos buscado posibles enhancers que estén controlando el promotor alternativo de THBS4, pero no hemos encontrado ningún candidato fiable. Por último, en humanos, se ha visto que hay dos haplotipos de THBS4 diferentes que se encuentran mantenidos mediante selección equilibradora. Sin embargo, la comparación experimental de ambos no muestra ningún efecto del genotipo sobre la expresión de THBS4. Aunque no se ha conseguido identificar la causa concreta del incremento en los niveles de THBS4 en humanos, en base a nuestros resultados sugerimos que la expresión diferencial del gen podría estar relacionada con una secuencia potenciadora específica del cerebro que no hemos conseguido localizar. Comprender como se encuentra regulada esta posible secuencia potenciadora podría ser relevante para entender cuales son las consecuencias funcionales de las diferencias de expresión de THBS4 sobre la evolución del cerebro y, en última instancia, darnos pistas sobre como nos convertimos en humanos.The last decades have seen a growing interest in what makes us humans and how the human brain differs from that of our closest relatives at the molecular level. Hundreds of genes with expression differences between human and non-human primates have been identified. However, it is important to study these genes in more detail to see if they are really involved in human brain characteristics. Thrombospondins are multimeric extracellular glycoproteins that modulate cell-cell and extracellular matrix interactions and have been implicated in synaptogenesis. Within the thrombospondin family, thrombospondin-2 (THBS2) and thrombospondin-4 (THBS4) show, respectively, a ~2-fold and ~6-fold upregulation in human cerebral cortex compared to chimpanzees and macaques. To analyze the causes of these expression differences, we have carried out a comparative and functional analysis of the THBS4 promoter region in humans and chimpanzees. We have identified and validated an alternative transcription start site (TSS) for THBS4 that is located ~44 kb upstream from the known TSS and generates a new mRNA isoform that might have appeared later that the reference one during evolution. To compare expression levels of both mRNAs, we performed quantitative RT-PCR in different human tissues and cortical regions of 11 humans, 11 chimpanzees and 8 macaques. Interestingly, the new isoform of THBS4 is expressed mainly in brain tissues. Moreover, expression differences between human and non-human primate cortex for this alternative isoform are consistent with those shown for total THBS4 expression. Increased THBS4 expression in the human brain therefore appears to be related to higher transcription from the alternative promoter. To evaluate the activity of both THBS4 promoter sequences we performed reporter assays from humans and chimpanzees in different human cell lines. We have found significant differences between both promoters, but not between species, in the neuroblastoma cell lines assayed. This result is consistent with the search for transcription factor binding sites (TFBS) in the alternative promoter region, which only detected three putative TFBS differentially predicted between both species. We also compared the DNA methylation in a CpG island upstream the new isoform in 5 humans and 5 chimpanzees detecting similar low methylation levels in all of them. Based in the computational predictions available online and ChIP-Seq pilot experiments, we searched for a putative enhancer region controlling the THBS4 alternative promoter without finding any reliable candidate. Finally, in humans, THBS4 has been associated to two different haplotypes that are maintained by balancing selection, but experimental analysis did not show any effect of the genotype over THBS4 gene expression. Although we have not been able to identify the ultimate cause of the increased THBS4 levels in humans, based on all our results we suggest that the differential gene expression might be related to a brain-specific enhancer sequence that has so far escaped our scrutiny. Understanding its regulation could be relevant to the functional consequences of THBS4 expression differences during human brain evolution and ultimately could give us clues of how we became humans

Molecular analysis of the mechanisms involved in THBS4 differential geneexpression in the human brain

Durante las últimas décadas ha crecido el interés en cuestiones como qué nos hace humanos o cómo difiere a nivel molecular el cerebro humano del de nuestros parientes más cercanos. Se han podido identificar cientos de genes con diferencias de expresión entre el ser humano y otros primates no humanos. Sin embargo, es importante estudiar más en detalle estos genes para comprobar si realmente están involucrados en las características específicas de nuestro cerebro. Las trombospondinas son glicoproteínas extracelulares multiméricas que modulan las interacciones entre células y con la matriz extracelular y que se han implicado en la sinaptogénesis. Dentro de la familia de las trombospondinas, los genes de la trombospondina-2 (THBS2) y trombospondina-4 (THBS4) se expresan, respectivamente, alrededor de 2 y 6 veces más en la corteza cerebral humana en comparación con la de chimpancés o macacos. Para conocer las causas de estas diferencias de expresión, hemos llevado a cabo un análisis comparativo y funcional de la región promotora de THBS4 en humanos y en chimpancés. Hemos identificado y validado un sitio de inicio de transcripción (TSS) alternativo para THBS4 que se encuentra 44 kb aguas arriba del TSS de referencia y que genera una nueva isoforma de ARNm que podría haber aparecido más tarde durante la evolución. Para comparar los niveles de expresión de ambos transcritos se realizó RT-PCR cuantitativa en diferentes tejidos humanos y en muestras de corteza cerebral de 11 humanos, 11 chimpancés y 8 macacos. Curiosamente, la nueva isoforma de THBS4 se expresa principalmente en los tejidos cerebrales. Por otra parte, la diferencia de expresión entre humanos y primates no humanos para la isoforma alternativa son consistentes con la encontrada al analizar la expresión total de THBS4. Por tanto, el aumento de la expresión de THBS4 en el cerebro humano parece estar relacionado con una mayor transcripción a partir del promotor alternativo. Para evaluar la actividad de ambas secuencias promotoras en humanos y en chimpancés, hemos llevado a cabo ensayos con un gen indicador en diferentes líneas celulares humanas. Se han encontrado diferencias significativas entre los dos promotores, aunque en las líneas de neuroblastoma que utilizamos no existen diferencias significativas entre especies. Este resultado es consistente con la búsqueda de sitios de unión de factores de transcripción en la región del promotor alternativo, ya que sólo se detectaron tres posibles sitios de unión diferentes entre ambas especies. Se ha comparado también la metilación del ADN en una isla CpG situada aguas arriba de la nueva isoforma de THBS4 en 5 humanos y en 5 chimpancés, detectando niveles bajos de metilación en ambas especies. Basándonos en las predicciones informáticas disponibles y en experimentos piloto de ChIP-Seq, hemos buscado posibles enhancers que estén controlando el promotor alternativo de THBS4, pero no hemos encontrado ningún candidato fiable. Por último, en humanos, se ha visto que hay dos haplotipos de THBS4 diferentes que se encuentran mantenidos mediante selección equilibradora. Sin embargo, la comparación experimental de ambos no muestra ningún efecto del genotipo sobre la expresión de THBS4. Aunque no se ha conseguido identificar la causa concreta del incremento en los niveles de THBS4 en humanos, en base a nuestros resultados sugerimos que la expresión diferencial del gen podría estar relacionada con una secuencia potenciadora específica del cerebro que no hemos conseguido localizar. Comprender como se encuentra regulada esta posible secuencia potenciadora podría ser relevante para entender cuales son las consecuencias funcionales de las diferencias de expresión de THBS4 sobre la evolución del cerebro y, en última instancia, darnos pistas sobre como nos convertimos en humanos.The last decades have seen a growing interest in what makes us humans and how the human brain differs from that of our closest relatives at the molecular level. Hundreds of genes with expression differences between human and non-human primates have been identified. However, it is important to study these genes in more detail to see if they are really involved in human brain characteristics. Thrombospondins are multimeric extracellular glycoproteins that modulate cell-cell and extracellular matrix interactions and have been implicated in synaptogenesis. Within the thrombospondin family, thrombospondin-2 (THBS2) and thrombospondin-4 (THBS4) show, respectively, a ~2-fold and ~6-fold upregulation in human cerebral cortex compared to chimpanzees and macaques. To analyze the causes of these expression differences, we have carried out a comparative and functional analysis of the THBS4 promoter region in humans and chimpanzees. We have identified and validated an alternative transcription start site (TSS) for THBS4 that is located ~44 kb upstream from the known TSS and generates a new mRNA isoform that might have appeared later that the reference one during evolution. To compare expression levels of both mRNAs, we performed quantitative RT-PCR in different human tissues and cortical regions of 11 humans, 11 chimpanzees and 8 macaques. Interestingly, the new isoform of THBS4 is expressed mainly in brain tissues. Moreover, expression differences between human and non-human primate cortex for this alternative isoform are consistent with those shown for total THBS4 expression. Increased THBS4 expression in the human brain therefore appears to be related to higher transcription from the alternative promoter. To evaluate the activity of both THBS4 promoter sequences we performed reporter assays from humans and chimpanzees in different human cell lines. We have found significant differences between both promoters, but not between species, in the neuroblastoma cell lines assayed. This result is consistent with the search for transcription factor binding sites (TFBS) in the alternative promoter region, which only detected three putative TFBS differentially predicted between both species. We also compared the DNA methylation in a CpG island upstream the new isoform in 5 humans and 5 chimpanzees detecting similar low methylation levels in all of them. Based in the computational predictions available online and ChIP-Seq pilot experiments, we searched for a putative enhancer region controlling the THBS4 alternative promoter without finding any reliable candidate. Finally, in humans, THBS4 has been associated to two different haplotypes that are maintained by balancing selection, but experimental analysis did not show any effect of the genotype over THBS4 gene expression. Although we have not been able to identify the ultimate cause of the increased THBS4 levels in humans, based on all our results we suggest that the differential gene expression might be related to a brain-specific enhancer sequence that has so far escaped our scrutiny. Understanding its regulation could be relevant to the functional consequences of THBS4 expression differences during human brain evolution and ultimately could give us clues of how we became humans

The Prospective COVID-19 Post-Immunization Serological Cohort in Munich (KoCo-Impf): Risk Factors and Determinants of Immune Response in Healthcare Workers

Reinkemeyer C, Khazaei Y, Weigert M, et al. The Prospective COVID-19 Post-Immunization Serological Cohort in Munich (KoCo-Impf): Risk Factors and Determinants of Immune Response in Healthcare Workers. Viruses. 2023;15(7): 1574.Antibody studies analyze immune responses to SARS-CoV-2 vaccination and infection, which is crucial for selecting vaccination strategies. In the KoCo-Impf study, conducted between 16 June and 16 December 2021, 6088 participants aged 18 and above from Munich were recruited to monitor antibodies, particularly in healthcare workers (HCWs) at higher risk of infection. Roche Elecsys® Anti-SARS-CoV-2 assays on dried blood spots were used to detect prior infections (anti-Nucleocapsid antibodies) and to indicate combinations of vaccinations/infections (anti-Spike antibodies). The anti-Spike seroprevalence was 94.7%, whereas, for anti-Nucleocapsid, it was only 6.9%. HCW status and contact with SARS-CoV-2-positive individuals were identified as infection risk factors, while vaccination and current smoking were associated with reduced risk. Older age correlated with higher anti-Nucleocapsid antibody levels, while vaccination and current smoking decreased the response. Vaccination alone or combined with infection led to higher anti-Spike antibody levels. Increasing time since the second vaccination, advancing age, and current smoking reduced the anti-Spike response. The cumulative number of cases in Munich affected the anti-Spike response over time but had no impact on anti-Nucleocapsid antibody development/seropositivity. Due to the significantly higher infection risk faced by HCWs and the limited number of significant risk factors, it is suggested that all HCWs require protection regardless of individual traits

Long-term monitoring of SARS-CoV-2 seroprevalence and variants in Ethiopia provides prediction for immunity and cross-immunity

Under-reporting of COVID-19 and the limited information about circulating SARS-CoV-2 variants remain major challenges for many African countries. We analyzed SARS-CoV-2 infection dynamics in Addis Ababa and Jimma, Ethiopia, focusing on reinfection, immunity, and vaccination effects. We conducted an antibody serology study spanning August 2020 to July 2022 with five rounds of data collection across a population of 4723, sequenced PCR-test positive samples, used available test positivity rates, and constructed two mathematical models integrating this data. A multivariant model explores variant dynamics identifying wildtype, alpha, delta, and omicron BA.4/5 as key variants in the study population, and cross-immunity between variants, revealing risk reductions between 24% and 69%. An antibody-level model predicts slow decay leading to sustained high antibody levels. Retrospectively, increased early vaccination might have substantially reduced infections during the delta and omicron waves in the considered group of individuals, though further vaccination now seems less impactful

Viaja con la mente

Este trabajo obtuvo la segunda mención especial de la modalidad B de los Premios Joaquín Sama 2006Se describe un concurso que consistía en realizar varias pruebas y que pretendía preparar a los alumnos para que tuvieran un comportamiento adecuado en el centro escolar. El objetivo principal del proyecto era mejorar la convivencia en el centro escolar, además de promover el trabajo en equipo, aumentar la motivación del alumnado, potenciar la búsqueda de soluciones alternativas ante los problemas diarios en el aula y el centro, dotar al alumno de los recursos necesarios para afrontar los conflictos de forma constructiva, etc. Se detalla la organización y el desarrollo del proyecto, su temporalización, la metodología seguida, los recursos necesarios para llevarlo a cabo, etc..ExtremaduraConsejería de Educación. Dirección General de Política Educativa; Calle Delgado Valencia, 6; 06800 Mérida (Badajoz); Tel. +34924006714; Fax +34924006716; [email protected]