SARS-CoV-2 seroprevalence and vaccine coverage from August to November 2021: A nationally representative survey in Mexico.

We aimed to estimate self-reported vaccine coverage and SARS-CoV-2 anti-N and anti-S seroprevalence in Mexico overall and for five vaccine types. We used a nationally representative survey with 7236 dried blood spot samples for adults 18 years and older collected from August to November 2021. Anti-N and anti-S seroprevalence were estimated adjusting for the sensitivity and specificity of the immunoassay test. A multivariate Poisson regression model was used to estimate seroprevalence by vaccine type and by age group adjusting for confounders and test performance. Vaccination coverage was 74%, being higher in women compared to men, high socioeconomic status (SES) compared to low and middle SES, graduates compared to people with high school, and formal workers compared to other employment statuses. Anti-N seroprevalence was 59.2%, compared to 84.1% anti-S seroprevalence. Anti-S seroprevalence was higher for vaccinated than unvaccinated participants. All vaccines were associated with more than 70% anti-S seroprevalence, with the lowest being observed for CoronaVac and Ad5-nCoV. Fully vaccinated participants over 60 years presented a lower seroprevalence (77.6%) compared to younger adults (91.1%), with larger differences for ChAdOx1 and CoronaVac vaccines. Between August and November 2021, three out of four Mexican adults had been vaccinated. Vaccination was associated with a higher positivity to anti-S antibodies. While antibodies do not reflect immunity, our results suggest that booster doses should be offered to people over 60 years of age and to adults who received Ad5-nCoV or CoronaVac as primary vaccination schemes.

Encuesta Nacional de Salud y Nutrición 2023: metodología y avances de la Ensanut Continua 2020-2024.

OBJETIVO: Presentar la metodología de la Encuesta Nacional de Salud y Nutrición 2023 (Ensanut 2023) y describir los procedimientos de inferencia para conjuntar la información colectada por la Ensanut Continua 2020-2024. Material y métodos. La Ensanut 2023 es la cuarta encuesta de la serie Ensanut Continua. Se describe el alcance de la Ensanut 2023 junto con sus procedimientos de muestreo, estimación, medición y organización logística. Además, se discute el procedimiento básico de estimación para analizar la integración de las encuestas Ensanut Continua 2020-2024. RESULTADOS: La Ensanut 2023 obtendrá a nivel nacional al menos 11 720 entrevistas completas de hogar y 13 378 cuestionarios completos de adulto. La unión de las Ensanut Continua 2020-2023 permitirá, en general, estimar a nivel estatal prevalencias p≥5% en adultos, con confiabilidad tolerable según las recomendaciones del Instituto Nacional de Estadística y Geografía. CONCLUSIONES: El análisis de la unión de la Ensanut Continua 2020-2023 permitirá iniciar la generación de estimaciones nacionales y estatales sobre el estado de salud y nutrición de la población mexicana.

Prevalencia de anticuerpos y vacunación contra SARS-CoV-2 en 2022 en México.

OBJETIVO: Describir la prevalencia de anticuerpos contra SARS-CoV-2, vacunación, barreras y rechazo a la vacunación Covid-19 en población mexicana. Material y métodos. Se utilizó información de los integrantes del hogar de uno y más años, incluidos en la Encuesta Nacional de Salud y Nutrición Continua 2022 (Ensanut Continua 2022) realizada de agosto-noviembre. Se estimó la prevalencia de anticuerpos antiproteínas N y S de SARS-CoV-2 en muestras de sangre capilar, dosis reportadas de vacunación a Covid-19 y las razones de barreras y rechazo a la vacunación. RESULTADOS: La prevalencia de anticuerpos anti-N fue de 94.4% y de anti-S 98.1%. La prevalencia de anticuerpos anti-S fue mayor en personas vacunadas con una, dos o tres o más dosis que en no vacunadas. Dentro de la población elegible a vacunación, 20.2% no estaba vacunada, 16.2% tenía una dosis, 30% dos dosis y 33.6% tres dosis o más. El 11.2% de la población elegible rechazó la vacunación, 5.5% reportó una barrera y 3.2% reportó que la vacuna no había llegado a su localidad. Conclusión. La prevalencia de anticuerpos por infección natural y por vacunación Covid-19 es alta en México. Las variaciones de rechazo y barreras a la vacunación entre grupos de edad y regiones deben tomarse en cuenta para intensificar esfuerzos específicos para la vacunación.

Prevalence of anti-SARS-CoV-2 antibodies and associated factors in healthcare workers of a Mexican Covid-19 hospital

OBJECTIVE: To determine the prevalence of SARS-CoV-2 antibodies among healthcare workers (HCW) and to identify factors associated with infection. Materials and meth-ods. A cross-sectional study was conducted in a Covid-19 hospital in Morelos, Mexico. Antibodies against SARS-CoV-2 spike and nucleocapsid proteins were detected by ELISA. A bivariate and multivariable Poisson regression model were performed to identify factors associated with infection. RESULTS: Among all participants, 31% had anti-SARS-CoV-2 antibodies, while only 13.1% had reported a history of positive RT-PCR. Individuals who reported cohabiting with someone with Covid-19, and those who had a previous RT-PCR test, were more likely to be seropositive. Laboratory personnel had the lowest seroprevalence (12.0%), while social workers had the highest (35.7%). CONCLUSIONS: The results of this study show the seroprevalence of SARS-CoV-2 antibodies among HCW in a hospital in Mexico, and underline the importance of serological tests for a better estimate of prevalence in health systems where only symptomatic cases are recorded.

Metodología de la Encuesta Nacional de Salud y Nutrición 2022 y Planeación y diseño de la Ensanut Continua 2020-2024.

OBJETIVO: Presentar el diseño de la Encuesta Nacional de Salud y Nutrición (Ensanut) 2022 y cuantificar el avance de la Ensanut Continua 2020-2024. Material y métodos. La Ensanut 2022 es la tercera encuesta de la serie de en-cuestas denominada Ensanut Continua 2020-2024. En este documento se describe el alcance de la Ensanut 2022 y sus procedimientos de muestreo, medición y organización logís-tica. Además, se presenta el avance esperado de la Ensanut Continua 2020-2024 al concluir la Ensanut 2022. Resulta-dos. La Ensanut 2022 obtendrá, a nivel nacional, al menos 10 160 entrevistas completas de hogar y 9 441 resultados de seropositividad a SARS-CoV-2. CONCLUSIONES: La Ensanut 2022 estimará la prevalencia de seropositividad a SARS-CoV-2 a nivel nacional y regional y avanzará en la acumulación de información para alcanzar los objetivos de la Ensanut Con-tinua 2020-2024.

Metodología de la Encuesta Nacional de Salud y Nutrición 2020 sobre Covid-19.

Objetivo. Describir el diseño y los resultados de campo de la Encuesta Nacional de Salud y Nutrición (Ensanut) 2020 so-bre Covid-19. Material y métodos. La Ensanut Covid-19 es una encuesta probabilística de hogares. En este artículo se describen los siguientes elementos del diseño: alcance, muestreo, medición, inferencia y logística. Resultados. Se obtuvieron 10 216 entrevistas de hogar completas y 9 464 resultados sobre seropositividad a SARS-CoV-2. La tasa de respuesta de hogar fue 80% y la de prueba de seropositividad de 44%. Conclusiones. El diseño probabilístico de la Ensa-nut Covid-19 permite hacer inferencias estadísticas válidas sobre parámetros de interés para la salud pública a nivel nacional y regional; en particular, permitirá hacer inferencias de utilidad práctica sobre la prevalencia de seropositividad a SARS-CoV-2 en México. Además, la Ensanut Covid-19 podrá ser comparada con Ensanut previas para identificar potenciales cambios en los estados de salud y nutrición de la población mexicana.

Metodología de la Encuesta Nacional de Salud y Nutrición 2021.

Objetivo. Describir el diseño de la Encuesta Nacional de Salud y Nutrición 2021 (Ensanut 2021). Material y métodos. La Ensanut 2021 es una encuesta probabilística de hogares que forma parte de la serie de Ensanut Continua 2020-2024. En esta ocasión se describen el alcance, el muestreo, la medición y la organización logística. Resultados. Se planea obtener al menos 12 060 entrevistas de hogar completas a nivel nacional y 9 837 muestras para determinar seropositividad a SARS-CoV-2 a nivel nacional. Conclusiones. La Ensanut 2021 permitirá realizar inferencias regionales sobre la prevalencia de seropositividad a SARS-CoV-2 y también acumular información para realizar inferencias estatales en el año 2024.

Adaptations in energy metabolism and gene family expansions revealed by comparative transcriptomics of three Chagas disease triatomine vectors.

BACKGROUND: Chagas disease is a parasitic infection caused by Trypanosoma cruzi. It is an important public health problem affecting around seven to eight million people in the Americas. A large number of hematophagous triatomine insect species, occupying diverse natural and human-modified ecological niches transmit this disease. Triatomines are long-living hemipterans that have evolved to explode different habitats to associate with their vertebrate hosts. Understanding the molecular basis of the extreme physiological conditions including starvation tolerance and longevity could provide insights for developing novel control strategies. We describe the normalized cDNA, full body transcriptome analysis of three main vectors in North, Central and South America, Triatoma pallidipennis, T. dimidiata and T. infestans. RESULTS: Two-thirds of the de novo assembled transcriptomes map to the Rhodnius prolixus genome and proteome. A Triatoma expansion of the calycin family and two types of protease inhibitors, pacifastins and cystatins were identified. A high number of transcriptionally active class I transposable elements was documented in T. infestans, compared with T. dimidiata and T. pallidipennis. Sequence identity in Triatoma-R. prolixus 1:1 orthologs revealed high sequence divergence in four enzymes participating in gluconeogenesis, glycogen synthesis and the pentose phosphate pathway, indicating high evolutionary rates of these genes. Also, molecular evidence suggesting positive selection was found for several genes of the oxidative phosphorylation I, III and V complexes. CONCLUSIONS: Protease inhibitors and calycin-coding gene expansions provide insights into rapidly evolving processes of protease regulation and haematophagy. Higher evolutionary rates in enzymes that exert metabolic flux control towards anabolism and evidence for positive selection in oxidative phosphorylation complexes might represent genetic adaptations, possibly related to prolonged starvation, oxidative stress tolerance, longevity, and hematophagy and flight reduction. Overall, this work generated novel hypothesis related to biological adaptations to extreme physiological conditions and diverse ecological niches that sustain Chagas disease transmission.

[Analysis of the evidence on the efficacy and safety of CYD-TDV dengue vaccine and its potential licensing and implementation through Mexico's Universal Vaccination Program]. / Análisis de la evidencia sobre eficacia y seguridad de la vacuna de dengue CYD-TDV y su potencial registro e implementación en el Programa de Vacunación Universal de México.

Dengue is a major global public health problem affecting Latin America and Mexico Prevention and control measures, focusing on epidemiological surveillance and vector control, have been partially effective and costly, thus, the development of a vaccine against dengue has created great expectations among health authorities and scientific communities worldwide. The CYD-TDV dengue vaccine produced by Sanofi-Pasteur is the only dengue vaccine evaluated in phase 3 controlled clinical trials. Notwithstanding the significant contribution to the development of a vaccine against dengue, the three phase 3 clinical studies of CYD-TDV and the meta-analysis of the long-term follow up of those studies, have provided evidence that this vaccine exhibited partial vaccine efficacy to protect against virologically confirmed dengue and lead to four considerations: a) adequate vaccine efficacy against dengue virus (DENV) infections 3 and 4, less vaccine efficacy against DENV 1 and no protection against infection by DENV 2; b) decreased vaccine efficacy in dengue seronegative individuals at the beginning of the vaccination; c) 83% and 90% protection against hospitalizations and severe forms of dengue, respectively, at 25 months follow-up; and d) increased hospitalization for dengue in the vaccinated group, in children under nine years of age at the time of vaccination, detected since the third year of follow-up. The benefit of the CYD-TDV vaccine can be summarized in the protection against infection by DENV 3 and 4, as well as protection for hospitalizations and severe cases in people over nine years, who have had previous dengue infection, working mainly as a booster. In this review we identified elements on efficacy and safety of this vaccine that must be taken into account in the licensing process and potential inclusion in the national vaccination program of Mexico. The available scientific evidence on the CYD-TDV vaccine shows merits, but also leads to relevant questions that should be answered to properly assess the safety profile of the product and the target populations of potential benefit. In this regard we consider it would be informative to complete the 6-year follow-up after starting vaccination, according to the company's own study protocol recommended by the World Health Organization. As with any new vaccine, the potential licensing and implementation of the CYD-TDV as part of Mexico's vaccination program, requires a clear definition of the balance between the expected benefits and risks. Particularly with a vaccine with variable efficacy and some signs of risk, in the probable case of licensing, the post-licensed period must involve the development of detailed protocols to immediately identify risks or any health event associated with vaccination.

Development of a multiplex-PCR probe system for the proper identification of Klebsiella variicola.

BACKGROUND: Klebsiella variicola was very recently described as a new bacterial species and is very closely related to Klebsiella pneumoniae; in fact, K. variicola isolates were first identified as K. pneumoniae. Therefore, it might be the case that some isolates, which were initially classified as K. pneumoniae, are actually K. variicola. The aim of this study was to devise a multiplex-PCR probe that can differentiate isolates from these sister species. RESULT: This work describes the development of a multiplex-PCR method to identify K. variicola. This development was based on sequencing a K. variicola clinical isolate (801) and comparing it to other K. variicola and K. pneumoniae genomes. The phylogenetic analysis showed that K. variicola isolates form a monophyletic group that is well differentiated from K. pneumoniae. Notably, the isolate K. pneumoniae 342 and K. pneumoniae KP5-1 might have been misclassified because in our analysis, both clustered with K. variicola isolates rather than with K. pneumoniae. The multiplex-PCR (M-PCR-1 to 3) probe system could identify K. variicola with high accuracy using the shared unique genes of K. variicola and K. pneumoniae genomes, respectively. M-PCR-1 was used to assay a collection of multidrug-resistant (503) and antimicrobial-sensitive (557) K. pneumoniae clinical isolates. We found K. variicola with a prevalence of 2.1% (23/1,060), of them a 56.5% (13/23) of the isolates were multidrug resistant, and 43.5% (10/23) of the isolates were antimicrobial sensitive. The phylogenetic analysis of rpoB of K. variicola-positive isolates identified by multiplex-PCR support the correct identification and differentiation of K. variicola from K. pneumoniae clinical isolates. CONCLUSIONS: This multiplex-PCR provides the means to reliably identify and genotype K. variicola. This tool could be very helpful for clinical, epidemiological, and population genetics studies of this species. A low but significant prevalence of K. variicola isolates was found, implying that misclassification had occurred previously. We believe that our multiplex-PCR assay could be of paramount importance to understand the population dynamics of K. variicola in both clinical and environmental settings.

A bioinformatics approach for integrated transcriptomic and proteomic comparative analyses of model and non-sequenced anopheline vectors of human malaria parasites.

Malaria morbidity and mortality caused by both Plasmodium falciparum and Plasmodium vivax extend well beyond the African continent, and although P. vivax causes between 80 and 300 million severe cases each year, vivax transmission remains poorly understood. Plasmodium parasites are transmitted by Anopheles mosquitoes, and the critical site of interaction between parasite and host is at the mosquito's luminal midgut brush border. Although the genome of the "model" African P. falciparum vector, Anopheles gambiae, has been sequenced, evolutionary divergence limits its utility as a reference across anophelines, especially non-sequenced P. vivax vectors such as Anopheles albimanus. Clearly, technologies and platforms that bridge this substantial scientific gap are required in order to provide public health scientists with key transcriptomic and proteomic information that could spur the development of novel interventions to combat this disease. To our knowledge, no approaches have been published that address this issue. To bolster our understanding of P. vivax-An. albimanus midgut interactions, we developed an integrated bioinformatic-hybrid RNA-Seq-LC-MS/MS approach involving An. albimanus transcriptome (15,764 contigs) and luminal midgut subproteome (9,445 proteins) assembly, which, when used with our custom Diptera protein database (685,078 sequences), facilitated a comparative proteomic analysis of the midgut brush borders of two important malaria vectors, An. gambiae and An. albimanus.

Single nucleotide polymorphisms of ANKK1, DDR4, and GRIN2B genes predict behavior in a prospective cohort of Mexican children and adolescents.

Numerous studies have established associations between single nucleotide polymorphisms (SNPs) and various behavioral and neurodevelopmental conditions. This study explores the links between SNPs in candidate genes involved in central nervous system (CNS) physiology and their implications for the behavioral and emotional aspects in children and teenagers. A total of 590 participants, aged 7-15 years, from the Early Life Exposures In Mexico To Environmental Toxicants (ELEMENT) cohort study in Mexico City, underwent genotyping for at least one of 15 CNS gene-related SNPs at different timepoints. We employed multiple linear regression models to assess the potential impact of genetic variations on behavioral and cognitive traits, as measured by the Behavioral Assessment System for Children (BASC) and Conners parent rating scales. Significant associations were observed, including the rs1800497 TC genotype (ANKK1) with the Cognitive Problems/Inattention variable (p value = 0.003), the rs1800955 CT genotype (DDR4) with the Emotional Lability Global index variable (p value = 0.01), and the rs10492138 GA and rs7970177 TC genotypes (GRIN2B) with the Depression variable (p values 0.007 and 0.012, respectively). These finds suggest potential genetic profiles associated with "risk" and "protective" behaviors for these SNPs. Our results provide valuable insights into the role of genetic variations in neurobehavior and highlight the need for further research in the early identification and intervention in individuals at risk for these conditions.

Presence of SARS-CoV-2-specific T cells before vaccination in the Mexican population.

The immune response to SARS-CoV-2 has been extensively studied following the pandemic outbreak in 2020; however, the presence of specific T cells against SARS-CoV-2 before vaccination has not been evaluated in Mexico. In this study, we estimated the frequency of T CD4+ and T CD8+ cells that exhibit a specific response to S (spike) and N (nucleocapsid) proteins in a Mexican population. We collected 78 peripheral blood samples from unvaccinated subjects, and the presence of antibodies against spike (RBD) and N protein was determined. Peripheral blood mononuclear cells were isolated and stimulated with a pool of S or N protein peptides (Wuhan-Hu-1 strain). IL-1ß, IL-4, IL-6, IL-10, IL-2, IL-8, TNF-α, IFN-γ, and GM-CSF levels were quantified in the supernatant of the activated cells, and the cells were stained to assess the activation and memory phenotypes. Differential activation frequency dependent on serological status was observed in CD4+ cells but not in CD8+ cells. The predominantly activated population was the central memory T CD4+ cells. Only 10% of the population exhibited the same phenotype with respect to the response to nucleocapsid peptides. The cytokine profile differed between the S and N responses. S peptides induced a more proinflammatory response compared with the N peptides. In conclusion, in a Mexican cohort before vaccination, there was a significant response to the S and N SARS-CoV-2 proteins resulting from previous infections with seasonal coronaviruses or previous undetected exposure to SARS-CoV-2.

Antimicrobial properties of Anopheles albimanus pericardial cells.

Insect pericardial cells (PCs) are strategically located along the dorsal vessel where they encounter a high hemolymph flow enabling them to undertake their osmoregulatory, detoxifying, and scavenging functions. In this location, PCs also encounter foreign molecules and microorganisms. The response of PCs of the mosquito Anopheles albimanus, one of the most important Plasmodium vivax vectors in Mexico and Latin America, to Saccharomyces cerevisiae was analyzed by using biochemical, cellular, ultrastructural, and bioinformatics approaches. Immune gene transcripts were identified in the PC transcriptome of A. albimanus. PCs responded to the presence of yeast and zymosan with increased lysosomal and phosphatase activities and produced lytic activity against bacteria. Our results indicate that mosquito PCs play a key role in the neutralization and elimination of pathogens.

Molecular epidemiology of Plasmodium vivax in Latin America: polymorphism and evolutionary relationships of the circumsporozoite gene.

BACKGROUND: The origins and dispersal of Plasmodium vivax to its current worldwide distribution remains controversial. Although progress on P. vivax genetics and genomics has been achieved worldwide, information concerning New World parasites remains fragmented and largely incomplete. More information on the genetic diversity in Latin America (LA) is needed to better explain current patterns of parasite dispersion and evolution. METHODS: Plasmodium vivax circumsporozoite protein gene polymorphism was investigated using polymerase chain reaction amplification and restriction fragment length polymorphism (PCR-RFLP), and Sanger sequencing in isolates from the Pacific Ocean coast of Mexico, Nicaragua, and Peru. In conjunction with worldwide sequences retrieved from the Genbank, mismatch distribution analysis of central repeat region (CRR), frequency estimation of unique repeat types and phylogenetic analysis of the 3' terminal region, were performed to obtain an integrative view of the genetic relationships between regional and worldwide isolates. RESULTS: Four RFLP subtypes, vk210a, b, c and d were identified in Southern Mexico and three subtypes vk210a, e and f in Nicaragua. The nucleotide sequences showed that Mexican vk210a and all Nicaraguan isolates were similar to other American parasites. In contrast, vk210b, c and d were less frequent, had a domain ANKKAEDA in their carboxyl end and clustered with Asian isolates. All vk247 isolates from Mexico and Peru had identical RFLP pattern. Their nucleotide sequences showed two copies of GGQAAGGNAANKKAGDAGA at the carboxyl end. Differences in mismatch distribution parameters of the CRR separate vk247 from most vk210 isolates. While vk247 isolates display a homogeneous pattern with no geographical clustering, vk210 isolates display a heterogeneous geographically clustered pattern which clearly separates LA from non-American isolates, except vk210b, c and d from Southern Mexico. CONCLUSIONS: The presence of vk210a in Mexico and vk210e, f and g in Nicaragua are consistent with other previously reported LA isolates and reflect their circulation throughout the continent. The vk210b, c and d are novel genotypes in LA. Their genetic relationships and low variability within these vk210 and/or within the vk247 parasites in Southern Mexico suggest its recent introduction and/or recent expansion to this region. The global analysis of P. vivax csp suggests this parasite introduction to the region and likely LA by different independent events.

Structural and immunological basis of cross-reactivity between dengue and Zika infections: Implications in serosurveillance in endemic regions.

Dengue and Zika are arthropod-borne viral diseases present in more than 100 countries around the world. In the past decade, Zika emerged causing widespread outbreaks in new regions, where dengue has been endemic-epidemic for a long period. The wide and extensive dissemination of the mosquito vectors, Aedes aegypti, and Ae. albopictus, favor the co-existence of both infections in the same regions. Together with an important proportion of asymptomatic infections, similar clinical manifestations, and a short time window for acute infection confirmatory tests, it is difficult to differentially estimate both dengue and Zika incidence and prevalence. DENV and ZIKV flavivirus share high structural similarity, inducing a cross-reactive immune response that leads to false positives in serological tests particularly in secondary infections. This results in overestimation of recent Zika outbreaks seroprevalence in dengue endemic regions. In this review, we address the biological basis underlying DENV and ZIKV structural homology; the structural and cellular basis of immunological cross reactivity; and the resulting difficulties in measuring dengue and Zika seroprevalence. Finally, we offer a perspective about the need for more research to improve serological tests performance.

Characterization of immunoglobulin loci in the gigantic genome of Ambystoma mexicanum.

Background: The axolotl, Ambystoma mexicanum is a unique biological model for complete tissue regeneration. Is a neotenic endangered species and is highly susceptible to environmental stress, including infectious disease. In contrast to other amphibians, the axolotl is particularly vulnerable to certain viral infections. Like other salamanders, the axolotl genome is one of the largest (32 Gb) and the impact of genome size on Ig loci architecture is unknown. To better understand the immune response in axolotl, we aimed to characterize the immunoglobulin loci of A. mexicanum and compare it with other model vertebrates. Methods: The most recently published genome sequence of A. mexicanum (V6) was used for alignment-based annotation and manual curation using previously described axolotl Ig sequences or reference sequences from other vertebrates. Gene models were further curated using A. mexicanum spleen RNA-seq data. Human, Xenopus tropicalis, Danio rerio (zebrafish), and eight tetrapod reference genomes were used for comparison. Results: Canonical A. mexicanum heavy chain (IGH), lambda (IGL), sigma (IGS), and the putative surrogate light chain (SLC) loci were identified. No kappa locus was found. More than half of the IGHV genes and the IGHF gene are pseudogenes and there is no clan I IGHV genes. Although the IGH locus size is proportional to genome size, we found local size restriction in the IGHM gene and the V gene intergenic distances. In addition, there were V genes with abnormally large V-intron sizes, which correlated with loss of gene functionality. Conclusion: The A. mexicanum immunoglobulin loci share the same general genome architecture as most studied tetrapods. Consistent with its large genome, Ig loci are larger; however, local size restrictions indicate evolutionary constraints likely to be imposed by high transcriptional demand of certain Ig genes, as well as the V(D)J recombination over very long genomic distance ranges. The A. mexicanum has undergone an extensive process of Ig gene loss which partially explains a reduced potential repertoire diversity that may contribute to its impaired antibody response.

Elevated levels of enteric IgA in an unimmunised mouse model of Hyper IgM syndrome derived from gut-associated secondary lymph organs even in the absence of germinal centres.

Introduction: Patients with Human Hyper IgM syndromes (HIGM) developed pulmonary and gastrointestinal infections since infancy and most patients have mutations in the CD40 ligand (CD40L) gene. Most HIGM patients compared to healthy subjects have higher/similar IgM and lower IgG, and IgA serum concentrations but gut antibody concentrations are unknown. CD40L on activated T-cells interacts with CD40 on B-cells, essential for the formation of germinal centres (GCs) inside secondary lymphoid organs (SLOs), where high-affinity antibodies, long-lived antibody-secreting plasma cells, and memory B-cells, are produced. C57BL6-CD40 ligand deficient mice (C57BL6-cd40l -/-), are a model of HIGM, because serum immunoglobulin concentrations parallel levels observed in HIGM patients and have higher faecal IgA concentrations. In mice, TGFß and other cytokines induce IgA production. Aims: To compare and evaluate B-cell populations and IgA-producing plasma cells in peritoneal lavage, non-gut-associated SLOs, spleen/inguinal lymph nodes (ILN), and gut-associated SLOs, mesenteric lymph nodes (MLN)/Peyer´s patches (PP) of unimmunised C57BL6-cd40l -/- and C57BL6-wild-type (WT) mice. Material and methods: Peritoneal lavages, spleens, ILN, MLN, and PP from 8-10 weeks old C57BL6-cd40l -/- and WT mice, were obtained. Organ cryosections were analysed by immunofluorescence and B-cell populations and IgA-positive plasma cell suspensions by flow cytometry. Results: In unimmunised WT mice, GCs were only observed in the gut-associated SLOs, but GCs were absent in all C57BL6-cd40l -/- SLOs. PP and MLN of C57BL6-cd40l -/- mice exhibited a significantly higher number of IgA-producing cells than WT mice. In the spleen and ILN of C57BL6-cd40l- /- mice IgA-producing cells significantly decreased, while IgM-positive plasma cells increased. C57BL6-cd40l -/- B-1 cells were more abundant in all analysed SLOs, whereas in WT mice most B-1 cells were contained within the peritoneal cavity. C57BL6-cd40l -/- B-cells in MLN expressed a higher TGFß receptor-1 than WT mice. Mouse strains small intestine microvilli (MV), have a similar frequency of IgA-positive cells. Discussion: Together our results confirm the role of PP and MLN as gut inductive sites, whose characteristic features are to initiate an IgA preferential immune response production in these anatomical sites even in the absence of GCs. IgA antibodies play a pivotal role in neutralising, eliminating, and regulating potential pathogens and microorganisms in the gut.

AIRR-C IG Reference Sets: curated sets of immunoglobulin heavy and light chain germline genes.

Introduction: Analysis of an individual's immunoglobulin (IG) gene repertoire requires the use of high-quality germline gene reference sets. When sets only contain alleles supported by strong evidence, AIRR sequencing (AIRR-seq) data analysis is more accurate and studies of the evolution of IG genes, their allelic variants and the expressed immune repertoire is therefore facilitated. Methods: The Adaptive Immune Receptor Repertoire Community (AIRR-C) IG Reference Sets have been developed by including only human IG heavy and light chain alleles that have been confirmed by evidence from multiple high-quality sources. To further improve AIRR-seq analysis, some alleles have been extended to deal with short 3' or 5' truncations that can lead them to be overlooked by alignment utilities. To avoid other challenges for analysis programs, exact paralogs (e.g. IGHV1-69*01 and IGHV1-69D*01) are only represented once in each set, though alternative sequence names are noted in accompanying metadata. Results and discussion: The Reference Sets include less than half the previously recognised IG alleles (e.g. just 198 IGHV sequences), and also include a number of novel alleles: 8 IGHV alleles, 2 IGKV alleles and 5 IGLV alleles. Despite their smaller sizes, erroneous calls were eliminated, and excellent coverage was achieved when a set of repertoires comprising over 4 million V(D)J rearrangements from 99 individuals were analyzed using the Sets. The version-tracked AIRR-C IG Reference Sets are freely available at the OGRDB website (https://ogrdb.airr-community.org/germline_sets/Human) and will be regularly updated to include newly observed and previously reported sequences that can be confirmed by new high-quality data.

Transcriptome of the adult female malaria mosquito vector Anopheles albimanus.

BACKGROUND: Human Malaria is transmitted by mosquitoes of the genus Anopheles. Transmission is a complex phenomenon involving biological and environmental factors of humans, parasites and mosquitoes. Among more than 500 anopheline species, only a few species from different branches of the mosquito evolutionary tree transmit malaria, suggesting that their vectorial capacity has evolved independently. Anopheles albimanus (subgenus Nyssorhynchus) is an important malaria vector in the Americas. The divergence time between Anopheles gambiae, the main malaria vector in Africa, and the Neotropical vectors has been estimated to be 100 My. To better understand the biological basis of malaria transmission and to develop novel and effective means of vector control, there is a need to explore the mosquito biology beyond the An. gambiae complex. RESULTS: We sequenced the transcriptome of the An. albimanus adult female. By combining Sanger, 454 and Illumina sequences from cDNA libraries derived from the midgut, cuticular fat body, dorsal vessel, salivary gland and whole body, we generated a single, high-quality assembly containing 16,669 transcripts, 92% of which mapped to the An. darlingi genome and covered 90% of the core eukaryotic genome. Bidirectional comparisons between the An. gambiae, An. darlingi and An. albimanus predicted proteomes allowed the identification of 3,772 putative orthologs. More than half of the transcripts had a match to proteins in other insect vectors and had an InterPro annotation. We identified several protein families that may be relevant to the study of Plasmodium-mosquito interaction. An open source transcript annotation browser called GDAV (Genome-Delinked Annotation Viewer) was developed to facilitate public access to the data generated by this and future transcriptome projects. CONCLUSIONS: We have explored the adult female transcriptome of one important New World malaria vector, An. albimanus. We identified protein-coding transcripts involved in biological processes that may be relevant to the Plasmodium lifecycle and can serve as the starting point for searching targets for novel control strategies. Our data increase the available genomic information regarding An. albimanus several hundred-fold, and will facilitate molecular research in medical entomology, evolutionary biology, genomics and proteomics of anopheline mosquito vectors. The data reported in this manuscript is accessible to the community via the VectorBase website (http://www.vectorbase.org/Other/AdditionalOrganisms/).