Structure vs. chemistry: Alternate mechanisms for controlling leaf microbiomes.

The analysis of phyllosphere microbiomes traditionally relied on DNA extracted from whole leaves. To investigate the microbial communities on the adaxial (upper) and abaxial (lower) leaf surfaces, swabs were collected from both surfaces of two garden plants, Rhapis excelsa and Cordyline fruticosa. Samples were collected at noon and midnight and at five different locations to investigate if the phyllosphere microbial communities change with time and location. The abaxial surface of Rhapis excelsa and Cordyline fruticosa had fewer bacteria in contrast to its adaxial counterpart. This observation was consistent between noon and midnight and across five different locations. Our co-occurrence network analysis further showed that bacteria were found almost exclusively on the adaxial surface while only a small group of leaf blotch fungi thrived on the abaxial surface. There are higher densities of stomata on the abaxial surface and these openings are vulnerable ports of entry into the plant host. While one might argue about the settling of dust particles and microorganisms on the adaxial surface, we detected differences in reactive chemical activities and microstructures between the adaxial and abaxial surfaces. Our results further suggest that both plant species deploy different defence strategies to deter invading pathogens on the abaxial surface. We hypothesize that chemical and mechanical defence strategies evolved independently for harnessing and controlling phyllosphere microbiomes. Our findings have also advanced our understanding that the abaxial leaf surface is distinct from the adaxial surface and that the reduced microbial diversity is likely a consequence of plant-microbe interactions.

Vertical stratification of the air microbiome in the lower troposphere.

The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising a meteorological tower and a research aircraft, we conducted synchronized measurements of meteorological parameters and airborne biomass (n = 480) in the vertical air column up to 3,500 m. The taxonomic analysis of metagenomic data revealed differing patterns of airborne microbial community composition with respect to time of day and height above ground. The temporal and spatial resolution of our study demonstrated that the diel cycle of airborne microorganisms is a ground-based phenomenon that is entirely absent at heights >1,000 m. In an integrated analysis combining meteorological and biological data, we demonstrate that atmospheric turbulence, identified by potential temperature and high-frequency three-component wind measurements, is the key driver of bioaerosol dynamics in the lower troposphere. Multivariate regression analysis shows that at least 50% of identified airborne microbial taxa (n = ∼10,000) are associated with either ground or height, allowing for an understanding of dispersal patterns of microbial taxa in the vertical air column. Due to the interconnectedness of atmospheric turbulence and temperature, the dynamics of microbial dispersal are likely to be impacted by rising global temperatures, thereby also affecting ecosystems on the planetary surface.

Humoral response to spike S1 and S2 and nucleocapsid proteins on microarray after SARS-CoV-2 infection.

Many aspects of the humoral immune response to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), such as its role in protection after natural infection, are still unclear. We evaluated IgA and IgG response to spike subunits 1 and 2 (S1 and S2) and Nucleocapsid proteins of SARS-COV-2 in serum samples of 109 volunteers with viral RNA detected or seroconversion with different clinical evolution (asymptomatic, mild, moderate, and severe coronavirus disease 2019), using the ViraChip® Test Kit. We observed that the quantification of antibodies to all antigens had a positive correlation to disease severity, which was strongly associated with the presence of comorbidities. Seroreversion was not uncommon even during the short (median of 77 days) observation, occurring in 15% of mild-asymptomatic cases at a median of 55 days for IgG and 46 days for IgA. The time to reach the maximal antibody response did not differ significantly among recovered and deceased volunteers. Our study illustrated the dynamic of anti-S1, anti-N, and anti-S2 IgA and IgG antibodies, and suggests that high production of IgG and IgA does not guarantee protection to disease severity and that functional responses that have been studied by other groups, such as antibody avidity, need further attention.

Inhibition of receptor-binding domain-ACE2 interaction after two doses of Sinovac's CoronaVac or AstraZeneca/Oxford's AZD1222 SARS-CoV-2 vaccines.

Practical laboratory proxies that correlate to vaccine efficacy may facilitate trials, identify nonresponders, and inform about boosting strategies. Among clinical and laboratory markers, assays that evaluate antibodies that inhibit receptor-binding domain (RBD) ligation to angiotensin-converting enzyme-2 receptor (receptor-binding inhibition [RBI]) may provide a surrogate for viral neutralization assays. We evaluated RBI before and after a median of 34 days (interquartile range [IQR]: 33-40) of the second dose of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Sinovac's CoronaVac (CN) or AstraZeneca/Oxford's AZD1222 (AZ) vaccines in 166 individuals. Both vaccines elicited high inhibitory titers in most subjects, 95% (158/166), with signal inhibition above 30% and 89% (127/143) with more than fourfold increase from prevaccination titers, but titers tend to decrease over time. Both postvaccination inhibitory titers (95%, IQR 85%-97% for AZ vs. 79%, IQR 60%-96% for CN, p = 0.004) and pre/post-titer increase (AZ 76%, IQR 51%-86% for AZ vs. 47%, IQR 24%-67% for CN, p < 0.0001) were higher among AZ vaccinees. Previous serological reactivity due to natural infection was associated with high prevaccination signal inhibition titers. The study documents a robust antibody response capable of interfering with RBD-angiotensin-converting enzyme binding. Evaluation of SARS-CoV-2 infection incidence in these populations is necessary to assess its association to protection and its duration.

Humoral response to spike S1 and S2 and nucleocapsidproteins on microarray after SARS­CoV­2 infection

Many aspects of the humoral immune response to severe acute respiratory syn-drome coronavirus 2 (SARS­CoV­2), such as its role in protection after natural in-fection, are still unclear. We evaluated IgA and IgG response to spike subunits 1 and2 (S1 and S2) and Nucleocapsid proteins of SARS­COV­2 in serum samples of 109volunteers with viral RNA detected or seroconversion with different clinical evolu-tion (asymptomatic, mild, moderate, and severe coronavirus disease 2019), using theViraChip®Test Kit. We observed that the quantification of antibodies to all antigenshad a positive correlation to disease severity, which was strongly associated with thepresence of comorbidities. Seroreversion was not uncommon even during the short(median of 77 days) observation, occurring in 15% of mild­asymptomatic cases at amedian of 55 days for IgG and 46 days for IgA. The time to reach the maximalantibody response did not differ significantly among recovered and deceased vo-lunteers. Our study illustrated the dynamic of anti­S1, anti­N, and anti­S2 IgA andIgG antibodies, and suggests that high production of IgG and IgA does not guaranteeprotection to disease severity and that functional responses that have been studiedby other groups, such as antibody avidity, need further attention. (AU)

Avaliação do desempenho de teste rápido e de dois imunoensaios automatizados para Sars-CoV-2 / Performance evaluation of a Sars-CoV-2 rapid test and two automated immunoassays

Introdução: Em função da urgência e demanda de uma resposta à pandemia do novo coronavírus (Covid-19), vários testes de detecção de anticorpos para a síndrome respiratória aguda grave do coronavírus 2 (Sars-CoV-2) têm sido desenvolvidos. Objetivo: Este estudo teve como objetivo avaliar o desempenho do teste rápido utilizado em um inquérito epidemiológico para Sars-CoV-2 em comparação com outros ensaios sorológicos. Métodos: Foram avaliadas 86 amostras de soro em três ensaios sorológicos: um imunoensaio de fluxo lateral ­ Wondfo Sars-CoV-2 Antibody Test (TRW) ­ e dois imunoensaios de quimioluminescência: Elecsys anti-Sars-CoV-2 (ECLIA) e Sars-CoV-2 IgG (CMIA-IgG). Resultados: As sensibilidades diagnósticas estimadas dos testes sorológicos na avaliação dessas amostras foram: TRW 59% [95% intervalo de confiança (IC) 43,4%-72,9%], ECLIA 66,7% (51%-79,4%) e CMIA-IgG 61,5% (47,1%-73%). Enquanto isso, a especificidade diagnóstica estimada para TRW foi 78,7% (95% CI 65,1%-88%), ECLIA 72,3% (58,2%-83,1%) e CMIA-IgG 76,6% (74%-95,5%). Os valores de sensibilidade e especificidade foram inferiores aos afirmados pelos fabricantes. Embora 16,2% (14/86) dos resultados tenham sido discordantes entre os três ensaios serológicos para Sars-CoV-2, o grau de concordância pelo índice Kappa foi adequado: TRW/CMIA-IgG [0,757 (95% IC 0,615-0,899)], TRW/ECLIA [0,715 (0,565-0,864)] e ECLIA/CMIA-IgG [0,858 (0,748-0,968)]. Conclusão: O teste sorológico pode ser uma ferramenta diagnóstica útil, o que reforça sua avaliação criteriosa, bem como o momento correto de sua utilização. (AU)

Introduction: Due to urgency and demand of a response to the Covid-19 pandemic, numerous Sars-CoV-2 immunoassays have been rapidly developed. Objective: This study aimed at assessing the performance of rapid Sars-CoV-2 antibody test in comparison to high-throughput serological assays. Methods: A total of 86 serum samples were evaluated in the three assays: a lateral flow immunoassay ­ Wondfo Sars-CoV-2 Antibody Test (WRT) ­ and two chemiluminescence immunoassays: Elecsys Anti-Sars-CoV-2 (ECLIA), and Sars-CoV-2 IgG (CMIA-IgG). Results: The estimated diagnostic sensitivities of serological tests in the evaluation of serum samples from the epidemiological survey were: WRT 59.0% [95% confidence interval (CI) 43.4%-72.9%], ECLIA 66.7% (51%-79.4%), and CMIA-IgG 61.5% (47.1%-73%). Meanwhile, the estimated diagnostic specificity was for WRT 78.7% (95% CI 65.1%-88%), ECLIA 72.3% (58.2%-83.1%), and CMIA-IgG 76.6% (74%-95.5%). The sensitivity and specificity values were lower than manufacturers' claimed. Although 16.2% (14/86) of serological results were discordant among the three Sars-CoV-2 serological assays, the degree of agreement by the kappa index was adequate: WRT/CMIA-IgG [0.757 (95% CI 0.615-0.899)], WRT/ECLIA [0.715 (0.565-0.864)], and ECLIA/CMIA-IgG [0.858 (0.748-0.968)]. Conclusion: The serological testing may be a useful diagnostic tool, which reinforces its careful evaluation, and, as well as the correct time to use it. (AU)

Performance evaluation of a Sars-CoV-2 rapid test and two automated immunoassays / Avaliação do desempenho de teste rápido e de dois imunoensaios automatizados para Sars-CoV-2

ABSTRACT Introduction: Due to urgency and demand of a response to the Covid-19 pandemic, numerous Sars-CoV-2 immunoassays have been rapidly developed. Objective: This study aimed at assessing the performance of rapid Sars-CoV-2 antibody test in comparison to high-throughput serological assays. Methods: A total of 86 serum samples were evaluated in the three assays: a lateral flow immunoassay - Wondfo Sars-CoV-2 Antibody Test (WRT) - and two chemiluminescence immunoassays: Elecsys Anti-Sars-CoV-2 (ECLIA), and Sars-CoV-2 IgG (CMIA-IgG). Results: The estimated diagnostic sensitivities of serological tests in the evaluation of serum samples from the epidemiological survey were: WRT 59% [95% confidence interval (CI) 43.4%-72.9%], ECLIA 66.7% (51%-79.4%), and CMIA-IgG 61.5% (47.1%-73%). Meanwhile, the estimated diagnostic specificity was for WRT 78.7% (95% CI 65.1%-88%), ECLIA 72.3% (58.2%-83.1%), and CMIA-IgG 76.6% (74%-95.5%). The sensitivity and specificity values were lower than manufacturers' claimed. Although 16.2% (14/86) of serological results were discordant among the three Sars-CoV-2 serological assays, the degree of agreement by the kappa index was adequate: WRT/CMIA-IgG [0.757 (95% CI 0.615-0.899)], WRT/ECLIA [0.715 (0.565-0.864)], and ECLIA/CMIA-IgG [0.858 (0.748-0.968)]. Conclusion: The serological testing may be a useful diagnostic tool, which reinforces its careful evaluation, and, as well as the correct time to use it.

RESUMEN Introducción: Debido a la urgencia y la demanda de una respuesta a la pandemia de Covid-19, se han desarrollado rápidamente numerosos inmunoensayos del Sars-CoV-2. Objetivo: Este estudio tuvo como objetivo evaluar el rendimiento de la prueba rápida de anticuerpos contra el Sars-CoV-2 en comparación con los ensayos serológicos de alto rendimiento. Métodos: Se evaluaron un total de 86 muestras de suero en los tres ensayos: un inmunoensayo de flujo lateral - Wondfo Sars-CoV-2 Antibody Test (TRW) - y dos inmunoensayos de quimioluminiscencia: Elecsys Anti-Sars-CoV-2 (ECLIA) y Sars-CoV-2 IgG (CMIA-IgG). Resultados: Las sensibilidades diagnósticas estimadas de las pruebas serológicas en la evaluación de muestras de suero de la encuesta epidemiológica fueron: WRT 59% [intervalo de confianza (IC) del 95%: 43,4%-72,9%], ECLIA 66,7% (51%-79,4%) y CMIA-IgG 61,5% (47,1%-73%). Mientras tanto, la especificidad diagnóstica estimada fue para WRT 78,7% (95% CI 65,1%-88%), ECLIA 72,3% (58,2%-83,1%) y CMIA-IgG 76,6% (74%-95,5%). Los valores de sensibilidad y especificidad fueron más bajos que los declarados por los fabricantes. Aunque el 16,2% (14/86) de los resultados fueron discordantes entre los tres ensayos serológicos del Sars-CoV-2, el grado de concordancia del índice kappa fue adecuado: WRT/CMIA-IgG [0,757 (IC del 95%: 0,615-0,899)], WRT/ECLIA [0,715 (0,565-0,864)] y ECLIA/CMIA-IgG [0,858 (0,748-0,968)]. Conclusión: La prueba serológica puede ser una herramienta diagnóstica útil, lo que refuerza su evaluación cuidadosa, así como el momento adecuado para usarla.

RESUMO Introdução: Em função da urgência e demanda de uma resposta à pandemia do novo coronavírus (Covid-19), vários testes de detecção de anticorpos para a síndrome respiratória aguda grave do coronavírus 2 (Sars-CoV-2) têm sido desenvolvidos. Objetivo: Este estudo teve como objetivo avaliar o desempenho do teste rápido utilizado em um inquérito epidemiológico para Sars-CoV-2 em comparação com outros ensaios sorológicos. Métodos: Foram avaliadas 86 amostras de soro em três ensaios sorológicos: um imunoensaio de fluxo lateral - Wondfo Sars-CoV-2 Antibody Test (TRW) - e dois imunoensaios de quimioluminescência: Elecsys anti-Sars-CoV-2 (ECLIA) e Sars-CoV-2 IgG (CMIA-IgG). Resultados: As sensibilidades diagnósticas estimadas dos testes sorológicos na avaliação dessas amostras foram: TRW 59% [95% intervalo de confiança (IC) 43,4%-72,9%], ECLIA 66,7% (51%-79,4%) e CMIA-IgG 61,5% (47,1%-73%). Enquanto isso, a especificidade diagnóstica estimada para TRW foi 78,7% (95% CI 65,1%-88%), ECLIA 72,3% (58,2%-83,1%) e CMIA-IgG 76,6% (74%-95,5%). Os valores de sensibilidade e especificidade foram inferiores aos afirmados pelos fabricantes. Embora 16,2% (14/86) dos resultados tenham sido discordantes entre os três ensaios serológicos para Sars-CoV-2, o grau de concordância pelo índice Kappa foi adequado: TRW/CMIA-IgG [0,757 (95% IC 0,615-0,899)], TRW/ECLIA [0,715 (0,565-0,864)] e ECLIA/CMIA-IgG [0,858 (0,748-0,968)]. Conclusão: O teste sorológico pode ser uma ferramenta diagnóstica útil, o que reforça sua avaliação criteriosa, bem como o momento correto de sua utilização.

Complete Genome Sequence of Penicillium oxalicum Strain SGAir0226 Isolated from Outdoor Tropical Air in Singapore.

Penicillium oxalicum strain SGAir0226 was isolated from a tropical air sample collected in Singapore. The complete genome was assembled from long reads obtained from single-molecule real-time sequencing and was further polished and error corrected using short read sequencing data. The assembly comprises 20 contigs with a total length of 30.7 Mb. The genome was predicted to contain 8310 protein-coding genes, 237 tRNAs and 83 rRNAs.

Complete Genome Sequence of Rhodococcus sp. Strain SGAir0479, Isolated from Indoor Air Collected in Singapore.

The complete genome sequence of Rhodococcus sp. strain SGAir0479 is presented here. This organism was isolated from an air sample collected in an indoor location in Singapore. The consensus assembly generated one chromosome of 4.86 Mb (G+C content of 69.8%) and one plasmid of 104,493 bp.

Effect of multiple freeze-thaw cycles on the stability of positive anti-treponemal serum samples / Efeito dos múltiplos ciclos de congelamento e descongelamento na estabilidade de amostras de soro antitreponêmico positivo

ABSTRACT Introduction: Biological samples have long been used in multiple laboratory investigations, and this procedure has been an issue of concern, as the samples are submitted to repeated freeze-thaw cycles, which may affect the results of a particular immunodiagnostic assay, due to the occurrence of physical damage to the antibody of interest. Objective: This study aimed at investigating the impact of successive freeze-thaw cycles on the stability of serum samples stored at -20ºC regarding the reactivity of anti-treponemal antibodies. Methods: At the Immunology Center-Instituto Adolfo Lutz (IAL), the analyzed serum samples analyzed were prepared and established as reference material for anti-treponemal immunodiagnostic assays. Sera stability was evaluated by chemiluminescence assay in samples submitted to 25 successive freeze-thaw cycles, ranging from 6 to 174 cycles. Results: Neither statistically significant effect on the reactivity of anti-treponemal antibodies (p-value > 0.05), nor adverse effect were observed in weakly reactive samples, such as the occurrence of false-negative results. Conclusion: It was shown that 174 freeze-thaw cycles of anti-treponemal sera did not affect the stability and the quality of samples, when evaluated by chemiluminescence assay.

RESUMO Introdução: As amostras biológicas têm sido utilizadas em múltiplas investigações por um longo período de tempo, e existe a preocupação a respeito dos seus repetidos ciclos de congelamento e descongelamento que podem afetar os resultados de determinado ensaio imunodiagnóstico pela ocorrência de dano físico do anticorpo de interesse. Objetivo: O objetivo deste estudo foi investigar o impacto dos sucessivos ciclos de congelamento e descongelamento na estabilidade das amostras de soro armazenadas a -20ºC quanto à reatividade de anticorpos antitreponêmicos. Métodos: No Centro de Imunologia do Instituto Adolfo Lutz (IAL), as amostras de soro analisadas foram preparadas e estabelecidas como material de referência de teste imunodiagnóstico antitreponêmico. A estabilidade dos soros foi avaliada por meio de ensaio de quimioluminescência, em amostras submetidas a 25 sucessivos ciclos de congelamento e descongelamento, que variaram de 6 a 174 ciclos. Resultados: Não houve efeito estatisticamente significante na reatividade dos anticorpos antitreponêmicos (valor de p > 0,05), e nenhum efeito adverso foi observado nas amostras fracamente reagentes, como a ocorrência de resultados falso negativos. Conclusão: Foi demonstrado que os 174 ciclos de congelamento e descongelamento dos soros antitreponêmicos não afetaram a estabilidade e a qualidade das amostras, quando avaliados por meio do ensaio de quimioluminescência.

Study on the stability of HIV and syphilis reference materials under varied temperature conditions during their transportation / Estudo da estabilidade de materiais de referência para HIV e sífilis sob condições de temperatura variadas durante o transporte

ABSTRACT Introduction: The objective of this study was to evaluate the short-term stability of the serum samples used as internal quality control (IQC) of human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome (Aids) and syphilis immunodiagnostic assays. These samples were produced at the Center of Immunology-Instituto Adolfo Lutz (IAL), and they were distributed to laboratories participating in the IAL Quality Control Program. Method: The sera analyzed by chemiluminescence assay were stored at varied temperature conditions: from 2ºC to 8ºC (refrigerator), from 15ºC to 25ºC (room temperature), at 37ºC (incubator) and at -20ºC (reference temperature) for 12 and 24 hours. Results: Comparative analysis of IQC results for anti-HIV and anti-T. pallidum (anti-treponemal) showed stability in the reference temperature and at the various simulated temperatures for transporting the samples at the established lengths of time. The data from the simple linear regression analysis of negative serum samples (incubator/24 hours) and in one batch of HIV IQC (room temperature/24 hours) were statistically significant at the level of 5% (p-value < 0.05). Conclusion: The sera presented necessary requirements as reference material to be transported to laboratories at refrigeration temperature (2ºC to 8ºC), at the maximum shipping time of 12 hours.

RESUMO Introdução: O objetivo deste estudo foi avaliar a estabilidade de curta duração de amostras de soro utilizadas como controle de qualidade interno (CQI) de testes imunodiagnósticos de vírus da imunodeficiência humana (HIV)/síndrome da imunodeficiência adquirida (Aids) e sífilis, produzidas no Centro de Imunologia do Instituto Adolfo Lutz (IAL) e distribuídas aos laboratórios participantes do Programa de Controle de Qualidade do IAL. Método: Os soros analisados por meio de ensaio de quimioluminescência foram armazenados em diferentes condições de temperaturas: de 2ºC a 8ºC (geladeira), de 15ºC a 25ºC (ambiente), 37ºC (estufa) e de -20ºC (referência) durante 12 e 24 horas. Resultados: A análise comparativa dos resultados do CQI HIV e T. pallidum (antitreponêmico) demonstrou que os materiais permaneceram estáveis, tanto na temperatura de referência quanto nas diferentes temperaturas simuladas para o transporte, no período de tempo estabelecido. No entanto, os resultados da análise de regressão linear simples das amostras de soro negativas (estufa/24 horas) e de um lote de CQI HIV (ambiente/24 horas) foram estatisticamente significativos ao nível de 5% (valor de p < 0,05). Conclusão: Os soros apresentaram requisitos necessários de material de referência para serem transportados aos laboratórios em temperatura de refrigeração (2ºC a 8ºC) no tempo máximo de 12 horas.

Avaliação de desempenho de um kit comercial de reagentes para detecção de anticorpos anti-toxocara canis frente ao kit padronizado in-house utilizado no Instituto Adolfo Lutz / Performance evaluation of a commercially available reagent kit for anti-Toxocara canis antibodies detection as compared to an in-house established kit used in Instituto Adolfo Lutz

A toxocaríase humana acomete o homem por meio da ingestão de ovosembrionados de T. canis. Geralmente, as infecções são assintomáticas,mas podem apresentar quadros graves como alterações pulmonares,distúrbios neurológicos e comportamentais e a perda da visão. Seu diagnóstico é principalmente imunológico. No Instituto Adolfo Lutz (IAL) o imunodiagnóstico de toxocaríase é realizado por meio de um ensaioimunoenzimático in-house (Elisa-IAL). O objetivo deste trabalho foiverificar o desempenho de um kit comercial Elisa (Ridascreen) paradetecção de toxocaríase, em comparação ao Elisa-IAL, empregando-se o índice Kappa e taxas de sensibilidade e especificidade relativas. Foram analisadas 170 amostras de soro da rotina laboratorial de toxocaríasehumana, paralelamente nos ensaios de Elisa-IAL e Ridascreen. Observouseuma concordância substancial e taxas de sensibilidade e especificidade relativas de 88% e 75%, respectivamente. Considerando esses resultados, sugerimos que o kit comercial avaliado pode ser empregado alternativamente ao Elisa-IAL para o diagnóstico datoxocaríase humana