Isothermal nucleic acid amplification combined with gold nanoparticles assisted electrochemical impedance for the sensitive and efficient porcine delta coronavirus detection.

The emergence of porcine delta coronavirus (PDCoV) has caused huge economic losses in the global pig industry. How to realize the sensitive and efficient detection for it is a difficult problem that need to be resolved. In this work, loop-mediated isothermal amplification (LAMP)-electrochemical impedance spectroscopy (EIS) detection platform for PDCoV based on nucleic acid level was constructed by combining the advantages of efficient amplification for LAMP and sensitive detection for EIS. Referring to a 159 bp fragment of PDCoV N gene (Genbank：KY078891, 641 bp-799 bp), primers (HS-FIP、BIP、F3、B3) were designed to screened and sulfhydryl groups were activated, and then loop-mediated isothermal amplification was carried out. Subsequently, gold nanoparticles were loaded on indium tin oxide glass by electrodeposition technology, and the amplified products were connected to the electrode surface through the formation of Au-S bonds. According to the difference of charge transfer resistance after double-stranded DNA was connected on the electrode surface, the detection platform can achieve valid detection of PDCoV in the concentration range of 102-107 copies/µL, the limit of detection is 28 copies/µL, and can be used for practical analysis of pig small intestine samples.

5 perguntas sobre sexo, coronavírus e ISTs

O novo coronavírus passa pelo sexo? As profilaxias Pré e Pós-Exposiçãi (PrEP e PEP) protegem do novo coronavírus? As unidades municipais de saúde especializadas em DST/Aids de São Paulo estão fechadas na pandemia? O Dr. Valdir Monteiro Pinto, médico do Programa Municipal de DST/Aids de São Paulo respondeu a essas e outras perguntas sobre sexo, coronavírus e infecções sexualmente transmissíveis!

A duplex nested RT-PCR method for monitoring porcine epidemic diarrhea virus and porcine delta-coronavirus.

BACKGROUND: Porcine epidemic diarrhea virus (PEDV) and porcine delta-coronavirus (PDCoV) are economically important pathogens that cause diarrhea in sows and acute death of newborn piglets. Moreover, the emerging PDCoV was reported to infect children. The current situation is that vaccine prevention has not met expectations, and emergency containment strategies following outbreaks cannot prevent the damages and losses already incurred. Therefore, a more sensitive detection method, that is both convenient and enables accurate and effective sequencing, that will provide early warning of PEDV and PDCoV is necessary. This will enable active, effective, and comprehensive prevention and control, which will possibly reduce disease occurrences. RESULTS: Duplex nested RT-PCR (dnRT-PCR) is an ideal method to achieve early warning and monitoring of PEDV and PDCoV diseases, and to additionally investigate any molecular epidemiological characteristics. In this study, two pairs of primers were designed for each virus based upon the highly conserved N protein sequences of both PEDV and PDCoV strains retrieved from the NCBI Genbank. After optimization of the reaction conditions, the dnRT-PCR assay amplified a 749-bp fragment specific to PEDV and a 344-bp fragment specific to PDCoV. Meanwhile, the specificity and sensitivity of the primers and clinical samples were tested to verify and establish this dnRT-PCR method. The limit of detection (LoD)for both PEDV and PDCoV was 10 copies/µL. The results showed that among 251 samples, 1 sample contained PEDV infection, 19 samples contained a PDCoV infection, and 8 samples were infected with both viruses, following the use of dnRT-PCR. Subsequently, the positive samples were sent for sequencing, and the sequencing results confirmed that they were all positive for the viruses detected using dnRT-PCR, and conventional RT-PCR detection was conducted again after the onset of disease. As these results were consistent with previous results, a detection method for PEDV and PDCoV using dnRT-PCR was successfully established. In conclusion, the dnRT-PCR method established in this study was able to detect both PEDV and PDCoV, concomitantly. CONCLUSIONS: The duplex nested RT-PCR method represents a convenient, reliable, specific, sensitive and anti-interference technique for detecting PEDV and PDCoV, and can additionally be used to simultaneously determine the molecular epidemiological background.

Gulls as a host for both gamma and deltacoronaviruses.

The coronaviruses (CoV) are ubiquitous pathogens found in wide variety of hosts that constantly pose a threat to human and animal health as a result of their enormous capacity to generate genetic changes. Constant monitoring of virus reservoirs can constitute an early-warning tool and control the spread and evolution of the virus. Coronaviruses are common in wild birds, globally, and birds of the Charadriiformes in particular have been demonstrated to be carriers of delta- (dCoV) and gammacoronaviruses (gCoV). In this paper, we present the genetic characterisation of five CoV strains from black-headed (Chroicocephalus ridibundus) and common (Larus canus) gulls. Whole genome sequence analysis showed high similarity of detected dCoV in gulls to previously identified strains from falcon, houbara, pigeon and gulls from Asia (UAE, China). However, phylogenetic analysis revealed bifurcation within a common branch. Furthermore, the accumulation of numerous amino acid changes within the S-protein was demonstrated, indicating further evolution of dCoV within a single gull host. In turn, phylogenetic analysis for the most of the structural and non-structural genes of identified gCoV confirmed that the strain belongs to the duck coronavirus 2714 (DuCoV2714) species within Igacovirus subgenera, while for the spike protein it forms a separate branch not closely related to any gCoV species known to date. The current study provides new and significant insights into the evolution and diversification of circulating coronaviruses in members of Laridae family.

#SPContraOCorona - EP3

Para combater o coronavírus, uma doença com alta capacidade de contágio, foi preciso agir desde cedo. Já foram direcionados investimentos para a criação de novos leitos, novas vagas para profissionais de saúde, divulgação da vacina contra a gripe, mais vagas em Centros de Acolhimento Emergenciais, entre outras entregas.

#SPContraOCorona - EP1

Para combater o coronavírus, uma doença com alta capacidade de contágio, foi preciso agir desde cedo. Já foram direcionados investimentos para a criação de novos leitos, novas vagas para profissionais de saúde, divulgação da vacina contra a gripe, mais vagas em Centros de Acolhimentos Emergenciais, entre outras entregas.

Large-scale real-life implementation of technology-enabled care to maximize hospitals' medical surge preparedness during future infectious disease outbreaks and winter seasons: a viewpoint.

Hospitals can be overburdened with large numbers of patients with severe infectious conditions during infectious disease outbreaks. Such outbreaks or epidemics put tremendous pressure on the admission capacity of care facilities in the concerned region, negatively affecting the elective program within these facilities. Such situations have been observed during the recent waves of the coronavirus disease pandemic. Owing to the imminent threat of a "tripledemic" by new variants of the coronavirus disease (such as the new Omicron XBB.1.16 strain), influenza, and respiratory syncytial virus during future winter seasons, healthcare agencies should take decisive steps to safeguard hospitals' surge capacity while continuing to provide optimal and safe care to a potentially large number of patients in their trusted home environment. Preparedness of health systems for infectious diseases will require dynamic interaction between a continuous assessment of region-wide available hospital capacity and programs for intensive home treatment of patients who can spread the disease. In this viewpoint, we describe an innovative, dynamic coupling system between hospital surge capacity and cascading activation of a nationwide system for remote patient monitoring. This approach was developed using the multi-criteria decision analysis methodology, considering previously published real-life experiences on remote patient monitoring.

The chaos law is a principal driver of natural selection: A proposition on the evolution of recently emerged coronaviruses.

Here we propose that viruses emerging in the human population undergo an evolution that is conditioned by the rules of chaos. Our data support the notion that the initial growth rate "r" affects the chances of the virus to establish a long-lasting relationship with the new host. Indeed, an emerging virus is able to spread and adapt only when it displays an initial r falling in a range frankly associated with chaotic growth.

Host Transcriptome Analysis of Ferret Tissues Following Henipavirus Infection.

Ferrets are commonly used as experimental models of infection for a variety of viruses due to their susceptibility to human respiratory viruses and the close resemblance of pathological outcomes found in human infections. Even though ferret-specific reagents are limited, the use of ferrets as a preclinical experimental model of infection has gained considerable interest since the publication of the ferret transcriptome and draft ferret genome. These advances have made it feasible to easily perform whole-genome gene expression analysis in the ferret infection model. Here, we describe methods for genome-wide gene expression analysis using RNA sequence (RNAseq) data obtained from the lung and brain tissues obtained from experimental infections of Hendra (HeV) and Nipah (NiV) viruses in ferrets. We provide detailed methods for RNAseq and representative data for host gene expression profiles of the lung tissues that show early activation of interferon pathways and later activation of inflammation-related pathways.

Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild.

Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans (Cygnus olor) and the diverse species that they interact with. We discovered and characterised the full genome of a divergent gammacoronavirus belonging to the Goose coronavirus CB17 species. We investigated the genetic diversity and dynamics of this gammacoronavirus using untargeted metagenomic sequencing of 223 faecal samples from swans of known age and sex, and RT-PCR screening of 1632 additional bird samples. The virus circulated persistently within the bird community; virus prevalence in mute swans exhibited seasonal variations, but did not change with swan age-class or epidemiological year. One whole genome was fully characterised, and revealed that the virus originated from a recombination event involving an undescribed gammacoronavirus species. Multiple lineages of this gammacoronavirus co-circulated within our study population. Viruses from this species have recently been detected in aquatic birds from both the Anatidae and Rallidae families, implying that host species habitat sharing may be important in shaping virus host range. As the host range of the Goose coronavirus CB17 species is not limited to geese, we propose that this species name should be updated to 'Waterbird gammacoronavirus 1'. Non-invasive sampling of bird coronaviruses may provide a tractable model system for understanding the evolutionary and cross-species dynamics of coronaviruses.

Wastewater-based epidemiology: the crucial role of viral shedding dynamics in small communities.

Background: Wastewater surveillance (WWS) of pathogens is a rapidly evolving field owing to the 2019 coronavirus disease pandemic, which brought about a paradigm shift in public health authorities for the management of pathogen outbreaks. However, the interpretation of WWS in terms of clinical cases remains a challenge, particularly in small communities where large variations in pathogen concentrations are routinely observed without a clear relation to clinical incident cases. Methods: Results are presented for WWS from six municipalities in the eastern part of Canada during the spring of 2021. We developed a numerical model based on viral kinetics reduction functions to consider both prevalent and incident cases to interpret the WWS data in light of the reported clinical cases in the six surveyed communities. Results: The use of the proposed numerical model with a viral kinetics reduction function drastically increased the interpretability of the WWS data in terms of the clinical cases reported for the surveyed community. In line with our working hypothesis, the effects of viral kinetics reduction modeling were more important in small communities than in larger communities. In all but one of the community cases (where it had no effect), the use of the proposed numerical model led to a change from a +1.5% (for the larger urban center, Quebec City) to a +48.8% increase in the case of a smaller community (Drummondville). Conclusion: Consideration of prevalent and incident cases through the proposed numerical model increases the correlation between clinical cases and WWS data. This is particularly the case in small communities. Because the proposed model is based on a biological mechanism, we believe it is an inherent part of any wastewater system and, hence, that it should be used in any WWS analysis where the aim is to relate WWS measurement to clinical cases.

Comparative virome analysis of individual shedding routes of Miniopterus phillipsi bats inhabiting the Wavul Galge cave, Sri Lanka.

Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were discovered in the past, the full picture of the bat viromes is not explored yet. In this study, the virome composition of Miniopterus phillipsi bats (formerly known as Miniopterus fuliginosus bats in Sri Lanka) inhabiting the Wavul Galge cave, Sri Lanka, was analyzed. To assess different possible excretion routes, oral swabs, feces and urine were collected and analyzed individually by using metagenomic NGS. The data obtained was further evaluated by using phylogenetic reconstructions, whereby a special focus was set on RNA viruses that are typically associated with bats. Two different alphacoronavirus strains were detected in feces and urine samples. Furthermore, a paramyxovirus was detected in urine samples. Sequences related to Picornaviridae, Iflaviridae, unclassified Riboviria and Astroviridae were identified in feces samples and further sequences related to Astroviridae in urine samples. No viruses were detected in oral swab samples. The comparative virome analysis in this study revealed a diversity in the virome composition between the collected sample types which also represent different potential shedding routes for the detected viruses. At the same time, several novel viruses represent first reports of these pathogens from bats in Sri Lanka. The detection of two different coronaviruses in the samples indicates the potential general persistence of this virus species in M. phillipsi bats. Based on phylogenetics, the identified viruses are closely related to bat-associated viruses with comparably low estimation of human pathogenic potential. In further studies, the seasonal variation of the virome will be analyzed to identify possible shedding patterns for particular viruses.

Assessing the coverage and timeliness of coronavirus vaccination among people experiencing homelessness in Wales, UK: a population-level data-linkage study.

BACKGROUND: People experiencing homelessness have elevated morbidity, increasing their risk of COVID-19 related complications and mortality. Achieving high vaccination coverage in a timely manner among homeless populations was therefore important during the mass vaccination programme in Wales to limit adverse outcomes. However, no systematic monitoring of vaccinations among people experiencing homelessness in Wales has been undertaken. METHODS: Retrospective cohort analysis was conducted using de-identified administrative data. Study cohort members were adults (≥ 18 years old) living in Wales on the 2 December 2020 and who had recently experienced homelessness, defined as experiencing homelessness between 1 July 2020 and 2 December 2020. The outcome of interest was first coronavirus vaccine dose. Follow-up started on 2 December 2020, and ended if the participant died, had a break in address history > 30 days, reached the end of follow up (30 November 2021), or had the outcome of interest. Median-time-to-vaccination was used as a crude measure of 'timeliness' of vaccine uptake. To account for competing risk of death prior to vaccination, vaccine coverage was described using cumulative incidence at 350-days, and at 50-day increments over follow-up (2 December 2020 to 17 November 2021). As a benchmark, all time-to-event measures were generated for the adult population in Wales with similar baseline individual and residential characteristics as the study cohort. RESULTS: 1,595 people with recent experiences of homelessness were identified and included in analysis. The study cohort were disproportionately male (68.8%) and concentrated in the most deprived areas in Wales. Median time-to-vaccination for the study cohort was 196 days (95% CI.: 184-209 days), compared to 141 days (95% CI.: 141-141 days) among the matched adult population in Wales. Cumulative incidence of vaccination after 350-days of follow-up was 60.4% (95% CI.: 57.8-62.8%) among the study cohort, compared to 81.4% (95% CI.: 81.3-81.5%) among the matched adult population. Visual analysis of cumulative incidence over time suggests that vaccine inequality, i.e., difference between study cohort and matched adult population, peaked after 200-days of follow-up, and declined slightly until last follow-up at 350-days. CONCLUSIONS: Despite being prioritised for vaccination, people experiencing homelessness in Wales appear to have been under-engaged, leading to lower vaccination coverage and greater time unvaccinated, potentially increasing their risk of COVID-19 complications and mortality.

Coronavírus: home office

O isolamento social continua sendo a principal orientação no enfrentamento ao coronavírus, produzindo novas dinâmicas de trabalho. A consultora de carreira e administradora Camila Viotto media oficinas nos Centros de Apoio ao Trabalho e Empreendedorismo e dá dicas para organizar o home office. Coleção: Acontece em SP

Coronavírus: cuidados com a saúde mental

Além de todos os cuidados para prevenir o contágio da Covid-19, doença causada pelo novo coronavírus, é preciso cuidar da saúde mental, que pode ser abalada pelo consumo intenso de notícias e pela necessidade do isolamento. Profissionais da Secretaria Municipal da Saúde falam sobre esse cuidado neste episódio de série sobre o coronavírus. Coleção: Acontece em SP.

Saiba mais sobre a COVID-19

Confira alguns cuidados importantes para se prevenir contra a COVID-19, causada pelo novo coronavírus. São cuidados simples, importantes e que devem ser frequentes para prevenir doenças contagiosas.

Prevenção ao novo coronavírus em Libras.

Na batalha contra o novo coronavírus, todos tem que fazer a sua parte! E a informação é ferramenta essencial nessa hora. Por isso, preparamos um vídeo com orientações sobre medidas preventivas à Covid-19 para deficientes auditivos e todos que carecem de cuidados especiais. Elas também servem para quem tem sequelas graves provocadas por paralisia cerebral, síndrome de Down, Transtorno do Espectro Autista (TEA), Doença Pulmonar Obstrutiva Crônica (DPOC), Esclerose Lateral Amiotrófica (ELA), Atrofia Muscular Espinhal (AME), Esclerose Múltipla (EM), distrofias musculares e outras semelhantes. As pessoas com deficiências visuais, auditivas e motoras também devem redobrar os cuidados. As orientações de permanecer em casa, reforçar a higiene, usar as etiquetas respiratórias, sair em casos extremamente necessários e evitar aglomerações devem ser levadas a sério. E os cuidadores também, gente! Aperte o play e confira as dicas aqui, compartilha o vídeo também afinal cuidar de si é cuidar do outro.

Como se prevenir do Coronavírus

Diante das medidas e informações para o enfrentamento da COVID-19, doença respiratória causada pelo novo Coronavírus, surgem dúvidas. E para te ajudar no enfrentamento das fake news e para se prevenir da melhor forma possível, o SPlica de hoje te mostra dicas importantes de higiene e cuidados nesse período. Coleção: SPlica

Família Nogueira

Neste período de isolamento social, a família Nogueira fez um vídeo para nos dar dicas e conselhos sobre como lidar com a quarentena e sua importância contra o coronavírus. Agora é todo mundo em casa pro bem de todo mundo.

Conheça a família Nogueira

Neste período de isolamento social, a família Nogueira fez um vídeo para nos dar dicas e conselhos sobre como lidar com a quarentena e sua importância contra o coronavírus. Agora é todo mundo em casa pro bem de todo mundo. Coleção: Família Nogueira