SARS-CoV-2 shedding, infectivity, and evolution in an immunocompromised adult patient

ABSTRACT This study aimed to provide further insight into the evolutionary dynamics of SARS-CoV-2 by analyzing the case of a 40-year-old man who had previously undergone autologous hematopoietic stem cell transplantation due to a diffuse large B-cell lymphoma. He developed a persistent SARS-CoV-2 infection lasting at least 218 days and did not manifest a humoral immune response to the virus during this follow-up period. Whole-genome sequencing and viral cultures confirmed a persistent infection with a replication-positive virus that had undergone genetic variation for at least 196 days after symptom onset.

SARS-CoV-2 Detection and Culture in Different Biological Specimens from Immunocompetent and Immunosuppressed COVID-19 Patients Infected with Two Different Viral Strains.

Introduction-The dynamics of SARS-CoV-2 shedding and replication in humans remain incompletely understood. Methods-We analyzed SARS-CoV-2 shedding from multiple sites in individuals with an acute COVID-19 infection by weekly sampling for five weeks in 98 immunocompetent and 25 immunosuppressed individuals. Samples and culture supernatants were tested via RT-PCR for SARS-CoV-2 to determine viral clearance rates and in vitro replication. Results-A total of 2447 clinical specimens were evaluated, including 557 nasopharyngeal swabs, 527 saliva samples, 464 urine specimens, 437 anal swabs and 462 blood samples. The SARS-CoV-2 genome sequences at each site were classified as belonging to the B.1.128 (ancestral strain) or Gamma lineage. SARS-CoV-2 detection was highest in nasopharyngeal swabs regardless of the virus strain involved or the immune status of infected individuals. The duration of viral shedding varied between clinical specimens and individual patients. Prolonged shedding of potentially infectious virus varied from 10 days up to 191 days, and primarily occurred in immunosuppressed individuals. Virus was isolated in culture from 18 nasal swab or saliva samples collected 10 or more days after onset of disease. Conclusions-Our findings indicate that persistent SARS-CoV-2 shedding may occur in both competent or immunosuppressed individuals, at multiple clinical sites and in a minority of subjects is capable of in vitro replication.

Shedding of infectious SARS-COV-2 in two asymptomatic children / Excreción de SARS-CoV-2 infeccioso en dos niños asin tomáticos

Abstract Asymptomatic infections with SARS-CoV-2 are associ ated with viral transmission and have a key role in the propagation of the pandemic. Understanding viral shed ding during asymptomatic infections is critical. Unfor tunately, data on asymptomatic SARS-CoV-2 infection in children is extremely limited. To determine the presence of viral viable shedding, we prospectively followed two healthy children of a family where both parents devel oped mild COVID-19 (April 2021). SARS-CoV-2 detection was made by RT-PCR and virus isolation by cell culture from saliva samples. Positive samples were sequenced to identify variants of SARS-CoV-2. Serum samples were evaluated to determine the presence of antibodies using a single enzyme-linked immunosorbent assay (ELISA, COVIDAR IgG). Both children were SARS-CoV-2 positive and asymptomatic. In addition, the virus grew in cell cul ture from saliva samples. Furthermore, one child showed viable SARS-CoV-2 for at least 17 days after the onset symptoms from his father. The recommended isolation period for asymptomatic contacts during the acquisition of data had been established for 10 days; however, this child remained with viable virus beyond that period. The positive samples from both children were consistent with B.1.1.28.1 lineage (Gamma). In both asymptomatic children, anti-Spike IgG was detected. Asymptomatic children may represent a source of infection that should not be underestimated during this pandemic.

Resumen Las infecciones asintomáticas por SARS-CoV-2 están asociadas a la transmisión viral y tienen un papel cla ve en la propagación de la pandemia. Comprender la excreción viral durante las infecciones asintomáticas es fundamental. Desafortunadamente, los datos sobre la infección asintomática por SARS-CoV-2 en niños son extremadamente limitados. Para determinar la presencia de excreción de virus viable, se siguió prospectivamente a dos niños sanos de una familia en la que ambos padres desarrollaron COVID-19 leve (abril 2021). La detección de SARS-CoV-2 se realizó por RT-PCR y el aislamiento del virus por cultivo celular a partir de muestras de saliva. Las muestras positivas se secuenciaron para identificar variantes de SARS-CoV-2. En las muestras de suero se determinó la presencia de anticuerpos utilizando un ensayo de ELISA (COVIDAR IgG). Ambos niños fueron positivos para SARS-CoV-2 y asintomáticos. Además, el virus creció en cultivos celulares a partir de muestras de saliva. Uno de los niños mantuvo SARS-CoV-2 via bles durante al menos 17 días después de la aparición de los síntomas de su padre. El período de aislamiento recomendado para contactos asintomáticos durante la adquisición de datos se había establecido en 10 días, sin embargo, este niño permaneció con virus viable más allá de ese período. Las muestras positivas de estos niños correspondieron al linaje B.1.1.28.1 (Gamma). En ambos niños asintomáticos se detectó anticuerpos IgG anti-Spike. Concluimos que los niños asintomáticos pueden representar una fuente de infección que no debe subestimarse durante esta pandemia.

Seroprevalence and Vaginal Shedding of Herpes Simplex Virus Type 2 in Pregnant Adolescents and Young Women from Morelos, Mexico.

Adolescents and young people are particularly vulnerable to contracting STIs, including HSV-2; furthermore, vaginal shedding of HSV-2 during pregnancy can cause vertical transmission and neonatal herpes. To evaluate the seroprevalence of HSV-2 and vaginal HSV-2 shedding in adolescent and young pregnant women, a cross-sectional study was carried out in 496 pregnant women-adolescents and young women. Venous blood and vaginal exudate samples were taken. The seroprevalence of HSV-2 was determined by ELISA and Western blot. Vaginal HSV-2 shedding was assessed by qPCR of the HSV-2 UL30 gene. The seroprevalence of HSV-2 in the study population was 8.5% (95% CI 6-11), of which 38.1% had vaginal HSV-2 shedding (95% CI 22-53). Young women presented a higher seroprevalence of HSV-2 (12.1%) than adolescents (4.3%), OR = 3.4, 95% CI 1.59-7.23. Frequent alcohol consumption was significantly associated with HSV-2 seroprevalence, OR = 2.9, 95% CI 1.27-6.99. Vaginal HSV-2 shedding is highest in the third trimester of pregnancy, but this difference is not significant. The seroprevalence of HSV-2 in adolescents and young women is similar to that previously reported in other studies. However, the proportion of women with vaginal shedding of HSV-2 is higher during the third trimester of pregnancy, increasing the risk of vertical transmission.

Shedding of infectious SARS-CoV-2 in two asymptomatic children.

Asymptomatic infections with SARS-CoV-2 are associated with viral transmission and have a key role in the propagation of the pandemic. Understanding viral shedding during asymptomatic infections is critical. Unfortunately, data on asymptomatic SARS-CoV-2 infection in children is extremely limited. To determine the presence of viral viable shedding, we prospectively followed two healthy children of a family where both parents developed mild COVID-19 (April 2021). SARS-CoV-2 detection was made by RT-PCR and virus isolation by cell culture from saliva samples. Positive samples were sequenced to identify variants of SARS-CoV-2. Serum samples were evaluated to determine the presence of antibodies using a single enzyme-linked immunosorbent assay (ELISA, COVIDAR IgG). Both children were SARS-CoV-2 positive and asymptomatic. In addition, the virus grew in cell culture from saliva samples. Furthermore, one child showed viable SARS-CoV-2 for at least 17 days after the onset symptoms from his father. The recommended isolation period for asymptomatic contacts during the acquisition of data had been established for 10 days; however, this child remained with viable virus beyond that period. The positive samples from both children were consistent with B.1.1.28.1 lineage (Gamma). In both asymptomatic children, anti-Spike IgG was detected. Asymptomatic children may represent a source of infection that should not be underestimated during this pandemic.

Las infecciones asintomáticas por SARS-CoV-2 están asociadas a la transmisión viral y tienen un papel clave en la propagación de la pandemia. Comprender la excreción viral durante las infecciones asintomáticas es fundamental. Desafortunadamente, los datos sobre la infección asintomática por SARS-CoV-2 en niños son extremadamente limitados. Para determinar la presencia de excreción de virus viable, se siguió prospectivamente a dos niños sanos de una familia en la que ambos padres desarrollaron COVID-19 leve (abril 2021). La detección de SARS-CoV-2 se realizó por RT-PCR y el aislamiento del virus por cultivo celular a partir de muestras de saliva. Las muestras positivas se secuenciaron para identificar variantes de SARS-CoV-2. En las muestras de suero se determinó la presencia de anticuerpos utilizando un ensayo de ELISA (COVIDAR IgG). Ambos niños fueron positivos para SARS-CoV-2 y asintomáticos. Además, el virus creció en cultivos celulares a partir de muestras de saliva. Uno de los niños mantuvo SARS-CoV-2 viables durante al menos 17 días después de la aparición de los síntomas de su padre. El período de aislamiento recomendado para contactos asintomáticos durante la adquisición de datos se había establecido en 10 días, sin embargo, este niño permaneció con virus viable más allá de ese período. Las muestras positivas de estos niños correspondieron al linaje B.1.1.28.1 (Gamma). En ambos niños asintomáticos se detectó anticuerpos IgG anti-Spike. Concluimos que los niños asintomáticos pueden representar una fuente de infección que no debe subestimarse durante esta pandemia.

SARS-CoV-2 infection-induced immunity and the duration of viral shedding: Results from a Nicaraguan household cohort study.

BACKGROUND: Much of the world's population has been infected with SARS-CoV-2. Thus, immunity from prior infection will play a critical role in future SARS-CoV-2 transmission. We investigated the impact of infection-induced immunity on viral shedding duration and viral load. METHODS: We conducted a household cohort study in Managua, Nicaragua, with an embedded transmission study that closely monitors participants regardless of symptoms. Real-time reverse-transcription polymerase chain reaction (RT-PCR) and enzyme-linked immunosorbent assays (ELISAs) were used to measure infections and seropositivity, respectively. Blood samples were collected twice annually and surrounding household intensive monitoring periods. We used accelerated failure time models to compare shedding times. Participants vaccinated ≥14 days prior to infection were excluded from primary analyses. RESULTS: There were 600 RT-PCR-confirmed SARS-CoV-2 infections in unvaccinated participants between May 1, 2020, and March 10, 2022, with prior ELISA data. Prior infection was associated with 48% shorter shedding times (event time ratio [ETR] 0.52, 95% CI: 0.39-0.69, mean shedding: 13.7 vs. 26.4 days). A fourfold higher anti-SARS-CoV-2 spike titer was associated with 17% shorter shedding (ETR 0.83, 95% CI: 0.78-0.90). Similarly, maximum viral loads (lowest cycle threshold [CT]) were lower for previously infected individuals (mean CT 29.8 vs. 28.0, p = 4.02 × 10-3 ), for adults and children ≥10 years, but not for children 0-9 years; there was little difference in CT levels for previously infected versus naïve adults aged above 60 years. CONCLUSIONS: Prior infection-induced immunity was associated with shorter viral shedding and lower viral loads, which may be important in the transition from pandemic to endemicity.

Assessment of mycoplasma vaccine efficacy in reducing infection with Newcastle disease virus

The present work recorded the impact of using Mycoplasma gallisepticum vaccines on post-vaccinal response and protection against challenge with Newcastle disease virus. Specific pathogen-free chickens were divided into eight groups of forty chickens each. Group G1 was vaccinated with Mycoplasma gallisepticum live attenuated and Mycoplasma gallisepticum inactivated vaccines. Group G2 was vaccinated with Mycoplasma gallisepticum live attenuated, Mycoplasma gallisepticum inactivated and Newcastle disease inactivated vaccines. Group G3 was vaccinated with Mycoplasma gallisepticum live attenuated vaccine. Group G4 was vaccinated with Mycoplasma gallisepticum live attenuated and Newcastle disease inactivated vaccines. Group G5 was vaccinated with Mycoplasma gallisepticum inactivated vaccine. Group G6 was vaccinated with Mycoplasma gallisepticum inactivated and Newcastle disease inactivated vaccines. Group G7 was vaccinated with Newcastle disease inactivated vaccine. Group G8 was kept as non-vaccinated control. The Newcastle disease hemagglutination inhibition antibodies and mortality percentages were measured. Group G7 recorded the best protective Newcastle disease hemagglutination inhibition antibody titer (7 log2). Group G2 recorded a marginal satisfactory antibody titer (6 log2) after vaccination by the three tested vaccines. The remaining groups revealed unsatisfactory titers ranged from 0-5. The protection levels for G2, G4, G6 and G7 ranged from 70percent to 100percent, but only G2 and G7 were considered protected. G1, G3, G5 and G8 showed typical clinical signs of Newcastle disease. The Mycoplasma gallisepticum vaccines couldn't improve the response to Newcastle disease inactivated vaccine. The results suggest that Mycoplasma gallisepticum vaccination is immunosuppressive rather than immunomodulatory in Newcastle disease vaccination(AU)

En el presente trabajo se registró el impacto de la utilización de vacunas contra Mycoplasma gallisepticum sobre la respuesta posvacunal y la protección frente al reto con el virus de la enfermedad de Newcastle. Pollos libres de patógenos específicos se distribuyeron en ocho grupos de cuarenta pollos cada uno. El grupo G1 se vacunó con vacunas vivas atenuadas e inactivadas contra Mycoplasma gallisepticum. Al grupo G2 se le aplicaron las vacunas: viva atenuada contra Mycoplasma gallisepticum, inactivada contra Mycoplasma gallisepticum e inactivada contra la enfermedad de Newcastle. El grupo G3 se inmunizó con la vacuna viva atenuada contra Mycoplasma gallisepticum; el G4, con las vivas atenuadas contra Mycoplasma gallisepticum e inactivada contra la enfermedad de Newcastle; el G5, con la vacuna inactivada contra Mycoplasma gallisepticum; el G6 con las vacunas inactivadas contra Mycoplasma gallisepticum y la enfermedad de Newcastle; el G7, con la vacuna inactivada contra la enfermedad de Newcastle y el G8 se mantuvo como control no vacunado. Se midieron los anticuerpos de inhibición de la hemaglutinación contra el virus de la enfermedad de Newcastle y los porcentajes de mortalidad. El grupo G7 registró el mejor título de anticuerpos inhibidores de la hemaglutinación contra la enfermedad de Newcastle (7 log2). El grupo G2 registró un título de anticuerpos marginalmente satisfactorio (6 log2) tras la vacunación con las tres vacunas ensayadas. Los demás grupos revelaron títulos insatisfactorios que oscilaban entre 0 y 5. Los niveles de protección de los grupos G2, G4, G6 y G7 oscilaron entre el 70 por ciento y el 100 por ciento, pero sólo G2 y G7 se consideraron protegidos. Los grupos G1, G3, G5 y G8 mostraron signos clínicos típicos de la enfermedad de Newcastle. Las vacunas contra Mycoplasma gallisepticum no pudieron mejorar la respuesta a la vacuna inactivada contra la enfermedad de Newcastle. Los resultados revelan que la vacunación con Mycoplasma gallisepticum es más inmunosupresora que inmunomoduladora en la vacunación contra la enfermedad de Newcastle(AU)

Local protection bubbles: an interpretation of the slowdown in the spread of coronavirus in the city of São Paulo, Brazil, in July 2020 / Bolhas de proteção locais: uma interpretação da diminuição da velocidade de disseminação do coronavírus na cidade de São Paulo, Brasil, em julho de 2020 / Burbujas de protección locales: una interpretación de la reducción de la velocidad de propagación del coronavirus en la ciudad de São Paulo, Brasil, en julio de 2020

Abstract: After four months of fighting the pandemic, the city of São Paulo, Brazil, entered a phase of relaxed social distancing measures in July 2020. Simultaneously, there was a decline in the social distancing rate and a reduction in the number of cases, fatalities, and hospital bed occupancy. To understand the pandemic dynamics in the city of São Paulo, we developed a multi-agent simulation model. Surprisingly, the counter-intuitive results of the model followed the city's reality. We argue that this phenomenon could be attributed to local bubbles of protection that emerged in the absence of contagion networks. These bubbles reduced the transmission rate of the virus, causing short and temporary reductions in the epidemic curve - but manifested as an unstable equilibrium. Our hypothesis aligns with the virus spread dynamics observed thus far, without the need for ad hoc assumptions regarding the natural thresholds of collective immunity or the heterogeneity of the population's transmission rate, which may lead to erroneous predictions. Our model was designed to be user-friendly and does not require any scientific or programming expertise to generate outcomes on virus transmission in a given location. Furthermore, as an input to start our simulation model, we developed the COVID-19 Protection Index as an alternative to the Human Development Index, which measures a given territory vulnerability to the coronavirus and includes characteristics of the health system and socioeconomic development, as well as the infrastructure of the city of São Paulo.

Resumo: Após quatro meses lutando contra a pandemia, a cidade de São Paulo, Brasil, entrou em uma fase de flexibilização das medidas de distanciamento social em julho de 2020. Simultaneamente, houve queda na taxa de distanciamento social e redução no número de casos, mortes e ocupação de leitos hospitalares. Um modelo de simulação multiagente foi desenvolvido para entender a dinâmica da pandemia na cidade de São Paulo. Ao contrário do esperado, os resultados contraintuitivos do modelo acompanharam a realidade da cidade. Argumentamos que este fenômeno pode ser atribuído às bolhas locais de proteção que surgiram na ausência de redes de contágio. Estas bolhas reduziram a taxa de transmissão do vírus, causando reduções curtas e temporárias na curva epidêmica - mas se manifestaram como um equilíbrio instável. Nossa hipótese está alinhada com a dinâmica da propagação do vírus observada até o momento, sem a necessidade de suposições ad hoc sobre limiares de imunidade coletiva natural ou heterogeneidade da taxa de transmissão da população, o que pode levar a previsões errôneas. Nosso modelo foi projetado para ser fácil de usar e não requer nenhum conhecimento científico ou de programação para gerar resultados sobre a transmissão do vírus em um determinado local. Além disso, como insumo para iniciar nosso modelo de simulação, desenvolvemos o Índice de Proteção contra a COVID-19 como alternativa ao Índice de Desenvolvimento Humano, que mede a vulnerabilidade de um determinado território ao coronavírus e inclui características do sistema de saúde e do desenvolvimento socioeconômico, além da infraestrutura da cidade de São Paulo.

Resumen: Tras cuatro meses luchando contra la pandemia, la ciudad de São Paulo, Brasil, empezó una fase de flexibilización de las medidas de alejamiento social en julio de 2020. A la vez, hubo una reducción en la tasa de alejamiento social y en el número de casos, muertes y ocupación de camas en los hospitales. Se desarrolló un modelo de simulación multiagente para entender la dinámica de la pandemia en la ciudad de São Paulo. Diferente de lo esperado, los resultados contradictorios del modelo reflejaron la realidad de la ciudad. Sostenemos que se puede atribuir este fenómeno a las burbujas locales de protección que surgieron durante la ausencia de redes de contagio. Estas burbujas redujeron la tasa de transmisión del virus, reduciendo de forma corta y temporal la curva epidémica -pero se manifestaron como un equilibrio inestable. Nuestra hipótesis se alinea con la dinámica de la propagación del virus observada hasta el momento, sin la necesidad de suposiciones ad hoc sobre umbrales de inmunidad colectiva natural o heterogeneidad de la tasa de transmisión de la población, lo que puede provocar previsiones equivocadas. Nuestro modelo se proyectó para ser fácil de usar y no necesita ningún conocimiento científico o de programación para generar resultados sobre la transmisión del virus en un determinado local. Además, como insumo para iniciar nuestro modelo de simulación, desarrollamos el Índice de Protección contra la COVID-19 como una alternativa al Índice de Desarrollo Humano, que mide la vulnerabilidad de un determinado territorio al coronavirus e incluye características del sistema de salud y del desarrollo socioeconómico, además de la infraestructura de la ciudad de São Paulo.

Non-random host tree infestation by the Neotropical liana Marcgravia longifolia.

The question whether or not tropical lianas infest host trees randomly or they exert host selection has implications for the structure and dynamics of tropical rainforests, particularly if colonization by lianas impacts host fitness. In this study, we present evidence that the Neotropical liana Marcgravia longifolia (Marcgraviaceae) infests host trees non-randomly. We identified host trees to species or genus level for 87 of the 100 M. longifolia individuals found in the study area of the Estación Biológica Quebrada Blanco (EBQB) in north-eastern Peruvian Amazonia. Data on host availability were taken from two 1-ha plots sampled at EBQB as part of a large-scale tree inventory in western Amazonia. Of the total of 88 tree genera with two or more individuals present in the inventory, 18 were represented amongst hosts. Host genera with a probability of colonization higher than expected by chance were Eschweilera (Lecythidaceae), Pouteria (Sapotaceae), Brosimum (Moraceae), and Hymenaea (Fabaceae). These findings suggest that M. longifolia exerts some level of host selectivity, but the mechanisms for this are completely unknown. Given the large number of animal species (41 bird species, three primate species) that are dispersing the seeds of M. longifolia and that have diverse ecological strategies, directed seed dispersal is unlikely to account for the observed patterns of host infestation.

Chikungunya Virus Shedding in Semen: A Case Series.

BACKGROUND: Chikungunya is a viral disease that is transmitted by mosquitoes. It is characterized by an acute onset of fever and severe arthralgia. METHODS: We describe six cases of acute and post-acute chikungunya in which viral RNA was detected in semen. CONCLUSIONS: The most prolonged detection period was 56 days after illness onset. We attempted to cultivate positive semen samples, but virus isolation was unsuccessful in all cases.

¿Cuál es el período de excreción viral e infectividad de la variante Ómicron del virus SARS-CoV-2?: reporte breve de evidencia / What is the period of viral shedding and infectivity of the omicron variant of Sars-cov-2 virus?: brief report of evidence

ANTECEDENTES Y OBJETIVO Han pasado 2 años y medio desde que la Organización Mundial de la Salud decretó emergencia sanitaria por la pandemia ocasionada por SARS-CoV-2. Durante este tiempo, se han presentado una serie de desafíos para evitar su propagación, uno de ellos corresponde a las mutaciones y cambios que ha sufrido el virus. En noviembre de 2021 se notificó la variante Ómicron B.1.1.529, que presenta algunas mutaciones de preocupación, asociándose con mayor transmisibilidad y menor susceptibilidad a los anticuerpos neutralizantes. En este contexto la Jefatura de la División de Planificación Sanitaria solicita este reporte breve de evidencia con el objetivo de conocer el período de excreción viral e infectividad de la variante Ómicron. METODOLOGÍA Se buscaron revisiones sistemáticas que respondieron la pregunta en las bases de datos MEDLINE y EMBASE a través de OVID y en Epistemonikos, con fecha 30 de agosto 2022. Debido a no encontrarse evidencia en los motores de búsqueda seleccionados, se realizó una búsqueda en Google académico, sin embargo, tampoco fue identificada evidencia alguna. Se incluyen revisiones sistemáticas, estudios que describieron o midieran los períodos de infectividad y excreción de la variante Ómicron del virus SARS-CoV-2. Se excluyen períodos de infectividad y excreción de otras variantes del Virus SARS-CoV-2. RESULTADOS -No se encontró evidencia que describiera el periodo de infectividad y excreción del virus en personas contagiadas con SARS-COV-2 variante Ómicron.

Evidence of recurrent selection of mutations commonly found in SARS-CoV-2 variants of concern in viruses infecting immunocompromised patients.

Chronically immunosuppressed patients infected with SARS-CoV-2 often experience prolonged virus shedding, and may pave the way to the emergence of mutations that render viral variants of concern (VOC) able to escape immune responses induced by natural infection or by vaccination. We report herein a SARS-CoV-2+ cancer patient from the beginning of the COVID-19 pandemic whose virus quasispecies across multiple timepoints carried several immune escape mutations found in more contemporary VOC, such as alpha, delta and omicron, that appeared to be selected for during infection. We hypothesize that immunosuppressed patients may represent the source of VOC seen throughout the COVID-19 pandemics.

SARS-CoV-2 loads in urine, sera and stool specimens in association with clinical features of COVID-19 patients.

Background: COVID-19 pandemic continues to be a priority in public health worldwide, and factors inherent to SARS-CoV-2 pathogenesis and genomic characteristics are under study. Investigations that evaluate possible risk factors for infection, clinical manifestations, and viral shedding in different specimens also need to clarify possible associations with COVID-19 prognosis and disease outcomes. Study design: In this study, we evaluated SARS-CoV-2 positivity and estimated viral loads by real-time RT-PCR in stool, sera, and urine samples from 35 patients, with a positive SARS-CoV-2 RNA molecular test in respiratory sample, attended at a University COVID-19 referral hospital in Goiania, Goias, Brazil. Whole-genome sequencing was also performed in samples with higher viral load. Results: The positivity index was 51.43%, 14.28%, and 5.71% in stool, sera, and urine specimens, respectively. The median viral load was 8.01 × 106 GC/g, 2.03 × 106 GC/mL, and 1.36 × 105 GC/mL in stool, sera, and urine, respectivelly. Of all patients, 88.57% had previous comorbidities, and 48.39% of them had detectable SARS-CoV-2 RNA in at least one type of clinical specimen evaluated by this study (stool, sera or urine). A higher viral load was observed in patients with more than two previous comorbidities and that were classified as severe or critical conditions. Samples with the highest viral loads were sequenced and characterized as B.1.1.33 variant. Conclusion: We conclude that SARS-CoV-2 RNA is present in more than one type of clinical specimen during the infection, and that the most critical patients had detectable viral RNA in more than one clinical specimen at the same time point.

Assessment of maternal immunity against Salmonella enterica serovar Heidelberg in progeny of broiler breeders vaccinated with different formulations of bacterins.

RESEARCH HIGHLIGHTSProgeny from vaccinated 30-week-old breeders presented less SH in caecal content compared to the control.High titres of maternal anti-Salmonella IgY could be associated with lower SH faecal shedding.

Prolonged SARS-CoV-2 nucleic acid conversion time in military personnel outbreaks with presence of specific IgG antibodies.

Coronavirus disease 2019 (COVID-19) is transmitted person-to-person mainly by close contact or droplets from respiratory tract. However, the actual time of viral shedding is still uncertain as well as the different routes of transmission. We aimed to characterize RNA shedding from nasopharyngeal and rectal samples in prolonged cases of mild COVID-19 in young male soldiers. Seventy patients from three different military locations were monitored after recommending to follow more strict isolation measures to prevent the spread of the virus. Then, nasopharyngeal, rectal, and blood samples were taken. SARS-CoV-2 RNA was detected by RT-PCR and specific antibodies by chemiluminescent immunoassays. The median nucleic acid conversion time (NACT) was 60 days (IQR: 7-85 days). Rectal swabs were taken in 60 % of patients. Seven patients (10 %) were positive in nasopharyngeal and rectal swabs, and five (7.14 %) remained positive in rectal swabs, but negative in nasopharyngeal samples. Four patients (5.71 %) that had been discharged, were positive again after 15 days. No significant difference was found in nucleic acid conversion time between age groups nor clinical classification. Maintaining distancing among different positive patients is essential as a possible re-exposure to the virus could cause a longer nucleic acid conversion time in SARS-COV-2 infections.

Human bocavirus detection and quantification in fecal and serum specimens from recipients of allogeneic hematopoietic stem cell transplantation: A longitudinal study.

OBJECTIVES: The aim of this study was to evaluate the occurrence of human bocavirus (HBoV) and to determine viral loads in samples of patients admitted for allogeneic hematopoietic stem cell transplantation (allo-HSCT). METHODS: Fecal and serum samples were collected from 19 patients, during a 24-month period. Samples were screened by quantitative polymerase chain reaction TaqMan assay, with specific probe and primers targeting the NP1 gene of all HBoVs genotypes (HBoV-1 to - 4), and viral loads were determined using serial dilutions of a recombinant plasmid. RESULTS: HBoV DNA was detected in 42.1% (8 of 19) of the patients in at least one type of sample (feces and/or serum) during the study period, with 75% (6 of 8) of the patients being positive in both types of sample. Viral shedding in feces had a median of 26 days (range, 5 to 121) and viremia was detected in 87.5% (7 of 8) of the patients. The HBoV loads in fecal samples were higher than in sera and, in most cases, HBoV was detected earlier in fecal than in sera samples. In six HBoV-positive patients (6 of 8) diarrhea was observed concomitantly to viral detection in fecal samples. CONCLUSIONS: A high frequency and loads of HBoV in allo-HSCT recipients was observed, especially in fecal samples. Positivity in fecal samples was an early predictor of HBoV presence.

Dynamic of Mycobacterium avium subspecies paratuberculosis infection in a domestic-wildlife interface: Domestic sheep and guanaco as reservoir community.

Natural herbivore populations have experienced uninterrupted pressures from direct and evident domestic-wildlife interactions and competition, to indirect or less obvious ones such as pathogen transmission. Thus, pathogen spillover between wild and domestic animals is a constant concern because the domestic-wildlife interface represents the ecological frontier in which pathogen transmission takes place in both directions. In Patagonian steppe communities, extensive sheep ranching and guanaco (Lama guanicoe) populations coexist, and guanaco have shown to be infected by pathogens such as Mycobacterium avium subspecies paratuberculosis (MAP) likely transmitted from livestock. MAP causes chronic enteritis and affects mostly domestic ruminants. We evaluated MAP prevalence and pathogen shedding in both species' faeces collected in non-shared and shared sites according to presence/absence of sheep and guanaco along a year, in four different seasons (autumn, winter, and spring 2018, and summer 2019). Our results indicate that MAP circulates in both sheep and guanaco populations with self-sustained transmission; however, both species differ in their levels of competence. We detected higher pathogen shedding in sites occupied by sheep, suggesting that sheep populations may be the main source of infection for susceptible animals due to their large numbers which drive MAP dynamics.

Atypical Prolonged Viral Shedding With Intra-Host SARS-CoV-2 Evolution in a Mildly Affected Symptomatic Patient.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is caused by a respiratory virus with a wide range of manifestations, varying from asymptomatic to fatal cases, with a generally short outcome. However, some individuals present long-term viral shedding. We monitored 38 individuals who were mildly affected by the SARS-CoV-2 infection. Out of the total studied population, three (7.9%) showed atypical events regarding the duration of positivity for viral RNA detection. In one of these atypical cases, a previously HIV-positive male patient presented a SARS-CoV-2 RNA shedding and subgenomic RNA (sgRNA) detected from the upper respiratory tract, respectively, for 232 and 224 days after the onset of the symptoms. The SARS-CoV-2 B.1.1.28 lineage, one of the most prevalent in Brazil in 2020, was identified in this patient in three serial samples. Interestingly, the genomic analyses performed throughout the infectious process showed an increase in the genetic diversity of the B.1.1.28 lineage within the host itself, with viral clearance occurring naturally, without any intervention measures to control the infection. Contrasting widely spread current knowledge, our results indicate that potentially infectious SARS-CoV-2 virus might be shed by much longer periods by some infected patients. This data call attention to better adapted non-pharmacological measures and clinical discharge of patients aiming at preventing the spread of SARS-CoV-2 to the population.

Shedding of Trypanosoma cruzi Surface Molecules That Regulate Host Cell Invasion Involves Phospholipase C and Increases Upon Sterol Depletion.

Metacyclic trypomastigote (MT) forms of Trypanosoma cruzi have been shown to release into medium gp82 and gp90, the stage-specific surface molecules that regulate host cell invasion, either in vesicles or in soluble form. Here, we found that during interaction of poorly invasive G strain with the host cell, gp82 and gp90 were released in vesicle-like forms, whereas no such release by highly invasive CL strain was observed. Shedding of vesicles of varying sizes by CL and G strains was visualized by scanning electron microscopy, and the protein profile of conditioned medium (CM) of the two strains was similar, but the content of gp82 and gp90 differed, with both molecules being detected in G strain as bands of high intensity in Western blotting, whereas in CL strain, they were barely detectable. Confocal images revealed a distinct distribution of gp82 and gp90 on MT surface of CL and G strains. In cell invasion assays, addition of G strain CM resulted in decreased CL strain internalization. Depletion of gp82 in G strain CM, by treatment with specific mAb-coupled magnetic beads, increased its inhibitory effect on CL strain invasion, in contrast to CM depleted in gp90. The effect of cholesterol-depleting drug methyl-ß-cyclodextrin (MßCD) on gp82 and gp90 release by MTs was also examined. G strain MTs, untreated or treated with MßCD, were incubated in serum-containing medium or in nutrient-depleted PBS++, and the CM generated under these conditions was analyzed by Western blotting. In PBS++, gp82 and gp90 were released at lower levels by untreated MTs, as compared with MßCD-treated parasites. CM from untreated and MßCD-treated G strain, generated in PBS++, inhibited CL strain internalization. Treatment of CL strain MTs with MßCD resulted in increased gp82 and gp90 shedding and in decreased host cell invasion. The involvement of phospholipase C (PLC) on gp82 and gp90 shedding was also investigated. The CM from G strain MTs pretreated with specific PLC inhibitor contained lower levels of gp82 and gp90, as compared with untreated parasites. Our results contribute to shed light on the mechanism by which T. cruzi releases surface molecules implicated in host cell invasion.

Clinical practice in COVID-19: The most frequently asked questions to infectious diseases specialists.

Since the emergence of the disease caused by the severe respiratory syndrome coronavirus 2 (SARS-CoV-2) - COVID-19 - in late December 2019, a vast number of publications on the subject appeared in peer-reviewed journals and preprints. Despite the significant amount of available information, infectious disease physicians are requested to solve questions from colleagues, patients, and relatives on a daily basis. Here, we aim to describe the evidence supporting the answers for frequently asked questions, based on a literature review. We created a web-based questionnaire which was distributed to a group of 70 infectious disease specialists and medical residents, asking what questions and issues they most frequently faced. The 10 most frequent questions guided the topics for a narrative review. We provide evidence and consensus-based information on subjects such as infection and transmission, isolation, management of COVID-19 confirmed cases, reinfection, clinical-therapeutic management, vaccination, and antibodies post-infection/vaccination. Correctly clarifying doubts and providing clear information to physicians, patients, and family members helps to better manage COVID-19 in the community and the hospital settings.