A single BNT162b2 dose protects against SARS-CoV-2: A case report of a family cluster of COVID-19.

Background. Coronavirus 2019 (COVID-19) disease is an infectious disease caused by the virus “Severe Acute Respiratory Syndrome Coronavirus 2” (SARS-CoV-2). This virus generated a pandemic in 2020 and has affected millions of people worldwide. Facing the need to prevent its contagion, the vaccine BNT162b2 was approved in December 2020 in Mexico and started being administered to healthcare workers. Case presentation. We presented two healthcare workers vaccinated with one single dose of BNT162b2, who lives in a family nucleus with a high transmission rate of SARS-CoV-2. These healthcare workers, identified in the manuscript as patients E and F, were asymptomatic and their real-time RT-PCR test for SARS-CoV-2 resulted negative, while the rest of the family (patients A-D) were SARS-CoV-2 positive. The antibody titers IgG anti-spike of patient F (after the second dose; 1080 Au/mL) turned out greater than patient E (before the second dose; 37.1 Au/mL). Discussion. To our knowledge, this is the first case report of the protective effect of a single BNT162b2 vaccine dose in the context of high transmission rates within a family nucleus. Despite changes induced by BNT162b2 in the antibody titers with single or double dose vaccination, a single dose of BNT162b2 showed to be sufficient for immunization of patients against COVID-19.Introducción. La enfermedad del Coronavirus 2019 (COVID-19) es una enfermedad infecciosa causada por el virus “Síndrome respiratorio agudo severo Coronavirus 2” (SARS-CoV-2). Este virus generó una pandemia en 2020 y ha afectado a millones de personas en todo el mundo. Ante la necesidad de prevenir su contagio, la vacuna BNT162b2 fue aprobada en México en diciembre de 2020 y comenzó a administrarse en trabajadores de la salud. Reporte de caso. Presentamos aquí, dos trabajadores de la salud vacunados con una sola dosis de BNT162b2, que viven en un núcleo familiar con alta tasa de transmisión del SARS-CoV-2. Estos trabajadores de la salud, identificados en el manuscrito como pacientes E y F, estaban asintomáticos y su prueba de RT-PCR en tiempo real para SARS-CoV-2 resultó negativa, mientras que el resto de la familia (pacientes A - D) fueron positivos para SARS-CoV-2. Los títulos de anticuerpos IgG anti-Spike del paciente F (después de la segunda dosis; 1080 Au/mL) resultaron mayores que los del paciente E (antes de la segunda dosis; 37.1 Au/mL). Discusión. Hasta donde sabemos, este es el primer informe de caso del efecto protector de una sola dosis de la vacuna BNT162b2 en el contexto de altas tasas de transmisión dentro de un núcleo familiar. A pesar de los cambios inducidos por BNT162b2 en los títulos de anticuerpos con vacunación de dosis única o doble, una dosis única de BNT162b2 demostró ser suficiente para la inmunización de pacientes contra COVID-19

Rhinovirus prevalence as indicator for efficacy of measures against SARS-CoV-2

Abstract Background Non-pharmaceutical measures to control the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) should be carefully tuned as they can impose a heavy social and economic burden. To quantify and possibly tune the efficacy of these anti-SARS-CoV-2 measures, we have devised indicators based on the abundant historic and current prevalence data from other respiratory viruses. Methods We obtained incidence data of 17 respiratory viruses from hospitalized patients and outpatients collected by 37 clinics and laboratories between 2010-2020 in Germany. With a probabilistic model for Bayes inference we quantified prevalence changes of the different viruses between months in the pre-pandemic period 2010-2019 and the corresponding months in 2020, the year of the pandemic with noninvasive measures of various degrees of stringency. Results We discovered remarkable reductions δ in rhinovirus (RV) prevalence by about 25% (95% highest density interval (HDI) [−0.35,−0.15]) in the months after the measures against SARS-CoV-2 were introduced in Germany. In the months after the measures began to ease, RV prevalence increased to low pre-pandemic levels, e.g. in August 2020 δ=−0.14 (95% HDI [−0.28,0.12]). Conclusions RV prevalence is negatively correlated with the stringency of anti-SARS-CoV-2 measures with only a short time delay. This result suggests that RV prevalence could possibly be an indicator for the efficiency for these measures. As RV is ubiquitous at higher prevalence than SARS-CoV-2 or other emerging respiratory viruses, it could reflect the efficacy of noninvasive measures better than such emerging viruses themselves with their unevenly spreading clusters

Respiratory viruses dynamics and interactions: ten years of surveillance in central Europe

Background Lower respiratory tract infections are among the main causes of death. Although there are many respiratory viruses, diagnostic efforts are focused mainly on influenza. The Respiratory Viruses Network (RespVir) collects infection data, primarily from German university hospitals, for a high diversity of infections by respiratory pathogens. In this study, we computationally analysed a subset of the RespVir database, covering 217,150 samples tested for 17 different viral pathogens in the time span from 2010 to 2019. Methods We calculated the prevalence of 17 respiratory viruses, analysed their seasonality patterns using information-theoretic measures and agglomerative clustering, and analysed their propensity for dual infection using a new metric dubbed average coinfection exclusion score (ACES). Results After initial data pre-processing, we retained 206,814 samples, corresponding to 1,408,657 performed tests. We found that Influenza viruses were reported for almost the half of all infections and that they exhibited the highest degree of seasonality. Coinfections of viruses are frequent; the most prevalent coinfection was rhinovirus/bocavirus and most of the virus pairs had a positive ACES indicating a tendency to exclude each other regarding infection. Conclusions The analysis of respiratory viruses dynamics in monoinfection and coinfection contributes to the prevention, diagnostic, treatment, and development of new therapeutics. Data obtained from multiplex testing is fundamental for this analysis and should be prioritized over single pathogen testing

Safe and effective pool testing for SARS-CoV-2 detection

Objectives: The global spread of SARS-CoV-2 is a serious public health issue. Large-scale surveillance screenings are crucial but can exceed test capacities. We (A) optimized test conditions and (B) implemented pool testing of respiratory swabs into SARS-CoV-2 diagnostics. Study design: (A) We determined the optimal pooling strategy and pool size. In addition, we measured the impact of vortexing prior to sample processing, compared a pipette-pooling method (by combining transport medium of several specimens) and a swab-pooling method (by combining several swabs into a test tube filled with PBS) as well as determined the sensitivities of three PCR assays. (B) Finally, we applied high-throughput pool testing for diagnostics. Results: (A) In a low prevalence setting, we defined a preferable pool size of ten in a two-stage hierarchical pool testing strategy. Vortexing of swabs (n = 33) increased cellular yield by a factor of 2.34. By comparing Ct-values of 16 pools generated with two different pooling strategies, pipette-pooling was more efficient compared to swab-pooling. Measuring dilution series of 20 SARS-CoV-2 positive samples in three PCR assays simultaneously revealed detection rates of 85% (assay I), 50% (assay II), and 95% (assay III) at a 1:100 dilution. (B) We systematically pooled 55,690 samples in a period of 44 weeks resulting in a reduction of 47,369 PCR reactions. Conclusions: For implementing pooling strategies into high-throughput diagnostics, we recommend utilizing a pipette-pooling method, performing sensitivity validation of the PCR assays used, and vortexing swabs prior to analyses. Pool testing for SARS-CoV-2 detection is feasible and effective in a low prevalence setting

High HPgV replication is associated with improved surrogate markers of HIV progression

<div><p>Background</p><p>Human Pegivirus (HPgV) may have a beneficial effect on HIV disease progression in co-infected patients; however, the virologic characteristics of this infection are not well defined. In this study, we determined HPgV viremia prevalence in Mexico and provide new insights to understand HPgV infection and HPgV/HIV co-infection.</p><p>Methods</p><p>We analyzed and quantified 7,890 serum samples for HPgV viremia by One-Step RT-Real-Time PCR, 6,484 from healthy blood donors and 1,406 from HIV-infected patients. Data on HIV progression were obtained from patients’ records. HPgV genotyping was performed in 445 samples by nested PCR of the 5’URT region. Finite Mixture Models were used to identify clustering patterns of HPgV viremia in blood donors and co-infected antiretroviral (ART)-naïve patients.</p><p>Results</p><p>HPgV was detected in 2.98% of blood donors and 33% of HIV patients, with a wide range of viral loads. The most prevalent genotypes were 3 (58.6%)and 2 (33.7%). HPgV viral loads from healthy blood donors and HPgV/HIV+ ART-naïve co-infected patients were clustered into two component distributions, low and high, with a cut-off point of 5.07log₁₀ and 5.06log₁₀, respectively. High HPgV viremia was associated with improved surrogate markers of HIV infection, independent of the estimated duration of HIV infection or HIV treatment.</p><p>Conclusions</p><p>HPgV prevalence in Mexico was similar to that reported for other countries. The prevalent genotypes could be related to Mexico’s geographic location and ethnicity, since genotype 2 is frequent in the United States and Europe and genotype 3 in Asia and Amerindian populations. HPgV viral load demonstrated two patterns of replication, low and high. The more pronounced beneficial response observed in co-infected patients with high HPgV viremia may explain discrepancies found between other studies. Mechanisms explaining high and low HPgV replication should be explored to determine whether the persistently elevated replication depends on host or viral factors.</p></div

Mean difference of HIV viral load in co-infected subjects according to time of HIV infection and HPgV viral load conditions.

<p>Mean difference of HIV viral load in co-infected subjects according to time of HIV infection and HPgV viral load conditions.</p

Effects of HPgV genotype (2 or 3) on surrogate markers of HIV progression.

<p>Each graph shows the differences between the means of: (A and B) HIV viral load/ml (log₁₀), (C and D) CD4⁺ cell counts (CD4⁺/mm³), and (E and F) CD4⁺/CD8⁺ ratio, in the ART-naïve population according to their HPgV condition (-negative, -low, or -high) and genotype 3 (A, C and E) and genotype 2 (B, D and F). Significant differences are considered at p<0.05.</p

Mean difference of CD4⁺/CD8⁺ ratio in co-infected subjects according to time of HIV infection and HPgV viral load condition.

<p>Mean difference of CD4⁺/CD8⁺ ratio in co-infected subjects according to time of HIV infection and HPgV viral load condition.</p

Diagram of pooling method for serum samples from blood donors.

<p>The diagram shows the construction of sample pools and analysis for HPgV viremia in healthy blood donors. Positive samples from the pool were re-tested in smaller pools each time until we detected the positive individual donor sample.</p

Mean difference of CD4⁺ cell counts (CD4⁺/mm³) in co-infected subjects according to time of HIV infection and HPgV viral load conditions.

<p>Mean difference of CD4⁺ cell counts (CD4⁺/mm³) in co-infected subjects according to time of HIV infection and HPgV viral load conditions.</p