Social distancing measures for COVID-19 are changing winter season

Health authorities worldwide have adopted measures of social distancing and movement restrictions, in addition to other public health measures to reduce exposure and to suppress interhuman SARS-CoV- 2 transmission. In Italy, a national lockdown with school closure was introduced from March to May 2020. From November 2020, Italy has been divided into zones according to regional epidemiological data, with primary schools reopened, associated with the mandatory use of face masks and different levels of social distance measures. For children with symptoms suggestive of COVID-19, the surveillance mechanism for the control of SARS-CoV- 2 infection is based on the performance of a real-time PCR on a nasopharyngeal swab. A diagnostic test has been introduced at the tertiary-level university hospital, Institute for Maternal and Child Health, IRCCS \u201cBurlo Garofolo\u201d of Trieste, consisting of a multiple nucleic acid amplification assay for 13 common viral respiratory pathogens on nasopharyngeal swab (Respiratory Flow Chip assay (Vitro, Sevilla, Spain), including SARS-CoV- 2, influenza A and B, adenovirus, other coronaviruses, parainfluenza virus 1\u20134, enteroviruses, bocavirus, metapneumovirus, respiratory syncytial virus (RSV), rhinoviruses, Bordetella pertussis, Bordetella parapertussis and Mycoplasma pneumoniae. Before routine utilisation, international standard quality control samples for each pathogen were used for test validation, and no cross-detection was found between the different pathogens. Criteria for testing referral did not change during the study period. Weekly variability of the number of total tests performed was due to the normal variations of acute illness. During the last winter season, from September 2020 (week 39) to February 2021 (week 7), 1138 nasopharyngeal swabs were tested for patients younger than 17 years old (figure 1). No influenza A or B nor RSV was detected during this period. The most common pathogen was rhinovirus (n=505), followed by adenoviruses (n=131), other coronaviruses (n=101) and SARS-CoV- 2 (n=57). Our data show that common winter pathogens circulation changed, and influenza virus and RSV did not produce a seasonal epidemic in the 2020\u20132021 winter season. These data suggest that social distancing measures and mask wearing profoundly changed the seasonality of winter paediatric respiratory infections that are mainly spread by respiratory droplets. The reasons why rhinovirus remains the main pathogen despite social distancing and face mask use are still a matter of debate. Similar data showing a decrease of common viral respiratory infections during the winter season have recently been reported in the southern hemisphere.1\u20134 Our data refer to a single institute, covering paediatric population of the Trieste Province (about 230 000 inhabitants), limiting the generalisation of our findings. However, our results highlight the need for continuing surveillance for the delayed spread of such viruses during spring and summer

Circulation of SARS-CoV-2 Variants among Children from November 2020 to January 2022 in Trieste (Italy)

Introduction: The ongoing coronavirus disease 19 (COVID-19) outbreak involves the pediatric population, but to date, few reports have investigated the circulation of variants among children. Material and Methods: In this retrospective study, non-hospitalized pediatric patients with SARS-CoV-2-positive nasopharyngeal swabs (NPS) were enrolled at the Institute for Maternal and Child Health-IRCCS Burlo Garofolo, Trieste (Italy), from November 2020 to January 2022. SARS-CoV-2 variants were identified by in vitro viral isolation, amplification, automatic sequencing of the receptor binding domain (RBD) of the SARS-CoV-2 spike coding gene, and subsequent nextgeneration sequencing. The growth curves of the isolated strains were defined in vitro by infecting Vero-E6 cells and quantifying the viral load in the supernatants up to 72 h post-infection by qRT– PCR. The neutralization activity of sera obtained from a COVID-19 vaccinated subject, recovered (2020) patient, vaccinated and recovered (2021) patient, and seronegative subject was assessed by microneutralization assay against the different variants. Results: In total, 32 SARS-CoV-2-positive children, 16 (50%) females, with a median age of 1.4 years (range: 1 day–13 years), were enrolled. The D614G amino acid substitution was detected in all isolated and amplified viral strains. Of the 32 isolates, 4 (12.5%) carried a nonsynonymous nucleotide mutation leading to the N439K (3/4), lineage B.1.258 (∆H69/∆V70), and S477N (1/4) substitution. In 7/32 (21.8%) isolates, amino acid substitutions allowed the identification of a delta variant, lineage B.1.617.2-AY.43, and in 1/32 (3.1%), the Omicron strain (B.1.1.529.BA1) was identified. The growth curves of the B.1, B.1.258 (∆H69/∆V70), B.1.617.2-AY.43, and B.1.1.529.BA1 variants did not show any significant differences. A reduction in the serum neutralizing activity against B.1.258 (∆H69/∆V70) only in a vaccinated subject (1.7-fold difference), against B.1.617.2-AY.43 in a vaccinated subject and in recovered patients (12.7 and ≥2.5-fold differences, respectively), and against B.1.1.529.BA1 variant (57.6-and 1.4-fold differences in vaccinated and in vaccinated and recovered patients) were observed compared to the B.1 variant. Conclusions: SARS-CoV-2 variants carrying the B.1.258 (∆H69/∆V70) and S477N substitutions were reported here in a pediatric population for the first time. Although the growth rates of the isolated strains (B.1.258, B.1.617.2-AY.43, B.1.1.529.BA1) did not differ from the B.1 variant, neutralizing activity of the sera from vaccinated subjects significantly decreased against these variants. Attention should be devoted to the pediatric population to prevent the spread of new SARS-CoV-2 variants in an unvaccinated and predominantly naive population

Oncogenic Virome Benefits from the Different Vaginal Microbiome-Immune Axes.

The picture of dynamic interaction between oncogenic viruses and the vaginal bacteria-immune host milieu is incomplete. We evaluated the impact of Polyomaviridae, Papillomaviridae, and Herpesviridae oncoviruses on the vaginal Community State Types (CSTs) and host immune response in reproductive-age women. In our cohort, only Polyomaviridae and Papillomaviridae were detected and were associated with changes in the resident bacteria of CST I and IV (p < 0.05). Lactobacillus crispatus increased in CST I while Prevotella timonensis and Sneathia sanguinegens increased in CST IV. Conversely, CST II and III showed an alteration of the immune response, with the decrease of Eotaxin, MCP-1, IL-7, IL-9, and IL-15 (p < 0.05), leading to reduced antiviral efficacy. An efficient viral clearance was observed only in women from CST I, dominated by Lactobacillus crispatus. Our in vivo study begins to address the knowledge gap with respect to the role of vaginal bacteria and immune response in susceptibility to oncoviral infections

Introduction of Probiotic-Based Sanitation in the Emergency Ward of a Children's Hospital During the COVID-19 Pandemic

Background: Antimicrobial resistance (AMR) represents a major threat to public health, especially in the hospital environment, and the massive use of disinfectants to prevent COVID-19 transmission might intensify this risk, possibly leading to future AMR pandemics. However, the control of microbial contamination is crucial in hospitals, since hospital microbiomes can cause healthcare-associated infections (HAIs), which are particularly frequent and severe in pediatric wards due to children having high susceptibility. Aim: We have previously reported that probiotic-based sanitation (PCHS) could stably decrease pathogens and their AMR in the hospital environment, reduce associated HAIs in adult hospitals, and inactivate enveloped viruses. Here, we aimed to test the effect of PCHS in the emergency room (ER) of a children's hospital during the COVID-19 pandemic. Methods: Conventional chemical disinfection was replaced by PCHS for 2 months during routine ER sanitation; the level of environmental bioburden was characterized before and at 2, 4, and 9 weeks after the introduction of PCHS. Microbial contamination was monitored simultaneously by conventional culture-based CFU count and molecular assays, including 16S rRNA NGS for bacteriome characterization and microarrays for the assessment of the resistome of the contaminating population. The presence of SARS-CoV-2 was also monitored by PCR. Results and conclusions: PCHS usage was associated with a stable 80% decrease in surface pathogens compared to levels detected for chemical disinfection (P &lt; 0.01), accompanied by an up to 2 log decrease in resistance genes (Pc &lt; 0.01). The effects were reversed when reintroducing chemical disinfection, which counteracted the action of the PCHS. SARS-CoV-2 was not detectable in both the pre-PCHS and PCHS periods. As the control of microbial contamination is a major issue, especially during pandemic emergencies, collected data suggest that PCHS may be successfully used to control virus spread without simultaneous worsening of the AMR concern

Principal variable selection to explain grain yield variation in winter wheat from features extracted from UAV imagery

Background: Automated phenotyping technologies are continually advancing the breeding process. However, collecting various secondary traits throughout the growing season and processing massive amounts of data still take great efforts and time. Selecting a minimum number of secondary traits that have the maximum predictive power has the potential to reduce phenotyping efforts. The objective of this study was to select principal features extracted from UAV imagery and critical growth stages that contributed the most in explaining winter wheat grain yield. Five dates of multispectral images and seven dates of RGB images were collected by a UAV system during the spring growing season in 2018. Two classes of features (variables), totaling to 172 variables, were extracted for each plot from the vegetation index and plant height maps, including pixel statistics and dynamic growth rates. A parametric algorithm, LASSO regression (the least angle and shrinkage selection operator), and a non-parametric algorithm, random forest, were applied for variable selection. The regression coefficients estimated by LASSO and the permutation importance scores provided by random forest were used to determine the ten most important variables influencing grain yield from each algorithm. Results: Both selection algorithms assigned the highest importance score to the variables related with plant height around the grain filling stage. Some vegetation indices related variables were also selected by the algorithms mainly at earlier to mid growth stages and during the senescence. Compared with the yield prediction using all 172 variables derived from measured phenotypes, using the selected variables performed comparable or even better. We also noticed that the prediction accuracy on the adapted NE lines (r = 0.58–0.81) was higher than the other lines (r = 0.21–0.59) included in this study with different genetic backgrounds. Conclusions: With the ultra-high resolution plot imagery obtained by the UAS-based phenotyping we are now able to derive more features, such as the variation of plant height or vegetation indices within a plot other than just an averaged number, that are potentially very useful for the breeding purpose. However, too many features or variables can be derived in this way. The promising results from this study suggests that the selected set from those variables can have comparable prediction accuracies on the grain yield prediction than the full set of them but possibly resulting in a better allocation of efforts and resources on phenotypic data collection and processing