Web search volume as a near-real-time complementary surveillance tool of tick-borne encephalitis (TBE) in Italy

The Internet is an important gateway for accessing health-related information, and data generated through web queries have been increasingly used as a complementary source for monitoring and forecasting of infectious diseases and they may partially address the issue of underreporting. In this study, we assessed whether tick-borne encephalitis (TBE)-related Internet search volume may be useful as a complementary tool for TBE surveillance in Italy. Monthly Google Trends (GT) data for TBE-related information were extracted for the period between January 2017 and September 2022, corresponding to the available time series of TBE notifications in Italy. Time series modeling was performed by applying seasonal autoregressive integrated moving average (SARIMA) models with or without GT data. The search terms relative to tick bites reflected best the observed temporal distribution of TBE cases, showing a correlation coefficient of 0.81 (95 % CI: 0.71-0.88). Particularly, both the reported number of TBE cases and GT searches occurred mainly during the summer. The peak of disease notifications coincided with that of Google searches in 4 of 6 years. Once calibrated, SARIMA models with or without GT data were applied to a validation set. Retrospective forecast made by the model with GT data was associated with a lower prediction error and accurately predicted the peak timing. By contrast, the traditional SARIMA model underestimated the actual number of TBE notifications by 65 %. Timeliness, easy availability, low cost and transparency make monitoring of the TBE-related Internet search queries a promising addition to the traditional methods of TBE surveillance in Italy.

RSV Disease Burden in Primary Care in Italy: A Multi-Region Pediatric Study, Winter Season 2022-2023

INTRODUCTION

Human respiratory syncytial virus (RSV) is one of the most frequent causes of respiratory infections in children under 5 years of age, but its socioeconomic impact and burden in primary care settings is still little studied.

METHODS

During the 2022/2023 winter season, 55 pediatricians from five Italian regions participated in our community-based study. They collected a nasal swab for RSV molecular test from 650 patients under the age of 5 with acute respiratory infections (ARIs) and performed a baseline questionnaire. The clinical and socioeconomic burden of RSV disease in primary care was evaluated by two follow-up questionnaires completed by the parents of positive children on Days 14 and 30.

RESULTS

RSV laboratory-confirmed cases were 37.8% of the total recruited ARI cases, with RSV subtype B accounting for the majority (65.4%) of RSV-positive swabs. RSV-positive children were younger than RSV-negative ones (median 12.5 vs. 16.5 months). The mean duration of symptoms for all children infected by RSV was 11.47 ± 6.27 days. We did not observe substantial differences in clinical severity between the two RSV subtypes, but RSV-A positive patients required more additional pediatric examinations than RSV-B cases. The socioeconomic impact of RSV infection was considerable, causing 53% of children to be absent from school, 46% of parents to lose working days, and 25% of families to incur extra costs.

CONCLUSIONS

Our findings describe a baseline of the RSV disease burden in primary care in Italy before the introduction of upcoming immunization strategies.

Influenza-like illness surveillance may underestimate the incidence of respiratory syncytial virus in adult outpatients

OBJECTIVES

Although respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections (ARIs), it is unclear which of the case definitions that prompt swab collection predicts RSV best. We aimed to profile RSV-positive adults and to identify possible RSV case definitions.

METHODS

This individual-based pooled analysis was based on influenza-like illness (ILI) surveillance conducted among Italian outpatient adults. All samples were tested for influenza, RSV and other respiratory viruses.

RESULTS

RSV was detected in 5.2% of the 1240 ILI adults tested. The prevalence of fever/feverishness was significantly lower (83.3%) in individuals positive for RSV and those negative for both viruses (79.4%) than in influenza-positive subjects (96.2%). Conversely, 98.3% of RSV-positive adults reported cough. Compared with subjects who tested negative, the adjusted relative risk ratio of cough in RSV-positive subjects was much higher than in influenza-positive subjects (6.89 vs 2.79). Using ARI with cough as the RSV case definition increased specificity.

CONCLUSION

As fever/feverishness is more common among influenza than RSV cases, ILI-based surveillance may underestimate RSV incidence in adult outpatients. While broad ARI definitions are useful for routine RSV surveillance, their low specificity may hamper vaccine effectiveness studies. The use of further ARI qualifiers like cough increases specificity.

Exploring missed opportunities for influenza vaccination and influenza vaccine co-administration patterns among Italian older adults: a retrospective cohort study

BACKGROUND

Missed opportunities constitute a main driver of suboptimal seasonal influenza vaccination (SIV) coverage in older adults. Vaccine co-administration is a way to reduce these missed opportunities. In this study, we quantified missed opportunities for SIV, identified some of their socio-structural correlates and documented SIV co-administration patterns.

METHODS

In this registry-based retrospective cohort study, we verified the SIV status of all subjects aged ≥65 years who received at least one dose of coronavirus disease 2019 (COVID-19), pneumococcal or herpes zoster vaccines during the 2022/23 influenza season. The frequency of concomitant same-day administration of SIV with other target vaccines was also assessed.

RESULTS

Among 41 112, 5482 and 3432 older adults who received ≥1 dose of COVID-19, pneumococcal and herpes zoster vaccines, missed opportunities for SIV accounted for 23.3%, 5.0% and 13.2%, respectively. Younger, male and foreign-born individuals were generally more prone to missing SIV. The co-administration of SIV with other recommended vaccines was relatively low, being 11.0%, 53.1% and 17.1% in COVID-19, pneumococcal and herpes zoster cohorts, respectively.

CONCLUSIONS

A sizeable proportion of older adults who received other recommended vaccines during the last influenza season did not receive SIV. This share of missed opportunities, which are subject to some social inequalities, may be addressed by increasing vaccine co-administration rates and implementing tailored health promotion interventions.

Rollout of the 2022/2023 Seasonal Influenza Vaccination and Correlates of the Use of Enhanced Vaccines among Italian Adults

In Italy, several types of seasonal influenza vaccines (SIVs) are available for older adults, but for the 2022/2023 season there were no guidelines on their specific use. This cross-sectional study assessed the frequency and determinants of the use of enhanced (adjuvanted and high-dose) SIVs in Italian older adults, as compared to standard-dose non-adjuvanted formulations. Of 1702 vaccines administered to a representative outpatient sample of adults aged ≥ 60 years and residing in Genoa, 69.5% were enhanced SIVs. Older age (adjusted odds ratio (aOR) for each 1-year increase 1.10; p < 0.001), and the presence of cardiovascular disease (aOR 1.40; p = 0.011) and diabetes (aOR 1.62; p = 0.005) were associated with the use of enhanced vaccines. Compared with the adjuvanted SIV, subjects immunized with the high-dose vaccine were older (aOR for each 1-year increase 1.05; p < 0.001) and had higher prevalence of respiratory diseases (aOR 1.85; p = 0.052). Moreover, usage of the enhanced SIVs was driven by the period of immunization campaign, place of vaccination and physician. Despite their superior immunogenicity and effectiveness, the adoption of enhanced SIVs in Italy is suboptimal, and should be increased. Enhanced formulations are mostly used in the oldest, and in subjects with some co-morbidities.

Increasing Influenza Vaccination Uptake by Sending Reminders: A Representative Cross-Sectional Study on the Preferences of Italian Adults

Evidence from countries that achieved a high seasonal influenza vaccination (SIV) coverage suggests that reminders to get vaccinated may increase SIV uptake. The goal of this study was to explore the experience and attitudes of Italian adults toward an active invitation to receive SIV, triggered by different sources and delivered via different communication channels, and to assess the projected benefits of this strategy. A cross-sectional survey on a representative sample of Italian adults was conducted by using computer-assisted web interviewing. Responses from 2513 subjects were analyzed. A total of 52.2% of individuals previously received invitations to undergo SIV and compared with people who did not receive any reminder were three times more likely (68.2% vs. 22.2%) to be vaccinated in the last season. Compared with other sources, reminders sent by general practitioners (GPs) were perceived as the most attractive. As for communication channels, most participants preferred text/instant messaging (24.6%) or email (27.2%), suggesting an acceleration in the Italian digital transformation triggered by the COVID-19 pandemic. Conversely, traditional postal letters or phone calls were preferred by only 17.0% and 8.6% of respondents, respectively. Reminders sent by GPs via text/instant messages or email are a valuable option for increasing SIV uptake among Italian adults.

Real-world performance of SARS-CoV-2 rapid antigen testing through the Alpha-, Delta- and Omicron-dominant waves of the COVID-19 pandemic

OBJECTIVES

Compared with reverse transcription polymerase chain reaction (RT-PCR), rapid antigen detection tests (RADTs) for SARS-CoV-2 diagnostics are faster, less expensive, but also less accurate. Performance of RADTs is context-specific and depends on disease prevalence. In this real-world study, we assessed impact of RADTs in an inpatient setting through the entire COVID-19 emergency phase.

METHODS

In this matched retrospective study, data on RT-PCR and RADT laboratory diagnoses of SARS-CoV-2 made between February 2020 and May 2023 in a large hospital were analyzed. To be included in the study, samples used for both RT-PCR and RADT had to be collected on the same day.

RESULTS

Of 278,867 RT-PCR tests available, 13,321 same-day RADTs could be matched to RT-PCR. Over the entire period, RADT sensitivity and specificity were 76.4% and 99.4%, respectively. With the observed positivity rate of 9.4%, positive and negative predictive values were 92.7% and 97.6%, respectively. Compared with the periods dominated by the Alpha and Delta variants of concern, RADT accuracy was slightly lower during the Omicron phase.

CONCLUSION

This real-world experience demonstrates that despite suboptimal sensitivity and some variation by predominant variants of concern and positivity prevalence, the use of RADTs is useful in hospital settings. Public health implications were discussed.

Population-level benefits of increasing influenza vaccination uptake among Italian older adults: results from a granular panel model

Background

The impact of seasonal influenza vaccination (SIV) on mortality is still controversial; some studies have claimed that increasing vaccination coverage rates is beneficial, while others have found no significant association. This study aimed to construct a granular longitudinal dataset of local VCRs and assess their effect on pneumonia- and influenza-related (P&I) mortality among Italian adults aged ≥ 65 years.

Methods

NUTS-3 (nomenclature of territorial units for statistics) level data on SIV coverage were collected via a survey of local data holders. Fixed- and random-effects panel regression modeling, when adjusted for potential confounders, was performed to assess the association between local SIV coverage rates and P&I mortality in older adults.

Results

A total of 1,144 local VCRs from 2003 to 2019 were ascertained. In the fully adjusted fixed-effects model, each 1% increase in vaccination coverage was associated (P < 0.001) with a 0.6% (95% CI: 0.3-0.9%) average over-time decrease in P&I mortality. With an annual average of 9,293 P&I deaths in Italy, this model suggested that 56 deaths could have been avoided each year by increasing SIV coverage by 1%. The random-effects model produced similar results. The base-case results were robust in a sensitivity analysis.

Conclusion

Over the last two decades, Italian jurisdictions with higher SIV uptake had, on average, fewer P&I deaths among older adults. Local policy-makers should implement effective strategies to increase SIV coverage in the Italian senior population.

Three seasons of enhanced safety surveillance of a cell culture-based quadrivalent influenza vaccine

The objective of this paper is to summarize annual enhanced safety surveillance activity across three seasons (2019/20-2021/22) for cell culture-based quadrivalent influenza vaccine (QIVc; Flucelvax® Tetra) in all age groups. This activity was conducted in primary care setting in Genoa (Italy) during the seasons 2019/20, 2020/21 and 2021/22. All adverse events registered within the first seven days following immunization were analyzed by season, type, age group and seriousness. Over three seasons, 3,603 QIVc exposures were recorded within the enhanced passive safety surveillance activity. No safety signals were identified. The overall reporting rates of individual case safety reports for the seasons 2019/20, 2020/21 and 2021/22 were 1.75%, 0.48% and 0.40%, respectively. The average number of adverse events per individual case safety report was similar (range 3.3-3.8 adverse events per case report) across the three seasons. Most adverse events were reactogenic in nature. The rate of adverse events was similarly low in all age groups. Enhanced passive safety surveillance activity is a feasible approach for the post-marketing monitoring of seasonal influenza vaccines. Within its limitations, results of this study support the favorable safety profile of QIVc. These safety data could further bolster public trust in influenza vaccines with the goal to increase vaccination uptake in all target groups.

Long follow-up of BNT162b2 mRNA vaccine in healthcare workers (2020-2022): A retrospective longitudinal SARS-CoV-2 serological surveillance

SARS-CoV-2 anti-spike IgG production and protection from severe respiratory illness should be explored in greater depth after COVID-19 booster vaccination. This longitudinal observational retrospective study investigated the anti-spike IgG response elicited by the first, second and booster doses of BNT162b2 mRNA vaccine in healthcare workers (HCW) at San Martino IRCCS Policlinico Hospital (Genoa) up to the 12th month. Sequential blood sampling was performed at T0 (prior to vaccination), T1 (21 days after the 1st dose of vaccine), T2, T3, T4, T5, T6 (7 days and 1, 3, 6 and 9 months after the 2nd dose, respectively), T7 and T8 (1 and 3 months after a booster dose). A SARS-CoV-2 IgG panel (Bio-Rad, Marnes-la-Coquette, France) was used to determine levels of receptor-binding domain (RBD), spike-1 (S1), spike-2 and nucleocapsid structural proteins of SARS-CoV-2. In the 51 HCWs evaluated, seroprevalence was 96% (49/51) at T1 and 100% (51/51) from T2 to T5 for RBD and S1. At T6, only one HCW was negative. T2 [RBD = 2945 (IQR:1693-5364); S1 = 1574 (IQR:833-3256) U/mL], and T7 [RBD = 8204 (IQR:4129-11,912); S1 = 4124 (IQR:2124-6326) U/mL] were characterized by the highest antibody values. Significant humoral increases in RBD and S1 were documented at T7 and T8 compared to T2 and T4, respectively (p-value < .001). Following vaccination with BNT162b2 and a booster dose in the 9th month, naïve and healthy subjects show high antibody titers up to 12 months and a protective humoral response against COVID-19 disease lasting up to 20 months after the last booster.

Influenza vaccine effectiveness in preventing hospital encounters for laboratory-confirmed infection among Italian adults, 2022/23 season

The effectiveness of seasonal influenza vaccination (SIV) varies from year to year. Interim estimates of vaccine effectiveness (VE) in outpatient settings have suggested that the 2022/23 northern hemisphere SIV was 54 % effective. The main goal of this study was to measure the 2022/23 SIV VE among Italian adults in a hospital setting. The study adopted a retrospective test-negative case-control design and was conducted in a large tertiary hospital (Genoa, Italy) between October 2022 and April 2023. Adult (≥18 years) patients accessing the hospital's Emergency Department for symptoms ascribable to an acute respiratory infection, for which a reverse-transcription real-time polymerase chain reaction test for the detection of influenza virus was prescribed, were potentially eligible. Of 33,692 referrals assessed, 487 patients were included in the study. A total of 13 % of patients were positive for influenza, most of which (63 %) belonged to the A(H3N2) subtype. SIV VE was 57 % (95 % CI: 11-81 %), 53 % (95 % CI: 2-80 %) and 38 % (95 % CI: -34-74 %) against any influenza, influenza A and A(H3N2), respectively. Although no cases caused by A(H1N1)pdm09 and B strains were observed among vaccinated individuals, VE estimates against the latter were imprecise, owing to their low detection rates. In conclusion, the 2022/23 SIV was moderately effective against hospital encounters for laboratory-confirmed influenza.

Epidemiology and molecular characteristics of respiratory syncytial virus (RSV) among italian community-dwelling adults, 2021/22 season

BACKGROUND

Respiratory syncytial virus (RSV) is a leading cause of acute respiratory infections worldwide. While historically RSV research has been focused on children, data on RSV infection in adults are limited. The goal of this study was to establish the prevalence of RSV in community-dwelling Italian adults and analyze its genetic variability during the 2021/22 winter season.

METHODS

In this cross-sectional study, a random sample of naso-/oropharyngeal specimens from symptomatic adults seeking for SARS-CoV-2 molecular testing between December 2021 and March 2022 were tested for RSV and other respiratory pathogens by means of reverse-transcription polymerase chain reaction. RSV-positive samples were further molecularly characterized by sequence analysis.

RESULTS

Of 1,213 samples tested, 1.6% (95% CI: 0.9-2.4%) were positive for RSV and subgroups A (44.4%) and B (55.6%) were identified in similar proportions. The epidemic peak occurred in December 2021, when the RSV prevalence was as high as 4.6% (95% CI: 2.2-8.3%). The prevalence of RSV detection was similar (p = 0.64) to that of influenza virus (1.9%). All RSV A and B strains belonged to the ON1 and BA genotypes, respectively. Most (72.2%) RSV-positive samples were also positive for other pathogens being SARS-CoV-2, Streptococcus pneumoniae and rhinovirus the most frequent. RSV load was significantly higher among mono-detections than co-detections.

CONCLUSION

During the 2021/22 winter season, characterized by the predominant circulation of SARS-CoV-2 and some non-pharmaceutical containment measures still in place, a substantial proportion of Italian adults tested positive for genetically diversified strains of both RSV subtypes. In view of the upcoming registration of vaccines, establishment of the National RSV surveillance system is urgently needed.

Rapid differential diagnosis of SARS-CoV-2, influenza A/B and respiratory syncytial viruses: Validation of a novel RT-PCR assay

BACKGROUND

Influenza and respiratory syncytial (RSV) viruses are expected to co-circulate with SARS-CoV-2 in the upcoming seasons and clinical differential diagnosis between them is difficult. Laboratory-based RT-PCR is a gold standard diagnostic method for influenza, RSV and SARS-CoV-2. The objective of this study was to estimate the diagnostic performance of a novel point-of-care RT-PCR assay STANDARD M10 Flu/RSV/SARS-CoV-2 (SD Biosensor) in a large number of clinical specimens with diversified (co)-infection patterns and viral loads.

METHODS

This was a retrospective study, in which all samples were tested in both STANDARD M10 Flu/RSV/SARS-CoV-2 index and Allplex SARS-CoV-2/Respiratory Panel 1 (Seegene) reference kits. Samples with discordant results were further processed in a third resolver test (Resp-4-Plex, Abbott).

RESULTS

A total of 1,019 naso-/oropharyngeal samples (50.3% positive for at least one virus) were processed in both STANDARD M10 Flu/RSV/SARS-CoV-2 and Allplex assays and the overall between-assay agreement was as high as 94.6%. Positive percent agreement of the STANDARD M10 Flu/RSV/SARS-CoV-2 was 100%, 96.6%, 97.3% and 99.4% for influenza A, B, RSV and SARS-CoV-2, respectively. The corresponding negative percent agreement was 99.7%. 100%, 100% and 98.4%, respectively. The expected positive and negative predictive values for all viruses were constantly above 96% in a reasonable range of disease prevalence.

CONCLUSIONS

STANDARD M10 Flu/RSV/SARS-CoV-2 is a reliable RT-PCR assay able to detect influenza A, influenza B, RSV and SARS-CoV-2 in one hour or less, fostering a rapid differential diagnosis of common respiratory viruses.

Sero-Epidemiological Study of Varicella in the Italian General Population

The aim of this study was to analyze the seroprevalence of varicella in Italy and to evaluate the impact of varicella vaccination, which has been mandatory for newborns since 2017. The levels of VZV-specific IgG antibodies were determined by the ELISA method in residual serum samples obtained from subjects aged between 6 and 64 years and residing in 13 Italian regions. Overall, 3746 serum samples were collected in the years 2019 and 2020. The overall seroprevalence was 91.6% (89.9% in males and 93.3% in females; p = 0.0002). Seroprevalence showed an increasing trend (p < 0.0001) starting in the younger age groups: 6-9 years: 84.1%; 10-14 years: 88.7%; 15-19 years: 89.3%; 20-39 years: 93.1% and >40 years: 97.0%. The seroprevalence data obtained in the present study were compared with those relating to previous sero-epidemiological surveys conducted, respectively, in the years 1996-1997, 2003-2004 and 2013-2014, taking into consideration only data from regions monitored in all surveillance campaigns. The comparison highlighted for the period 2019-2020 showed significantly higher values in the age groups 6-9 (p < 0.001), 10-14 (p = 0.018) and 15-19 years (p = 0.035), while in adults, the trend did not change over time (ns). These results highlight the positive impact of varicella vaccination in Italy.

Systemic sclerosis and vaccinations: a three-year register-based cohort study about vaccination rate and uptake from Liguria referral center, northwest Italy

Patients with diffused Systemic Sclerosis (dSSc) are more subject to severe respiratory complications with higher rates of intensive care unit (ICU) admission. Vaccination represents the most effective means of prevention and care for frail patients, such as SSc patients, preventing infections, reducing mortality and morbidity, and granting a better quality of life. Both vaccinations against seasonal influenza and Streptococcus pneumoniae are currently recommended by the European League Against Rheumatism (EULAR) guidelines on vaccination. The aim of this study is to give an updated analysis on S. pneumoniae and seasonal influenza vaccination coverage in a cohort of 91 patients with SSc and to investigate demographic and clinical variables significantly related to vaccine acceptance. The correlation between vaccine administration and other factors was investigated using a binomial logistic regression to evaluate the adjusted odds ratio (aOR). The patients followed up in this study reached higher percentages than the general population, passing the 75% target for both influenza and anti-pneumococcal vaccinations and reaching for influenza vaccine coverage rates of 83.8% for subjects undergoing immunosuppressive therapies and 88.9% for elderly subjects. For the latter group, it is important to emphasize the strong correlation between older age groups and vaccination acceptance.

Prevalence of Pneumococcal Serotypes in Community-Acquired Pneumonia among Older Adults in Italy: A Multicenter Cohort Study

Pneumococcal community-acquired pneumonia (CAP) is a leading cause of mortality. Following the introduction of pneumococcal conjugate vaccines (PCVs) in children, a decrease in the burden of the disease was reported. In parallel, an increase in non-vaccine serotypes was also noted. The objective of this study was to assess the current serotype-specific epidemiology of pneumococci among Italian older adults hospitalized for CAP. A prospective study was conducted between 2017 and 2020 in four Italian regions. Subjects aged ≥65 years hospitalized with confirmed CAP were tested for pneumococci using both pneumococcal urinary antigen and serotype-specific urine antigen tests able to identify all 24 serotypes included in the available vaccines. Of the 1155 CAP cases, 13.1% were positive for pneumococci. The most prevalent serotypes were 3 (2.0%), 8 (1.7%), 22F (0.8 %) and 11A (0.7%). These serotypes are all included in the newly licensed PCV20. The serotypes included in PCV13, PCV15 and PCV20 contributed to 3.3%, 4.4% and 7.5% of the CAP cases, respectively. In the context of a low PCV13 coverage among older adults and a high PCV coverage in children, a substantial proportion of CAP is caused by PCV13 serotypes. Higher valency PCV15 and PCV20 may provide additional benefits for the prevention of CAP in vaccinated older adults.

Epidemiological and Clinical Features of SARS-CoV-2 Variants Circulating between April-December 2021 in Italy

SARS-CoV-2 is constantly evolving, leading to new variants. We analysed data from 4400 SARS-CoV-2-positive samples in order to pursue epidemiological variant surveillance and to evaluate their impact on public health in Italy in the period of April-December 2021. The main circulating strain (76.2%) was the Delta variant, followed by the Alpha (13.3%), the Omicron (5.3%), and the Gamma variants (2.9%). The B.1.1 lineages, Eta, Beta, Iota, Mu, and Kappa variants, represented around 1% of cases. There were 48.2% of subjects who had not been vaccinated, and they had a lower median age compared to the vaccinated subjects (47 vs. 61 years). An increasing number of infections in the vaccinated subjects were observed over time, with the highest proportion in November (85.2%). The variants correlated with clinical status; the largest proportion of symptomatic patients (59.6%) was observed with the Delta variant, while subjects harbouring the Gamma variant showed the highest proportion of asymptomatic infection (21.6%), albeit also deaths (5.4%). The Omicron variant was only found in the vaccinated subjects, of which 47% had been hospitalised. The diffusivity and pathogenicity associated with the different SARS-CoV-2 variants are likely to have relevant public health implications, both at the national and international levels. Our study provides data on the rapid changes in the epidemiological landscape of the SARS-CoV-2 variants in Italy.

Effect of the 2020/21 season influenza vaccine on SARS-CoV-2 infection in a cohort of Italian healthcare workers

OBJECTIVES

Healthcare workers (HCWs) are a priority group for seasonal influenza vaccination (SIV). The 2020/21 SIV campaign was conducted during the second wave of the COVID-19 pandemic. Vaccines, including SIV, may exert non-specific protective effects on other infectious diseases which may be ascribable to the concept of trained immunity. The aim of this study was to explore the association between 2020/21 SIV and SARS-CoV-2 positivity in a cohort of Italian HCWs.

METHODS

In this observational study, a cohort of HCWs employed by a large (ca 5000 employees) referral tertiary acute-care university hospital was followed up retrospectively until the start of the COVID-19 vaccination campaign. The independent variable of interest was the 2020/21 SIV uptake. Both egg-based and cell culture-derived quadrivalent SIVs were available. The study outcome was the incidence of new SARS-CoV-2 infections, as determined by RT-PCR. Multivariable Cox regression was applied in order to discern the association of interest.

RESULTS

The final cohort consisted of 2561 HCWs who underwent ≥1 RT-PCR test and accounted for a total of 94,445 person-days of observation. SIV uptake was 35.6%. During the study period, a total of 290 new SARS-CoV-2 infections occurred. The incidence of new SARS-CoV-2 was 1.62 (95% CI: 1.22-2.10) and 3.91 (95% CI: 3.43-4.45) per 1000 person-days in vaccinated and non-vaccinated HCWs, respectively, with an adjusted non-proportional hazard ratio of 0.37 (95% CI: 0.22-0.62). E-values suggested that unmeasured confounding was unlikely to explain the association.

CONCLUSIONS

A lower risk of SARS-CoV-2 infection was observed among SIV recipients.

Increase in taxonomic assignment efficiency of viral reads in metagenomic studies

Metagenomics studies have revolutionized the field of biology by revealing the presence of many previously unisolated and uncultured micro-organisms. However, one of the main problems encountered in metagenomic studies is the high percentage of sequences that cannot be assigned taxonomically using commonly used similarity-based approaches (e.g. BLAST or HMM). These unassigned sequences are allegorically called « dark matter » in the metagenomic literature and are often referred to as being derived from new or unknown organisms. Here, based on published and original metagenomic datasets coming from virus-like particle enriched samples, we present and quantify the improvement of viral taxonomic assignment that is achievable with a new similarity-based approach. Indeed, prior to any use of similarity based taxonomic assignment methods, we propose assembling contigs from short reads as is currently routinely done in metagenomic studies, but then to further map unassembled reads to the assembled contigs. This additional mapping step increases significantly the proportions of taxonomically assignable sequence reads from a variety -plant, insect and environmental (estuary, lakes, soil, feces) - of virome studies.

Discovery of parvovirus-related sequences in an unexpected broad range of animals

Our knowledge of the genetic diversity and host ranges of viruses is fragmentary. This is particularly true for the Parvoviridae family. Genetic diversity studies of single stranded DNA viruses within this family have been largely focused on arthropod- and vertebrate-infecting species that cause diseases of humans and our domesticated animals: a focus that has biased our perception of parvovirus diversity. While metagenomics approaches could help rectify this bias, so too could transcriptomics studies. Large amounts of transcriptomic data are available for a diverse array of animal species and whenever this data has inadvertently been gathered from virus-infected individuals, it could contain detectable viral transcripts. We therefore performed a systematic search for parvovirus-related sequences (PRSs) within publicly available transcript, genome and protein databases and eleven new transcriptome datasets. This revealed 463 PRSs in the transcript databases of 118 animals. At least 41 of these PRSs are likely integrated within animal genomes in that they were also found within genomic sequence databases. Besides illuminating the ubiquity of parvoviruses, the number of parvoviral sequences discovered within public databases revealed numerous previously unknown parvovirus-host combinations; particularly in invertebrates. Our findings suggest that the host-ranges of extant parvoviruses might span the entire animal kingdom.

Role of the phosphatidylinositol-3-kinase/Akt/target of rapamycin pathway during ambidensovirus infection of insect cells

The phosphatidylinositol-3-kinase (PI3K)/Akt/target of rapamycin (TOR) signalling pathway controls cell growth and survival, and is targeted by a number of viruses at different phases of their infection cycle to control translation. Whether and how insect viruses interact with this pathway remain poorly addressed. Here, we investigated the role of PI3K/Akt/TOR signalling during lethal infection of insect cells with an insect parvovirus. Using Junonia coenia densovirus (JcDV; lepidopteran ambidensovirus 1) and susceptible insect cells as experimental models, we first described JcDV cytopathology, and showed that viral infection affects cell size, cell proliferation and survival. We deciphered the role of PI3K/Akt/TOR signalling in the course of infection and found that non-structural (NS) protein expression correlates with the inhibition of TOR and the shutdown of cellular synthesis, concomitant with the burst of viral protein expression. Together, these results suggest that NS proteins control the cellular translational machinery to favour the translation of viral mRNAs at the expense of cellular mRNAs. As a consequence of TOR inhibition, cell autophagy is activated. These results highlight new functions for NS proteins in the course of multiplication of an insect parvovirus.

Annotation pattern of ESTs from Spodoptera frugiperda Sf9 cells and analysis of the ribosomal protein genes reveal insect-specific features and unexpectedly low codon usage bias

MOTIVATION

A whole set of Expressed Sequence Tags (ESTs) from the Sf9 cell line of Spodoptera frugiperda is presented here for the first time. By this way we want to identify both conserved and specific genes of this pest species. We also expect from this analysis to find a class of protein sequences providing a tool to explore genomic features and phylogeny of Lepidoptera.

RESULTS

The ESTs display both housekeeping as well as developmentally regulated genes, and a high percentage of sequences with unknown function. Among the identified ORFs, almost all ribosomal proteins (RPs) were found with high EST redundancy and hence sequence accuracy. The codon usage found among RP genes is in average surprisingly much less biased in Lepidoptera than in other organisms. Other Spodoptera genes also displayed a low bias, suggesting a general genome expression feature in this Lepidoptera. We also found that the L35A and L36 RP sequences, respectively, display 40 and 10 amino-acid insertions, both being present only in insects. Sequence analysis suggests that they are probably not subjected to a strong selective pressure and may be good phylogenetic markers for Lepidoptera. Most interestingly, the Lepidoptera sequences of 9 RP genes displayed a specific signature different from the canonical one. We conclude that the RP family allows valuable comparative genomics and phylogeny of Lepidoptera.

AVAILABILITY

All EST sequence data are available from the private 'Spodo-Base' upon request.

Characterization of the cDNA encoding the 90 kDa heat-shock protein in the Lepidoptera Bombyx mori and Spodoptera frugiperda

This report presents the first hsp90 complete cDNA sequences from two Lepidoptera. The Bombyx mori full sequence was reconstituted from 15 partial cDNA clones belonging to expressed sequence tag libraries obtained from different tissues or cultured cells, thus showing the ubiquitous expression of the hsp90 gene. The Spodoptera frugiperda cDNA was isolated as a full-length clone from a cDNA library established from the Sf9 cell line. Both cDNAs are highly homologous and display the classical amino acid (aa) stretches representing the HSP90 signature. They potentially encode a 716 aa (B. mori) and a 717 aa (S. frugiperda) protein, with a calculated molecular mass of 83 kDa similar to the Drosophila homologous protein. We show that, unlike the vertebrates, hsp90 is a unique gene in both S. frupiperda and B. mori genomes. Sequencing of the corresponding genomic region shows that, contrary to the dipteran homologous gene, the lepidopteran hsp90 gene does not display any intron. Phylogenetic analysis based on the two lepidopteran and 23 other HSP90 aa sequences displays a high consistency with known phylogeny at both high and low taxonomic levels. Transcriptional analysis performed in S. frugiperda shows that the induction of the hsp90 gene only occurs 14 degrees C above physiological growth conditions (42 degrees C).