BA.2.86 variant emergence and spread dynamics through wastewater monitoring in Paris, France

Numerous SARS-CoV-2 variants are emerging as the epidemic continues, inducing new waves of contamination. In July 2023, a new variant named BA.2.86 was identified, raising concerns about its potential for viral escape, even in an immune population. The reduction in patient-centered testing and the identification of variants by sequencing means that we are now blind to the spread of this new variant. The aim of this study was to track the signature of this variant in wastewater in Paris, France. This variant showed a very rapid spread, highly correlated with national flash studies involving sequencing of clinical samples, but with a moderate impact on virus circulation. This easy-to-implement approach enabled us to monitor the emergence and spread of this new variant in real time at low cost.

From Alpha to Omicron BA.2: New digital RT-PCR approach and challenges for SARS-CoV-2 VOC monitoring and normalization of variant dynamics in wastewater

Throughout the COVID-19 pandemic, new variants have continuously emerged and spread in populations. Among these, variants of concern (VOC) have been the main culprits of successive epidemic waves, due to their transmissibility, pathogenicity or ability to escape the immune response. Quantification of the SARS-CoV-2 genomes in raw wastewater is a reliable approach well-described and widely deployed worldwide to monitor the spread of SARS-CoV-2 in human populations connected to sewage systems. Discrimination of VOCs in wastewater is also a major issue and can be achieved by genome sequencing or by detection of specific mutations suggesting the presence of VOCs. This study aimed to date the emergence of these VOCs (from Alpha to Omicron BA.2) by monitoring wastewater from the greater Paris area, France, but also to model the propagation dynamics of these VOCs and to characterize the replacement kinetics of the prevalent populations. These dynamics were compared to various individual-centered public health data, such as regional incidence and the proportions of VOCs identified by sequencing of strains isolated from patient. The viral dynamics in wastewater highlighted the impact of the vaccination strategy on the viral circulation within human populations but also suggested its potential effect on the selection of variants most likely to be propagated in immunized populations. Normalization of concentrations to capture population movements appeared statistically more reliable using variations in local drinking water consumption rather than using PMMoV concentrations because PMMoV fecal shedding was subject to variability and was not sufficiently relevant in this study. The dynamics of viral spread was observed earlier (about 13 days on the wave related to Omicron VOC) in raw wastewater than the regional incidence alerting to a possible risk of decorrelation between incidence and actual virus circulation probably resulting from a lower severity of infection in vaccinated populations.

SARS-CoV-2 genome quantification in wastewaters at regional and city scale allows precise monitoring of the whole outbreaks dynamics and variants spreading in the population

SARS-CoV-2 is a coronavirus causing a globalized outbreak called COVID-19. SARS-CoV-2 transmission is associated with inhalation of contaminated respiratory droplets and could causes severe complications. Until today several "waves" of infections have been observed despite implementation of strict health policies. Decisions for such sanitary measures are based on population health monitoring. Unfortunately, for COVID-19, a significant proportion of individuals are asymptomatic but play a role in the virus transmission. To overcome these limitations, several strategies were developed including genome quantification in wastewater that could allow monitoring of the health status of population, since shedding of SARS-CoV-2 in patient stool is frequent. Wastewater-based epidemiology (WBE) was established and several countries implemented this approach to allow COVID-19 outbreak monitoring. In France, the OBEPINE project performed a quantitative analysis of SARS-CoV-2 in raw wastewater samples collected from major wastewater treatment plants (WWTP) since March 2020. In the greater Paris area 1101 samples (507 for five WWTP and 594 for sewer) were collected. This 16 months monitoring allows us to observe the outbreak dynamics. Comparison of WBE indicators with health data lead to several important observation; the good level of correlation with incidence rates, the average 3 days lead time, and the sensitivity (WBE change when incidence is > to 7/100000 inhabitants). We also compared the local monitoring (city level) with the regional monitoring, to help cluster identification. Moreover, variants of concern (VOC) emerged due to the selection pressure. We developed a specific RT-qPCR method targeting the deletion H69-V70 in the spike protein, using this deletion as a proxy of the B.1.1.7 presence in the wastewater. With this data we demonstrate the predominant role played by this strain in the third wave. All these results allow a better description and understanding of the pandemic and highlight the role of such WBE indicators.

Structural and functional studies of the metalloregulator Fur identify a promoter-binding mechanism and its role in Francisella tularensis virulence

Francisella tularensis is a Gram-negative bacterium causing tularaemia. Classified as possible bioterrorism agent, it may be transmitted to humans via animal infection or inhalation leading to severe pneumonia. Its virulence is related to iron homeostasis involving siderophore biosynthesis directly controlled at the transcription level by the ferric uptake regulator Fur, as presented here together with the first crystal structure of the tetrameric F. tularensis Fur in the presence of its physiological cofactor, Fe²⁺. Through structural, biophysical, biochemical and modelling studies, we show that promoter sequences of F. tularensis containing Fur boxes enable this tetrameric protein to bind them by splitting it into two dimers. Furthermore, the critical role of F. tularensis Fur in virulence and pathogenesis is demonstrated with a fur-deleted mutant showing an attenuated virulence in macrophage-like cells and mice. Together, our study suggests that Fur is an attractive target of new antibiotics that attenuate the virulence of F. tularensis.

Pérard et al. report the structure of Francisella tularensis Fur (FtFur) with its physiological cofactor Fe²⁺, and show that FtFur is important for virulence. This study identifies a promoter-driven tetramer splitting mechanism that may provide insight into future antibiotics development.

[Helical CT pelvimetry: advantages of a low dose volume acquisition technique]

The authors evaluate the accuracy of a new CT pelvimetry technique that allows faster and low dose acquisition, and provides an axial view of the true conjugate as well as a 3D view of the maternal pelvis. Made possible by the availability of MDCT, this new technique may be a good alternative to standard CT pelvimetry even if MR pelvimetry still appears as the gold standard.

[Local investigation concerning psychic and sexual functioning a short time after hysterectomy]

Hysterectomy is one of the most common operations done throughout the world. Patients' concerns about sexual functioning after hysterectomy is great.

OBJECTIVE

We wanted to evaluate, through a local investigation based on a questionnaire, the psychosexual impact of this operation and to compare our data to those available in the literature.

PATIENTS AND METHODS

534 patients operated between of 01.01.1997 and 31.12.1997 for a benign uterine pathology (prolapse excluded) were included. Questions were about sexual and psychological functioning after hysterectomy. The main outcome measures were changes in the sexual life, sexual desire, orgasm, dyspareunia, frequency of sexual relations. Abdominal and vaginal surgical approaches were compared for some items when possible.

RESULTS

After the operation, 83.3% of the patients felt better, 30.4% of the patients mentioned changes in their sexual life, 32% of low libido rates was noticed (and there was a significant difference between abdominal and vaginal surgical approaches), 27.6% of the patients had less frequent orgasm and only 8.8% experienced orgasm more frequently, 15% suffer from dyspareunia, and 15% were more engaged in sexual intercourse.

CONCLUSION

Psychosexual impact of hysterectomy is limited and is not more frequent when vaginal surgery is performed, but pre- and post-operative prevention can be useful.

[Human papillomavirus typing in routine cervical smears. Results from a series of 3778 patients]

AIM

As human papillomavirus (HPV) infection is a significant risk factor for cervical cancer, the aim of this study was to assess the efficacy of HPV detection techniques in predicting the presence or the development of a high-grade squamous intra epithelial lesion. Additional reasons for carrying out this investigation were as follows. It was considered that the clinical value of HPV typing may have been underestimated in certain previous reports, which based their findings on first-generation assays. Moreover, until the present investigation most studies only investigated the cases with abnormal smear findings and did not include long-term follow-up, nor detailed follow-up of women with a normal smear but positive HPV typing, although this patient subgroup is of particular interest. The patient population included 3778 women who underwent routine cytological cervical screening and who gave their informed consent to participate in this study, consisting of a cervical smear, HPV testing via a second-generation Hybrid Capture II assay (which is more sensitive than first-generation tests, and can detect 18 different HPV types, i.e., 13 oncogenic and five non-oncogenic types); and in the case of abnormal smear findings, colposcopic examination and directed biopsies of the sites of suspected lesions. The women with cytomorphologically normal cervical smears but which who HPV-positive were reexamined six months later.

RESULTS

HPV findings were positive in 66 cases where the initial smear indicated the presence of a high-grade lesion with the diagnosis confirmed by biopsy in 65 cases; in 155 cases (76.1%) where the initial smear indicated the presence of a low-grade lesion; in 44 (57.1%) out of 77 smears indicating the presence of ASCUS-type (atypical squamous cells of undetermined significance) lesions; and in 366 cases (10.5%) of apparently normal initial smears. After colposcopy and follow-up, a final diagnosis of high-grade lesion was made for 85 patients. All these patients were found to have high-risk (oncogene-positive) HPV at the first examination, but in only 65 cases (76.5%) was the initial smear indicative of a high-grade lesion. Finally, in the patient groups with low-grade or ASCUS-type smear findings or with an apparently normal smear, a high-grade lesion was only found in those patients with persistent high-risk HPV infection. In all, the sensitivity of the Hybrid Capture II assay in detecting high-grade lesions was 100% versus 85.9% for standard cytology. However, its specificity (86.3%) and positive predictive value were not as high as the latter.

CONCLUSION

The results of this study indicate that HPV typing via this second-generation assay displays good sensitivity for the detection of at-risk cases, i.e., those involving the presence or development of high-grade cervical lesions. However, a number of issues have to be addressed before HPV typing is adopted in clinical practice, such as the fairly high HPV prevalence in women aged over 60 years, and whether the implications of this are the same as for younger age groups. Also, the present cost of complete typing remains too high for it to be used on a widespread scale. Nevertheless, HPV typing may have a useful role to play in the detection of cervical cancer.

Human papillomavirus detection by the hybrid capture II assay: a reliable test to select women with normal cervical smears at risk for developing cervical lesions

The reliability of the Hybrid Capture II (HC-II; Digene, Silver Spring, MD, U.S.A.) assay was tested in detecting 18 human Papillomavirus (HPV) types for the screening of cervical lesions. Cytology, HPV testing, colposcopy, and biopsy were used to monitor 204 women with normal smears at the first entry. The median follow-up was 15 months (range, 4-27 months). The primary endpoint was clinical progression defined as the presence of a cervical intraepithelial lesion at the biopsy. In the patient population of 204 HPV-infected women, 81 (39.7%) had a persistent HPV infection at two or three examinations with a final histologic diagnosis of 14 high-grade and 13 low-grade squamous intraepithelial lesions (SIL) within 4 to 22 months. Women with regressive HPV infection did not develop any lesion during the same period. The evaluation of the viral load of high-risk HPV by the HC-II did not represent a sensitive approach to predict the persistence or the apparition of high-grade lesions. Thus, persistent high-risk HPV infection detected with HC-II represents a reliable tool to select populations at risk for the development of high-grade cervical lesions.