Incidental diagnosis of mpox virus infection in patients undergoing sexually transmitted infection screening-findings from a study in France

OBJECTIVES

This study aimed to investigate the prevalence of mpox virus (MPXV) infections in the general population consulting for routine sexually transmitted infections (STIs) in our Marseille public hospital. In fact, the recent worldwide MPXV outbreak mainly impacted men who have sex with men and the prevalence of MPXV infections in the general population remains poorly defined.

METHODS

All samples addressed routinely to our microbiological laboratory for STIs between July 1 and October 15, 2022 were screened with MPXV-specific quantitative polymerase chain reaction.

RESULTS

A total of 2688 samples from 1896 patients suspected of having STIs were tested and eight (0.4%) patients were incidentally diagnosed with MPXV infection, including six men and two women. MPXV was detected in rectal swabs (n = 2), urine (n = 2), vaginal swabs (n = 2), a urethral swab (n = 1), and a skin swab (n = 1).

CONCLUSIONS

This study suggests that some MPXV infections are likely to be underdiagnosed because of their non-specific clinical presentation and/or insufficient clinical knowledge of the disease. Our data showed that systematic screening was particularly useful for detecting MPXV in patients without classic lesions or cases of asymptomatic carriage in patients reporting recent high-risk exposure and in patients presenting no obvious risk factor.

How to distinguish mpox from its mimickers: An observational retrospective cohort study

During the current global outbreak of mpox (formerly monkeypox), atypical features were frequently described outside endemic areas, raising concerns around differential diagnosis. In this study, we included 372 adult patients who had clinical signs consistent with mpox and who were screened using non-variola orthopoxvirus specific quantitative polymerase chain reaction (PCR) between 15 May and 15 November 2022 at the University Hospital Institute Méditerranée Infection, Marseille, France. At least one clinical sample was positive for 143 (38.4%) of these patients and 229 (61.6%) were negative. Clinically, patients who had mpox presented more frequently with systemic signs (69.9% vs. 31.0%, p < 10-6 ) including fever (51.0% vs. 30.1%, p < 10-3 ), myalgia (33.5% vs. 17.9%, p = 0.002), and lymphadenopathy (38.5% vs. 13.1%, p < 10-6 ). Among the patients who were negative for the non-variola orthopoxvirus, an alternative diagnosis was identified in 58 of them (25.3%), including chickenpox (n = 30, 13.1%), syphilis (n = 9, 4%), bacterial skin infection (n = 8, 3.5%), gonococcus (n = 5, 2.2%), HSV infection (n = 5, 2.2%), and histoplasmosis (n = 1, 0.4%). Overall, in the current outbreak, we show that mpox has a poorly specific clinical presentation. This reinforces the importance of microbiological confirmation. In symptomatic patients who are negative for the monkeypox virus by PCR, a broad differential diagnosis should be maintained.

Temporal Shift of the Respiratory Syncytial Virus Epidemic Peak for the Years 2020-2023 in Marseille, Southern France

Respiratory syncytial virus is among the most common causes of respiratory infections. Typically, this viral infection has a seasonality during the cold months but with the SARS-CoV-2 pandemic this has been considerably modified. Here, we studied the epidemiology of this virus in university hospitals of Marseille, South of France, over the period 2020 to 2023. We tested in our laboratory from July 2020 to October 2021 16,516 nasopharyngeal swabs from 16,468 patients for RSV infection using different qPCR assays. We then analyzed data from previous and subsequent winters (from 2018 to 2023) and previous summers (from 2015 to 2021). A total of 676 patients were RSV-positive; their mean age was 3 years and 91 were under 5 years of age. We observed a delay of 4 months of the RSV epidemic's onset compared to other years with an epidemic that peaked in March 2021. We had significantly more RSV-positive cases during summer 2021 compared to previous summers, whereas the incidence of RSV infections was not significantly higher during winter 2022 versus previous winters. Moreover, 494 patients were diagnosed as RSV-positive in the emergency unit and 181 were subsequently hospitalized, and 34 patients were diagnosed RSV-positive while already in the intensive care unit. Over all the study periods, 38 patients diagnosed as RSV-positive died, the majority of whom (23/28) were over 65 years of age. These data show an atypical evolution of the incidence of RSV infections in our city and is another example of the unpredictability of infectious disease epidemiology.

Sequencing of monkeypox virus from infected patients reveals viral genomes with APOBEC3-like editing, gene inactivation, and bacterial agents of skin superinfection

A large outbreak of Monkeypox virus (MPXV) infections has arisen in May 2022 in nonendemic countries. Here, we performed DNA metagenomics using next-generation sequencing with Illumina or Nanopore technologies for clinical samples from MPXV-infected patients diagnosed between June and July 2022. Classification of the MPXV genomes and determination of their mutational patterns were performed using Nextclade. Twenty-five samples from 25 patients were studied. A MPXV genome was obtained for 18 patients, essentially from skin lesions and rectal swabbing. All 18 genomes were classified in clade IIb, lineage B.1, and we identified four B.1 sublineages (B.1.1, B.1.10, B.1.12, B.1.14). We detected a high number of mutations (range, 64-73) relatively to a 2018 Nigerian genome (genome GenBank Accession no. NC_063383.1), which were harbored by a large part of a set of 3184 MPXV genomes of lineage B.1 recovered from GenBank and Nextstrain; and we detected 35 mutations relatively to genome ON563414.3 (a B.1 lineage reference genome). Nonsynonymous mutations occurred in genes encoding central proteins, among which transcription factors and core and envelope proteins, and included two mutations that would truncate a RNA polymerase subunit and a phospholipase d-like protein, suggesting an alternative start codon and gene inactivation, respectively. A large majority (94%) of nucleotide substitutions were G > A or C > U, suggesting the action of human APOBEC3 enzymes. Finally, >1000 reads were identified as from Staphylococcus aureus and Streptococcus pyogenes for 3 and 6 samples, respectively. These findings warrant a close genomic monitoring of MPXV to get a better picture of the genetic micro-evolution and mutational patterns of this virus, and a close clinical monitoring of skin bacterial superinfection in monkeypox patients.

Protection from successive Omicron variants with SARS-CoV-2 vaccine and monoclonal antibodies in kidney transplant recipients

Introduction

Kidney transplant recipients (KTRs) are at high risk of severe COVID-19, even when they are fully vaccinated. Additional booster vaccinations or passive immunization with prophylactic monoclonal antibodies are recommended to increase their protection against severe COVID-19.

Methods

Here, we describe the neutralization of SARS-CoV-2 Delta, Omicron BA.1, BA.2, BA.4, and BA.5 variants, firstly by 39 serum samples from vaccinated KTRs exhibiting anti-spike antibody concentrations ≥264 binding antibody units (BAU)/mL and, secondly, by tixagevimab/cilgavimab.

Results

No neutralization was observed for 18% of the KTRs, while serum from only 46% of patients could neutralize the five variants. Cross-neutralization of the Delta and Omicron variants occurred for 65–87% of sera samples. The anti-spike antibody concentration correlated with neutralization activity for all the variants. The neutralization titers against the Delta variant were higher in vaccinated KTRs who had previously presented with COVID-19, compared to those KTRs who had only been vaccinated. Breakthrough infections occurred in 39% of the KTRs after the study. Tixagevimab/cilgavimab poorly neutralizes Omicron variants, particularly BA.5, and does not neutralize BQ.1, which is currently the most prevalent strain.

Discussion

As a result, sera from seropositive vaccinated KTRs had poor neutralization of the successive Omicron variants. Several Omicron variants are able to escape tixagevimab/cilgavimab.

Observational Cohort Study of Evolving Epidemiologic, Clinical, and Virologic Features of Monkeypox in Southern France

We enrolled 136 patients with laboratory-confirmed monkeypox during June 4-August 31, 2022, at the University Hospital Institute Méditerranée Infection in Marseille, France. The median patient age was 36 years (interquartile range 31-42 years). Of 136 patients, 125 (92%) were men who have sex with men, 15 (11%) reported previous smallpox vaccinations, and 21 (15.5%) were HIV-positive. The most frequent lesion locations were the genitals (68 patients, 53%), perianal region (65 patients, 49%), and oral/perioral area (22 patients, 17%). Lesion locations largely corresponded with the route of contamination. Most (68%) patients had isolated anal, genital, or oral lesions when they were first seen, including 56 (61%) who had >1 positive site without a visible lesion. Concurrent sexually transmitted infections were diagnosed in 19 (15%) patients, and 7 patients (5%) were asymptomatic. We recommend vaccination campaigns, intensified testing for sexually transmitted infections, and increased contact tracing to control the ongoing monkeypox outbreak.

Matrix-Encoding Gene Diversity of 624 Influenza A/H3N2 Genomes Does Not Show Association with Impaired Viral Detection by Commercialized qPCR Assays

As for the case of SARS-CoV-2, genome sequencing of influenza viruses is of potential interest to raise and address virological issues. Recently, false-negativity of real-time reverse transcription-PCR (qPCR) assays that detect influenza A/H3N2 virus RNA were reported and associated with two mutations (A37T and C161T) in the Matrix-encoding (M1) gene located on viral segment 7. This triggered a national alert in France. The present study sought to assess the association between the presence of these mutations and potential false negative results of influenza A/H3N2 virus RNA detection by commercialized qPCR assays at the clinical virology laboratory of our university hospitals in southern France. This study focused on the genetic diversity in the M1 gene and segment 7 of 624 influenza A/H3N2 virus genomes obtained from respiratory samples having tested qPCR-positive with M1 gene-targeting assays in our clinical virology laboratory. A total of 585 among the 624 influenza A/H3N2 virus genomes (93.7%) were of clade 3C.2a1b.2a.2, and 39 (6.3%) were of clade 3C.2a1b.1a. M1 gene substitutions A37T and C161T were both present in 582 (93.3%) genomes, only of clade 3C.2a1b.2a.2. Substitution A37T was present in 621 (99.5%) genomes. Substitution C161T was present in 585 genomes (93.8%), all of clade 3C.2a1b.2a.2. Moreover, 21 other nucleotide positions were mutated in ≥90% of the genomes. The present study shows that A37T/C and C161T mutations, and other mutations in the M1 gene and segment 7, were widely present in influenza A/H3N2 virus genomes recovered from respiratory samples diagnosed qPCR-positive with commercialized assays.

Choosing a cellular model to study SARS-CoV-2

As new pathogens emerge, new challenges must be faced. This is no different in infectious disease research, where identifying the best tools available in laboratories to conduct an investigation can, at least initially, be particularly complicated. However, in the context of an emerging virus, such as SARS-CoV-2, which was recently detected in China and has become a global threat to healthcare systems, developing models of infection and pathogenesis is urgently required. Cell-based approaches are crucial to understanding coronavirus infection biology, growth kinetics, and tropism. Usually, laboratory cell lines are the first line in experimental models to study viral pathogenicity and perform assays aimed at screening antiviral compounds which are efficient at blocking the replication of emerging viruses, saving time and resources, reducing the use of experimental animals. However, determining the ideal cell type can be challenging, especially when several researchers have to adapt their studies to specific requirements. This review strives to guide scientists who are venturing into studying SARS-CoV-2 and help them choose the right cellular models. It revisits basic concepts of virology and presents the currently available in vitro models, their advantages and disadvantages, and the known consequences of each choice.

Antiviral Activity of Repurposing Ivermectin against a Panel of 30 Clinical SARS-CoV-2 Strains Belonging to 14 Variants

Over the past two years, several variants of SARS-CoV-2 have emerged and spread all over the world. However, infectivity, clinical severity, re-infection, virulence, transmissibility, vaccine responses and escape, and epidemiological aspects have differed between SARS-CoV-2 variants. Currently, very few treatments are recommended against SARS-CoV-2. Identification of effective drugs among repurposing FDA-approved drugs is a rapid, efficient and low-cost strategy against SARS-CoV-2. One of those drugs is ivermectin. Ivermectin is an antihelminthic agent that previously showed in vitro effects against a SARS-CoV-2 isolate (Australia/VI01/2020 isolate) with an IC50 of around 2 µM. We evaluated the in vitro activity of ivermectin on Vero E6 cells infected with 30 clinically isolated SARS-CoV-2 strains belonging to 14 different variants, and particularly 17 strains belonging to six variants of concern (VOC) (variants related to Wuhan, alpha, beta, gamma, delta and omicron). The in vitro activity of ivermectin was compared to those of chloroquine and remdesivir. Unlike chloroquine (EC50 from 4.3 ± 2.5 to 29.3 ± 5.2 µM) or remdesivir (EC50 from 0.4 ± 0.3 to 25.2 ± 9.4 µM), ivermectin showed a relatively homogeneous in vitro activity against SARS-CoV-2 regardless of the strains or variants (EC50 from 5.1 ± 0.5 to 6.7 ± 0.4 µM), except for one omicron strain (EC50 = 1.3 ± 0.5 µM). Ivermectin (No. EC50 = 219, mean EC50 = 5.7 ± 1.0 µM) was, overall, more potent in vitro than chloroquine (No. EC50 = 214, mean EC50 = 16.1 ± 9.0 µM) (p = 1.3 × 10-34) and remdesivir (No. EC50 = 201, mean EC50 = 11.9 ± 10.0 µM) (p = 1.6 × 10-13). These results should be interpreted with caution regarding the potential use of ivermectin in SARS-CoV-2-infected patients: it is difficult to translate in vitro study results into actual clinical treatment in patients.

Control of common viral epidemics but not of SARS-CoV-2 through the application of hygiene and distancing measures

Background

We systematically survey respiratory and gastrointestinal infections of viral origin in samples sent to our university hospital institute in Marseille, southern France. Here, we evaluated whether the measures implemented to fight COVID-19 had an effect on the dynamics of viral respiratory or gastrointestinal infections.

Methods

We analysed PCR performed and positive for the diagnoses of viral respiratory and gastrointestinal infections over five years (January 2017-February 2021). Data were collected from our epidemiological surveillance system (MIDaS). Dates and contents of French measures against SARS-CoV-2 were collected from: https://www.gouvernement.fr/info-coronavirus/les-actions-du-gouvernement.

Results

Over the 2017-2021 period, 990,364 analyses were carried out for respiratory infections not including SARS-CoV-2, 510,671 for SARS-CoV-2 and 27,719 for gastrointestinal infections. During winter 2020–2021, when the most restrictive lockdown measures were in place in France, a marked decrease of infections with influenza viruses (one case versus 1,839-1,850 cases during 2017-2020 cold seasons) and with the RSV (56 cases versus 988-1,196 cases during 2017-2020 cold seasons) was observed, demonstrating the relative effectiveness of these measures on their occurrence. SARS-CoV-2 incidence seemed far less affected. Rhinoviruses, parainfluenza 3 virus, and the coronavirus NL63 remained at comparable levels. Also, the norovirus winter season positivity rates decreased continuously and significantly over time from 9.3% in 2017–2018 to 2.0% in 2020–2021.

Conclusion

The measures taken to control COVID-19 were effective against lower respiratory tract infections viruses and gastroenteritis agents, but not on the agents of the common winter cold and SARS-CoV-2. This suggests that more specific measures to prevent COVID-19 and upper respiratory tract infections need to be discovered to limit the spread of this epidemic.

First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France

The SARS‐CoV‐2 21K/BA.1, 21L/BA.2, and BA.3 Omicron variants have recently emerged worldwide. To date, the 21L/BA.2 Omicron variant has remained very minority globally but became predominant in Denmark instead of the 21K/BA.1 variant. Here, we describe the first cases diagnosed with this variant in south‐eastern France. We identified 13 cases using variant‐specific qPCR and next‐generation sequencing between 28/11/2021 and 31/01/2022, the first two cases being diagnosed in travelers returning from Tanzania. Overall, viral genomes displayed a mean (±standard deviation) number of 65.9 ± 2.5 (range, 61–69) nucleotide substitutions and 31.0 ± 8.3 (27–50) nucleotide deletions, resulting in 49.6 ± 2.2 (45–52) amino acid substitutions (including 28 in the spike protein) and 12.4 ± 1.1 (12–15) amino acid deletions. Phylogeny showed the distribution in three different clusters of these genomes, which were most closely related to genomes from England and South Africa, from Singapore and Nepal, or from France and Denmark. Structural predictions highlighted a significant enlargement and flattening of the surface of the 21L/BA.2 N‐terminal domain of the spike protein compared to that of the 21K/BA.1 Omicron variant, which may facilitate initial viral interactions with lipid rafts. Close surveillance is needed at global, country, and center scales to monitor the incidence and clinical outcome of the 21L/BA.2 Omicron variant.

Bioaccumulation and biomagnification in elasmobranchs: A concurrent assessment of trophic transfer of trace elements in 12 species from the Indian Ocean

We provided the first multi-species study investigating the presence and organotropism of trace elements in three tissues of 12 elasmobranch species. Shark species showed comparable TE loads, although milk sharks and juvenile scalloped hammerhead sharks exhibited the highest Cd and Hg levels, respectively. Fins accumulated higher levels of Pb, Co, and Cr; muscles higher V, As, and Hg; livers higher Se and Cd levels. The organotropism of TEs calls for cautious when choosing a tissue to be sampled since certain tissues, like fin clips, do not provide reliable surrogate for the internal loads of some TEs. Strong correlations between essential and toxic TEs indicated detoxification mechanisms, while the TMF provided evidence for Hg, As and Se biomagnification along the food-web. Considering the difficulties in assessing elasmobranchs contamination from different areas, the proposed multi-species approach represents a valuable way to estimate the species-specific accumulation and transfer of pollutants in sharks.

Épidémiologie des Coronavirus 229E dans les infections respiratoires

Introduction

Les infections respiratoires représentent une part majeure des infections humaines. Certaines études ont centré le cadre de leur prospection à des services hospitaliers délimités comme les soins intensifs, à des pathogènes déterminés (Souty et al., 2019) ou encore à des zones géographiques restreintes (Masse et al., 2017) afin d’en déterminer les risques pour la population. Ce sont les infections à Picornavirus qui sont le plus fréquemment diagnostiquées (Ambrosioni et al., 2014 ; Monto et al., 2001) mais on observe également une part importante d’infections virales multiples. L’utilisation récente de systèmes de détection multiplexés permet actuellement d’énumérer avec précision les agents étiologiques rencontrés en France. Nous décrivons ici les caractéristiques épidémiologiques et cliniques de 72 cas d’infections à Coronavirus 229E diagnostiquées sur une période couvrant janvier 2017 à décembre 2019.

Matériels et méthodes

Les prélèvements par écouvillonnage pharyngé et nasal ainsi que les prélèvements de liquide bronchoalvéolaire, réalisés entre janvier 2017 à décembre 2019 et testés par biologie moléculaire, ont été adressés au laboratoire de diagnostic pour recherche de virus respiratoires. Le diagnostic de 16 357 échantillons a été réalisé par PCR temps réel avec les trousses FTD Respiratory pathogens 21 (Fast Track Diagnosis, Luxembourg) ou Biofire Filmarray Respiratory panel 2 plus (Biomérieux, France).

Résultats

Un total de 16 357 prélèvements respiratoires issus de 11 976 patients a été testé sur la période de janvier 2017 à décembre 2019. Parmi ceux-ci, on distingue 554 prélèvements positifs à Coronavirus pour 483 patients. L’identification des Coronavirus a permis de déterminer que 79 prélèvements étaient positifs à Coronavirus 229E issues de 72 patients soit 14,9 % (72/483). Parmi eux, 4 patients présentaient une co-infection avec un autre sous-type de Coronavirus : 2 avec les sous-types OC43 et 2 avec les sous-types NL63. Un des 72 patients est décédé en service de réanimation en novembre 2019 et nous avons détecté 5 jours après son admission la présence de Coronavirus 229E dans son liquide bronchoalvéolaire. Il présentait un tableau clinique dégradé avec un syndrome de détresse respiratoire. Ce patient de 62 ans avait reçu une greffe bi-pulmonaire en janvier 2019 suite à une pneumopathie interstitielle non spécifique compliquée d’une hypertension artérielle pulmonaire. Il se trouvait en situation de rejet de greffe et a présenté aux cours de son hospitalisation des co-infections pulmonaires à Klebsiella pneumoniae BLSE et Mycoplasma pneumoniae.

Conclusion

Sur la période étudiée, nous avons pu détecter et classifier 554 prélèvements positifs à Coronavirus. Soixante-douze patients ont présenté le sous-type 229E, ce qui représente une proportion plus importantes qu’une étude réalisée chez les enfants (Vabret et al., 2008). Ce sous-type 229E a été in vitro associé à une mortalité des cellules dendritiques (Mesel-Lemoine et al., 2012).

Caractéristiques épidémiologiques et cliniques de 136 infections à coronavirus OC43 diagnostiquées dans des hôpitaux universitaires de 2017 à 2019

Introduction

Matériels et méthodes

Résultats

Conclusion

Children account for a small proportion of diagnoses of SARS-CoV-2 infection and do not exhibit greater viral loads than adults

Previous reports have suggested that children are less affected than adults by SARS-CoV-2. We analyzed SARS-CoV-2 diagnoses between February 27, 2020, and March 14, 2020, and mortality among positive patients in Marseille university hospitals. Of 4050 tested individuals, 228 were positive. Deaths occurred in 2/99 documented cases (both > 85 year-old). Children were majorly asymptomatic. Incidence increased by 7.4-fold between 1–5 and 45–65 years then decreased. It was significantly lower among 0–1 year- (0%) and 1–5 (1.1%) and 5–10 (3.6%)-year-old children than among subjects > 18 years (6.5%). Viral loads did not differ between children and adults. Children may not contribute significantly to virus circulation.

[Regional differentials in cancer mortality in the state of Rio de Janeiro, Brazil, 1979-1981]

In 1980, malignant neoplasms ranked 3rd as a cause of death in the State of Rio de Janeiro, Brazil, with a crude mortality rate of 89.8 per 100,000. Cancer mortality data for 1979-1981 are presented for the State, with the objective of analyzing regional differentials. For the purpose of comparing mortality from the most important cancers, the State was divided into three regions: Capital, Metropolitan Belt and Interior, on the basis of the geographical structure of the State--which gave rise to the present urbanization patterns. Average annual age and sex-specific mortality rates per 100,000 were calculated for the period 1979-1981 for each cancer site and for 5-year age groups up to 79 years and for 80 years and above. Age standardized rates (ASR) were calculated by direct standardization to the world population and standardized mortality ratios (SMR) were also calculated with the objective of comparing different geographical areas. It was found that the most important malignant neoplasms among males were those of the lung (ASR 27.9), stomach (ASR 24.0), prostate, oesophagus and liver. The breast was the most important site for females (ASR 16.0), followed by the stomach (ASR 10.8), lung, cervix uteri and uterus (unspecified). The highest ASR were in the Capital (164.4 in males, 106.2 in females) and the lowest in the Interior (126.5 in males, and 91.3 in females). The highest SMR were found for breast (1.28), colon (1.71) and lung (1.70) cancers, the mortality rates for which were almost two-times higher in the Capital than in the Interior.(ABSTRACT TRUNCATED AT 250 WORDS)