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Objectives: We attempted to establish a molecular investigation by Next Generation sequencing of the measles virus (MeV) strains circulating in Marseille-France during the last outbreak that occurred between 2017 and 2019.Methods: The circulating MeV were isolated from clinical samples using cell culture method and whole genomes were sequenced by Illumina Miseq Next Generation. Genotyping and comparative analyses were assessed by phylogenetic reconstructions. Clinical and epidemiological data from cases were also recorded.Results: A total of 110 MeV strains were isolated in cell culture. Our analysis based on whole genome sequences of 98 isolates confirmed that 93 strains belonged to the genotype D8 and 5 to the genotype B3. Phylogenetic analyses revealed 4 distinct MeV circulating clones in Marseille. Measles mostly occured in children < 5 years-old and in adults 30-50 years-old. Measles infection also occurred in 2 adequately vaccinated cases (2 doses). Among 63 measles cases of whom we had available clinical data informations, a total of 35 patients were hospitalized and 19 developed complications including one death case recorded.Conclusions: Whole Genome Sequencing seems to be a useful tool for more refined genomic characterization of large measles outbreak. Vaccination strategies for measles eradication need to be re-evaluated in the current context. [ABSTRACT FROM AUTHOR]

The SARS-CoV-2 pandemic and large-scale genomic surveillance provided an exceptional opportunity to analyze mutations that appeared over three years in viral genomes. Here we studied mutations and their epidemic consequences for SARS-CoV-2 genomes from our center. We analyzed 61,397 SARS-CoV-2 genomes we sequenced from respiratory samples for genomic surveillance. Mutations frequencies were calculated using Nextclade, Microsoft Excel, and an in-house Python script. A total of 22,225 nucleotide mutations were identified, 220 (1.0%) being each at the root of ≥836 genomes, classifying mutations as 'hyperfertile'. Two seeded the European pandemic: P323L in RNA polymerase, associated with an increased mutation rate, and D614G in spike that improved fitness. Most 'hyperfertile' mutations occurred in areas not predicted with increased virulence. Their mean number was 8±6 (0–22) per 1000 nucleotides per gene. They were 3.7-times more frequent in accessory than informational genes (13.8 versus 3.7/1000 nucleotides). Particularly, they were 4.1-times more frequent in ORF8 than in the RNA polymerase gene. Interestingly, stop codons were present in 97 positions, almost only in accessory genes, including ORF8 (21/100 codons). most 'hyperfertile' mutations did not predict emergence of a new epidemic, and some were stop codons indicating the existence of so-named 'non-virulence' genes. • Mutations and their epidemic consequences for 61,397 SARS genomes were studied. • Among 22,225 nucleotide mutations, 220 (1.0%) were classified as 'hyperfertile'. • These latter were 3.7-times more frequent in accessory than informational genes. • Stop codons were present almost only in accessory genes including ORF8. • Most 'hyperfertile' mutations did not predict emergence of a new epidemic. [ABSTRACT FROM AUTHOR]

Background Health care–associated infections (HAIs) are a major cause of morbidity and mortality in intensive care unit (ICU) patients. Our objective was to evaluate the impact of daily bathing with chlorhexidine gluconate (CHG) on the incidence rates of HAIs, with a focus on their causative bacteria, in a French ICU. Methods From March 2012-May 2013, we enrolled 325 patients with at least 1 episode of suspected sepsis in the ICU, during two 6-month periods. The intervention group was subjected daily to skin cleansing with 2% CHG–impregnated cloths, whereas the control group was bathed daily with soap and water. HAI included bloodstream infections, ventilator-associated pneumonia, and urinary tract infections. Incidence rates corresponded to the number of infections per 1,000 patient days. Results Incidence of HAI was significantly decreased in the intervention group (29 vs 56; P = .01). After adjustment for baseline patient characteristics, the increased risk of HAI in the water and soap group was significant (odds ratio = 1.993; 95% confidence interval [CI], 1.132-3.508; P = .017). The incidence rate of clinical cultures positive for gram-negative bacteria, including Enterobacteriaceae and nonfermenting bacilli, decreased in the intervention group (risk ratio = 0.588; 95% CI, 0.346-0.978; P = .04). Conclusions CHG daily cleansing reduced the incidence rate of HAI caused by gram-negative bacteria, highlighting the role of the transient gram-negative bacteria skin colonization in the pathogenesis of HAI. [ABSTRACT FROM AUTHOR]

We describe the epidemiology of the first cases diagnosed in our institute of infections with the SARS-CoV-2 Beta variant and how this variant was imported to Marseille. The Beta variant was identified based on analyses of sequences of viral genomes or of a spike gene fragment obtained by next-generation sequencing using Illumina technology, or by a real-time reverse-transcription-PCR (qPCR) specific of the Beta variant. The first patient diagnosed as infected with the SARS-CoV-2 Beta variant was sampled on January 15, 2021. Twenty-nine patients were diagnosed in January 2021 (two weeks). Fifteen (52%) patients were of Comorian nationality. Eight (28%) had travelled abroad, including six who had returned from Comoros. Phylogeny based on SARS-CoV-2 genomes from 11 of these patients and their best BLAST hits from the GISAID database showed that seven patients, including the four returning from Comoros, were clustered with 27 other genomes from GISAID that included the six first Beta variant genomes described in Comoros in January 2021. Our analyses highlight that, as for the case of other SARS-CoV-2 variants that have been diagnosed in Marseille, the Beta variant was imported to Marseille through travel from abroad. It had limited spread in our geographical area. • First cases with the SARS-CoV-2 Beta variant in Marseille were in Comorian people. • The Beta variant had limited spread in our geographical area. • Travels abroad create favourable conditions for the spread of SARS-CoV-2 variants. • Genomic surveillance is needed to decipher variants' epidemiological features. [ABSTRACT FROM AUTHOR]

Summary: A patient presented diffuse pulmonary parenchymal micronodules. Tropheryma whipplei was detected in the saliva, a bronchial biopsy and bronchoalveolar fluid. PAS staining, immunohistochemistry and PCR for T. whipplei were negative in the duodenal biopsies. T. whipplei was isolated from the bronchoalveolar fluid, reinforcing its role as a respiratory pathogen. [Copyright &y& Elsevier]

The purpose of the study was to challenge the hypothesis of an introduction of influenza viruses by international travellers and subsequent local circulation in Marseille, France. We analysed the epidemiological data of PCR-confirmed cases over an eight-year period and compared the genomic data of local and imported influenza viruses during a six-month period. Between June 2013 and December 2020, 12,434 patients in the Assistance Publique–Hospitaux de Marseille were diagnosed with an influenza virus infection at the laboratory of the Institut Hospitalo-Universitaire Méditerranéee Infection of Marseille. Half of the patients were below the age of 20. Most of the imported cases were diagnosed outside of epidemic periods. Fourteen genomes of the influenza A virus, including six in international travellers returning from Europe or from the Arabian Peninsula and eight from patients who had not travelled were analysed. Sequences of influenza A/H1N1 virus genomes detected in subjects who had travelled to Saudi Arabia were in the same clade and differed from sequences detected later in a traveller returning from Italy, and in non-travellers who were infected in Marseille. This suggests that influenza viruses imported from Saudi Arabia did not subsequently circulate in Marseille. Future studies with higher numbers of genomes are needed to confirm this result. [ABSTRACT FROM AUTHOR]

Using an amoebal co-culture procedure, a novel α-Proteobacterium phylogenetically close to two uncultured aquatic bacteria was isolated. On the basis of phenotypic characterization and 16S rRNA gene sequence analysis, we propose the new genus and species Nordella oligomobilis gen. nov., sp. nov. The genus Nordella forms a well separated taxon in the order Rhizobiales within the α-2 subgroup of Proteobacteria. Its close relatives are environmental uncultured bacteria. [Copyright &y& Elsevier]

In December 2019, a new severe acute respiratory syndrome coronavirus (SARS-CoV-2) causing coronavirus diseases 2019 (COVID-19) emerged in Wuhan, China. African countries see slower dynamic of COVID-19 cases and deaths. One of the assumptions that may explain this later emergence in Africa, and more particularly in malaria endemic areas, would be the use of antimalarial drugs. We investigated the in vitro antiviral activity against SARS-CoV-2 of several antimalarial drugs. Chloroquine (EC 50 = 2.1 μM and EC 90 = 3.8 μM), hydroxychloroquine (EC 50 = 1.5 μM and EC 90 = 3.0 μM), ferroquine (EC 50 = 1.5 μM and EC 90 = 2.4 μM), desethylamodiaquine (EC 50 = 0.52 μM and EC 90 = 1.9 μM), mefloquine (EC 50 = 1.8 μM and EC 90 = 8.1 μM), pyronaridine (EC 50 = 0.72 μM and EC 90 = 0.75 μM) and quinine (EC 50 = 10.7 μM and EC 90 = 38.8 μM) showed in vitro antiviral effective activity with IC 50 and IC 90 compatible with drug oral uptake at doses commonly administered in malaria treatment. The ratio C lung /EC 90 ranged from 5 to 59. Lumefantrine, piperaquine and dihydroartemisinin had IC 50 and IC 90 too high to be compatible with expected plasma concentrations (ratio C max /EC 90 < 0.05). Based on our results, we would expect that countries which commonly use artesunate-amodiaquine or artesunate-mefloquine report fewer cases and deaths than those using artemether-lumefantrine or dihydroartemisinin-piperaquine. It could be necessary now to compare the antimalarial use and the dynamics of COVID-19 country by country to confirm this hypothesis. [ABSTRACT FROM AUTHOR]

In our institute in Marseille, France, we initiated early and massive screening for coronavirus disease 2019 (COVID-19). Hospitalization and early treatment with hydroxychloroquine and azithromycin (HCQ-AZ) was proposed for the positive cases. We retrospectively report the clinical management of 3,737 screened patients, including 3,119 (83.5%) treated with HCQ-AZ (200 mg of oral HCQ, three times daily for ten days and 500 mg of oral AZ on day 1 followed by 250 mg daily for the next four days, respectively) for at least three days and 618 (16.5%) patients treated with other regimen ("others"). Outcomes were death, transfer to the intensive care unit (ICU), ≥10 days of hospitalization and viral shedding. The patients' mean age was 45 (sd 17) years, 45% were male, and the case fatality rate was 0.9%. We performed 2,065 low-dose computed tomography (CT) scans highlighting lung lesions in 592 of the 991 (59.7%) patients with minimal clinical symptoms (NEWS score = 0). A discrepancy between spontaneous dyspnoea, hypoxemia and lung lesions was observed. Clinical factors (age, comorbidities, NEWS-2 score), biological factors (lymphocytopenia; eosinopenia; decrease in blood zinc; and increase in D-dimers, lactate dehydrogenase, creatinine phosphokinase, troponin and C-reactive protein) and moderate and severe lesions detected in low-dose CT scans were associated with poor clinical outcome. Treatment with HCQ-AZ was associated with a decreased risk of transfer to ICU or death (Hazard ratio (HR) 0.18 0.11–0.27), decreased risk of hospitalization ≥10 days (odds ratios 95% CI 0.38 0.27–0.54) and shorter duration of viral shedding (time to negative PCR: HR 1.29 1.17–1.42). QTc prolongation (>60 ms) was observed in 25 patients (0.67%) leading to the cessation of treatment in 12 cases including 3 cases with QTc> 500 ms. No cases of torsade de pointe or sudden death were observed. Although this is a retrospective analysis, results suggest that early diagnosis, early isolation and early treatment of COVID-19 patients, with at least 3 days of HCQ-AZ lead to a significantly better clinical outcome and a faster viral load reduction than other treatments. [ABSTRACT FROM AUTHOR]

Rapid virological diagnosis is needed to limit the length of isolation for suspected COVID-19 cases. We managed the first 280 patients suspected to have COVID-19 through a rapid care circuit and virological diagnosis in our infectious disease reference hospital in Marseille, France. Rapid viral detection was performed on sputum and nasopharyngeal samples. Over our study period, no SARS-CoV-2 was detected. Results were obtained within approximately 3 h of the arrival of patient samples at the laboratory. Other viral infections were identified in 49% of the patients, with most common pathogens being influenza A and B viruses, rhinovirus, metapneumovirus and common coronaviruses, notably HKU1 and NL63. Early recognition of COVID-19 is critical to isolate confirmed cases and prevent further transmission. Early rule-out of COVID-19 allows public health containment measures to be adjusted by reducing the time spent in isolation. [ABSTRACT FROM AUTHOR]

An ongoing epidemic of respiratory diseases caused by a novel coronavirus (COVID 2019, SARS-CoV2) started in Wuhan, Hubei, in China at the end of December 2019. The French government decided to repatriate the 337 French nationals living in Wuhan and place them in quarantine in their home country. We decided to test them all for SARS-Cov2 twice in order to reduce anxiety among the population and decision-makers. We investigated the presence of SARS-CoV-19 in asymptomatic carriers by testing all repatriated patients within the first 24 h of their arrival in France and at day 5. Viral RNA was extracted from pooled nasal and oropharyngeal swab fluids or sputum in the absence of nasal/oropharyngeal swabs. Detection of SARS-CoV-2 RNA was then carried out using several real-time reverse transcription (RT)-PCR assays. We tested 337 passengers at day 0 and day 5. All the tests for SARS-CoV2 were negative. By optimising the sampling process, sending samples sequentially and reducing the time-scale for biological analysis, we were able to test the samples within 5 h (including sampling, shipment and biological tests). Optimising our procedures reduces anxiety and reassures the population and decision makers. [ABSTRACT FROM AUTHOR]

Since 2003, dozens of giant viruses that infect amoebas (GVA), including mimiviruses and marseilleviruses, have been discovered. These giants appear to be common in our biosphere. From the onset, their presence and possible pathogenic role in humans have been serendipitously observed or investigated using a broad range of technological approaches, including culture, electron microscopy, serology and various techniques based on molecular biology. The link between amoebal mimiviruses and pneumonia has been the most documented, with findings that fulfill several of the criteria considered as proof of viral disease causation. Regarding marseilleviruses, they have been mostly described in asymptomatic persons, and in a lymph node adenitis. The presence and impact of GVA in humans undoubtedly deserve further investigation in medicine. [ABSTRACT FROM AUTHOR]

Acanthamoeba are natural hosts for giant viruses and their life cycle comprises two stages: a trophozoite and a cryptobiotic cyst. Encystment involves a massive turnover of cellular components under molecular regulation. Giant viruses are able to infect only the trophozoite, while cysts are resistant to infection. Otherwise, upon infection, mimiviruses are able to prevent encystment. This review highlights the important points of Acanthamoeba and giant virus interactions regarding the encystment process. The existence of an acanthamoebal non-permissive cell for Acanthamoeba polyphaga mimivirus, the prototype member of the Mimivirus genus, is analyzed at the molecular and ecological levels, and compared to a similar phenomenon previously described for Emiliana huxleyi and its associated phycodnaviruses: the ‘Cheshire Cat’ escape strategy. [ABSTRACT FROM AUTHOR]

Almost fifteen years ago, the discovery of Acanthamoeba polyphaga mimivirus , the first giant virus, changed how we define a virus. It was discovered incidentally in a process of isolating Legionella sp. from environmental samples in the context of pneumonia epidemics using a co-culture system with Acanthamoeba . Since then, much effort and improvement has been put into the original technique. In addition to the known families of Mimiviridae and Marseilleviridae , four new proposed families of giant viruses have been isolated: Pandoravirus, Pithovirus, Faustovirus and Mollivirus. Major improvements were based on enrichment systems, targeted use of antibiotics and high-throughput methods. The most recent development, using flow cytometry for isolation and presumptive identification systems, opens a path to large environmental surveys that may discover new giant virus families in new protozoa supports used for culture support. [ABSTRACT FROM AUTHOR]

• The prevalence of mpox virus (MPXV) infections in the general population remains poorly defined. • A total of 0.4% of incidental MPXV cases were found in individuals screened for other sexually transmitted infections. • MPXV screening allows the detection of occult infection and asymptomatic carriage. • A syndromic diagnostic approach to sexually transmitted infections is essential for better patient management. 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. 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. 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). 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. [ABSTRACT FROM AUTHOR]

• The COVID19 pandemics affected suddenly the Jewish community of Marseille, France. The investigations of COVID-19 epidemic clusters showed that many small gathering for Purim Jewish celebration, in March 2020 accelerated the virus spreading in community settings. • A total of 6 clusters were linked to religious and social activities: a ski trip, organized meals for the Purim Jewish celebration in community and family settings on March 10, a religious service and a charity gala. • A considerable proportion (40%) of the patients were infected by index patients during the presymptomatic period. • Clinical and PCR attack rates were 3.3 and 2.7 fold lower in children than in adults, especially when children were in close contacts with the infected adults; and thus suggesting a lower susceptibility of children for the COVID19. We investigated possible COVID-19 epidemic clusters and their common sources of exposure that led to a sudden increase in the incidence of COVID-19 in the Jewish community of Marseille between March 15 and March 20, 2020. All data were generated as part of routine work at Marseille university hospitals. Biological diagnoses were made by RT-PCR testing. A telephone survey of families in which a laboratory confirmed case was diagnosed was conducted to determine possible exposure events. As of March 30, 2020, 63 patients were linked to 6 epidemic clusters. The 6 clusters were linked to religious and social activities: a ski trip, organized meals for the Purim Jewish celebration in community and family settings on March 10, a religious service and a charity gala. Notably, 40% of the patients were infected by index patients during the presymptomatic period, which was 2.5 days before symptom onset. When considering household members, all 12 patients who tested negative and who did not develop any relevant clinical symptoms compatible with COVID-19 were 1–16 years of age. The clinical attack rate (symptoms compatible with COVID-19, and biologically confirmed by PCR) in adults was 85% compared to 26% in children. Family and community gatherings for the Purim Jewish celebration probably accelerated the spread of COVID-19 in the Marseille Jewish community, leading to multiple epidemic clusters. This investigation of family clusters suggested that all close contacts of patients with confirmed COVID-19 who were not infected were children. [ABSTRACT FROM AUTHOR]

At the end of November 2019, a novel coronavirus responsible for respiratory tract infections (COVID-19) emerged in China. Despite drastic containment measures, this virus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), spread in Asia and Europe. The pandemic is ongoing with a particular hotspot in Southern Europe and America; many studies predicted a similar epidemic in Africa, as is currently seen in Europe and the United States of America. However, reported data have not confirmed these predictions. One of the hypotheses that could explain the later emergence and spread of COVID-19 pandemic in African countries is the use of antimalarial drugs to treat malaria, and specifically, artemisinin-based combination therapy (ACT). The antiviral activity of fixed concentrations of ACT at concentrations consistent with those observed in human plasma when ACT is administered at oral doses for uncomplicated malaria treatment was evaluated in vitro against a clinically isolated SARS-CoV-2 strain (IHUMI-3) in Vero E6 cells. Mefloquine-artesunate exerted the highest antiviral activity with % inhibition of 72.1 ± 18.3 % at expected maximum blood concentration (C max) for each ACT drug at doses commonly administered in malaria treatment. All the other combinations, artesunate-amodiaquine, artemether-lumefantrine, artesunate-pyronaridine, or dihydroartemisinin-piperaquine, showed antiviral inhibition in the same ranges (27.1 to 34.1 %). Antimalarial drugs for which concentration data in the lungs are available are concentrated from 10 to 160 fold more in the lungs than in blood. These in vitro results reinforce the hypothesis that antimalarial drugs could be effective as an anti-COVID-19 treatment. [ABSTRACT FROM AUTHOR]

• There were fewer common respiratory virus-associated deaths in Southeastern France hospitals during 2019–2020 vs 2018–2019. • The majority were due to decreases in influenza A virus and respiratory syncytial virus (RSV)-associated deaths. • 55 deaths were associated with a SARS-CoV-2 diagnosis. • There was similar respiratory virus-associated mortality among hospitalized patients. • SARS-CoV-2 infections had a limited impact on the number of deaths of any cause among hospitalized people. Respiratory viruses are a major cause of mortality worldwide and in France, where they cause several thousands of deaths every year. University Hospital Institute-Méditerranée Infection performs real-time surveillance of all diagnoses of infections and associated deaths in public hospitals in Marseille, Southeastern France. This study compared mortality associated with diagnoses of respiratory viruses during the colder months of 2018–2019 and 2019–2020 (week 47–week 14). In 2018–2019, 73 patients (0.17% of 42,851 hospitalized patients) died after being diagnosed with a respiratory virus; 40 and 13 deaths occurred in patients diagnosed with influenza A virus and respiratory syncytial virus (RSV), respectively. In 2019–2020, 50 patients (0.10% of 49,043 patients hospitalized) died after being diagnosed with a common respiratory virus; seven and seven deaths occurred in patients diagnosed with influenza A virus and RSV, respectively. Additionally, 55 patients died after being diagnosed with SARS-CoV-2. The proportion of respiratory virus-associated deaths among hospitalized patients was thus significantly lower for common respiratory viruses in 2019–2020 than in 2018–2019 (102 versus 170 per 100,000 hospitalized patients; p = 0.003), primarily as a consequence of a decrease in influenza A virus (–83%) and RSV (–46%)-associated deaths. Overall, the proportion of respiratory virus-associated deaths among hospitalized patients was higher, but not significantly, in 2019–2020 than in 2018–2019 (214 versus 170 per 100,000 hospitalized patients; p = 0.08, Yates-corrected Chi-square test). These findings put into perspective the death burden of SARS-CoV-2 infections in this geographical area. [ABSTRACT FROM AUTHOR]

Chlamydiae are pathogenic and symbiotic bacteria, which form an important part of amoeba-associated microorganisms. In this paper, we report the isolation, developmental cycle and genome analysis of Protochlamydia phocaeensis sp. nov., an obligate intracellular parasite with a large host spectrum, able to infect Acanthamoeba castellanii , Acanthamoeba polyphaga , and Vermamoeba vermiformis . The genome size is 3,424,182 bp with a GC content of 42%. This bacterium displayed a particular developmental cycle depending on the infected host. The P. phocaeensis showed typical inclusion vacuoles in A. castellanii , while these were absent in V. vermiformis . Since “ Chlamydiae –amoebae” interactions are supposed to depend on the chlamydial species, our findings speculate that variations in the developmental cycle of certain Chlamydiae are also host dependent. [ABSTRACT FROM AUTHOR]

Among the multiple SARS-CoV-2 variants identified since summer 2020, several have co-circulated, creating opportunities for coinfections and potentially genetic recombinations that are common in coronaviruses. Viral recombinants are indeed beginning to be reported more frequently. Here, we describe a new SARS-CoV-2 recombinant genome that is mostly that of a Omicron 21L/BA.2 variant but with a 3′ tip originating from a Omicron 21K/BA.1 variant. Two such genomes were obtained in our institute from adults sampled in February 2022 in university hospitals of Marseille, southern France, by next-generation sequencing carried out with the Illumina or Nanopore technologies. The recombination site was located between nucleotides 26,858-27,382. In the two genomic assemblies, mean sequencing depth at mutation-harboring positions was 271 and 1362 reads and mean prevalence of the majoritary nucleotide was 99.3 ± 2.2% and 98.8 ± 1.6%, respectively. Phylogeny generated trees with slightly different topologies according to whether genomes analyzed were depleted or not of the 3′ tip. This 3′ terminal end brought in the Omicron 21L/BA.2 genome a short transposable element of 41 nucleotides named S2m that is present in most SARS-CoV-2 except a few variants among which the Omicron 21L/BA.2 variant and may be involved in virulence. Importantly, this recombinant is not detected by currently used qPCR that screen for variants in routine diagnosis. The present observation emphasizes the need to survey closely the genetic pathways of SARS-CoV-2 variability by whole genome sequencing, and it could contribute to gain a better understanding of factors that lead to observed differences between epidemic potentials of the different variants. • We described a new recombinant consiting in a Omicron 21L/BA.2 variant with the 3′ tip of a Omicron 21K/BA.1 variant. • This recombinant is not detected by routine variants screening qPCR. • It recovered from a 21K/BA.1 genome a short transposable element named S2m that lacks in 21L/BA.2 genomes. • S2m might increase viral virulence. [ABSTRACT FROM AUTHOR]

Abstract: Acanthamoeba polyphaga mimivirus (APMV) is a giant, double-stranded virus of the Mimiviridae family that was discovered in 2003. Recent studies have shown that this virus is able to replicate in murine and human phagocytes and might be considered a putative human pathogen that causes pneumonia. However, there is little data regarding APMV and its host defense relationship. In the present study, we investigated how some components of the interferon (IFN) system are stimulated by APMV in human peripheral blood mononuclear cells (PBMCs) and how APMV replication is affected by IFN treatment. Our results demonstrated that APMV is able to replicate in human PBMCs, inducing type I Interferons (IFNs) but inhibiting interferon stimulated genes (ISG) induction by viroceptor and STAT-1 and STAT-2 dephosphorylation independent mechanisms. We also showed that APMV is resistant to the antiviral action of interferon-alpha2 (IFNA2) but is sensitive to the antiviral action of interferon-beta (IFNB1). Our results demonstrated the productive infection of professional phagocytes with APMV and showed that this virus is recognized by the immune system of vertebrates and inhibits it. It provides the first data regarding APMV and the IFN system interaction and raise new and relevant evolutional questions about the relationship between APMV and vertebrate hosts. [Copyright &y& Elsevier]

Abstract: Background: Megavirales is a proposed new virus order composed of Mimivirus, Marseillevirus and closely related viruses, as well as members of the families Poxviridae, Iridoviridae, Ascoviridae, Phycodnaviridae and Asfarviridae. The Megavirales virome, which we refer to as the megavirome, has been largely neglected until now because of the use of technical procedures that have jeopardized the discovery of giant viruses, particularly the use of filters with pore sizes in the 0.2–0.45-μm range. Concurrently, there has been accumulating evidence supporting the role of Mimivirus, discovered while investigating a pneumonia outbreak using amoebal coculture, as a causative agent in pneumonia. Objectives: In this paper, we describe the detection of sequences related to Mimivirus and Marseillevirus in the gut microbiota from a young Senegalese man. We also searched for sequences related to Megavirales in human metagenomes publicly available in sequence databases. Results: We serendipitously detected Mimivirus- and Marseillevirus-like sequences while using a new metagenomic approach targeting bacterial DNA that subsequently led to the isolation of a new member of the family Marseilleviridae, named Senegalvirus, from human stools. This discovery demonstrates the possibility of the presence of giant viruses of amoebae in humans. In addition, we detected sequences related to Megavirales members in several human metagenomes, which adds to previous findings by several groups. Conclusions: Overall, we present convergent evidence of the presence of mimiviruses and marseilleviruses in humans. Our findings suggest that we should re-evaluate the human megavirome and investigate the prevalence, diversity and potential pathogenicity of giant viruses in humans. [Copyright &y& Elsevier]

Abstract: Background: Acanthamoeba polyphaga mimivirus (APMV), the largest known virus, has been studied as a putative pneumonia agent, especially in hospital environments. Despite the repercussions of the discovery of APMV, there has been no study related to the control of APMV and the susceptibility of this virus to disinfectants. Objectives: This work investigated the virucidal activity against mimivirus of chemical biocides commonly used in clinical practice for the disinfection of hospital equipment and rooms. Study design: APMV was dried on sterilized steel coupons, exposed to different concentrations of alcohols (ethanol, 1-propanol and 2-propanol) and commercial disinfectants (active chlorine, glutaraldehyde and benzalkonium chloride) and titrated in amoebas using the TCID50 value. The stability of APMV on an inanimate surface was also tested in the presence and absence of organic matter for 30 days. Results: APMV showed a high level of resistance to chemical biocides, especially alcohols. Only active chlorine and glutaraldehyde were able to decrease the APMV titers to undetectable levels. Dried APMV showed long-lasting stability on an inanimate surface (30 days), even in the absence of organic matter. Conclusions: The data presented herein may help health and laboratory workers plan the best strategy to control this putative pneumonia agent from surfaces and devices. [Copyright &y& Elsevier]

Surveillance of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic epidemiology led us to detect several variants since summer 2020. We report the recent spread of a new SARS-CoV-2 spike 501Y variant. SARS-CoV-2 sequences obtained from human nasopharyngeal samples by Illumina next-generation sequencing were analysed using Nextclade and an in-house Python script and were compared using BLASTn to the GISAID database. Phylogeny was investigated using the IQ-TREE software. We identified that SARS-CoV-2 genomes from four patients diagnosed in our institute harboured a new set of amino acid substitutions including L18F, L452R, N501Y, A653V, H655Y, D796Y, G1219V ± Q677H. These spike N501Y genomes are the first of Nextstrain clade 19B. We obtained partial spike gene sequences of this genotype for an additional 43 patients. All patients infected with this genotype were diagnosed since mid-January 2021. We detected 42 other genomes of this genotype in GISAID, which were obtained from samples collected in December 2020 in four individuals and in 2021 in 38 individuals. The 89 sequences obtained in our institute or other laboratories originated from the Comoros archipelago, western European countries (mostly metropolitan France), Turkey and Nigeria. These findings warrant further studies to investigate the spread, epidemiological and clinical features, and sensitivity to immune responses of this variant. [ABSTRACT FROM AUTHOR]

A novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is responsible for the current coronavirus disease 2019 global pandemic. Only a few laboratories routinely isolate the virus, which is because the current co-culture strategy is highly time-consuming and requires a biosafety level 3 laboratory. This work aimed to develop a new high-throughput isolation strategy using novel technologies for rapid and automated isolation of SARS-CoV-2. We used an automated microscope based on high-content screening (HCS), and we applied specific image analysis algorithms targeting cytopathic effects of SARS-CoV-2 on Vero E6 cells. A randomized panel of 104 samples, including 72 that tested positive by RT-PCR and 32 that tested negative, were processed with our HCS strategy and were compared with the classical isolation procedure. The isolation rate was 43% (31/72) with both strategies on RT-PCR-positive samples and was correlated with the initial RNA viral load in the samples, in which we obtained a positivity threshold of 27 Ct. Co-culture delays were shorter with the HCS strategy, where 80% (25/31) of the positive samples were recovered by the third day of co-culture, compared with only 26% (8/30) with the classic strategy. Moreover, only the HCS strategy allowed us to recover all the positive samples (31 with HCS versus 27 with classic strategy) after 1 week of co-culture. This system allows the rapid and automated screening of clinical samples with minimal operator workload, which reduces the risk of contamination and paves the way for future applications in clinical microbiology, such as large-scale drug susceptibility testing. [ABSTRACT FROM AUTHOR]

• Methylene blue (MB) has a 50% cytotoxic concentration (CC 50) >100 μM in Vero E6 cells. • MB inhibited SARS-CoV-2 replication in Vero E6 cells (EC 50 = 0.30 ± 0.03 μM and EC 90 = 0.75 ± 0.21 μM). • In comparison, EC 50 and EC 90 of 1.5 and 3.0 μM for hydroxychloroquine and 20.1 and 41.9 μM for azithromycin. • C max /EC 50 and C max /EC 90 for MB were estimated at 10.1 and 4.0 after oral and 33.3 and 13.3 after i.v. administration. • EC 50 and EC 90 values of MB consistent with concentrations observed in human blood. In December 2019, a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causing coronavirus diseases 2019 (COVID-19) emerged in Wuhan, China. Currently there is no antiviral treatment recommended against SARS-CoV-2. Identifying effective antiviral drugs is urgently required. Methylene blue has already demonstrated in vitro antiviral activity in photodynamic therapy as well as antibacterial, antifungal and antiparasitic activities in non-photodynamic assays. In this study. non-photoactivated methylene blue showed in vitro activity at very low micromolar range with an EC 50 (median effective concentration) of 0.30 ± 0.03 μM and an EC 90 (90% effective concentration) of 0.75 ± 0.21 μM at a multiplicity of infection (MOI) of 0.25 against SARS-CoV-2 (strain IHUMI-3). The EC 50 and EC 90 values for methylene blue are lower than those obtained for hydroxychloroquine (1.5 μM and 3.0 μM) and azithromycin (20.1 μM and 41.9 μM). The ratios C max /EC 50 and C max /EC 90 in blood for methylene blue were estimated at 10.1 and 4.0, respectively, following oral administration and 33.3 and 13.3 following intravenous administration. Methylene blue EC 50 and EC 90 values are consistent with concentrations observed in human blood. We propose that methylene blue is a promising drug for treatment of COVID-19. In vivo evaluation in animal experimental models is now required to confirm its antiviral effects on SARS-CoV-2. The potential interest of methylene blue to treat COVID-19 needs to be confirmed by prospective comparative clinical studies. [ABSTRACT FROM AUTHOR]

Chloroquine and hydroxychloroquine have been found to be efficient on SARS-CoV-2, and reported to be efficient in Chinese COV-19 patients. We evaluate the effect of hydroxychloroquine on respiratory viral loads. French Confirmed COVID-19 patients were included in a single arm protocol from early March to March 16th, to receive 600mg of hydroxychloroquine daily and their viral load in nasopharyngeal swabs was tested daily in a hospital setting. Depending on their clinical presentation, azithromycin was added to the treatment. Untreated patients from another center and cases refusing the protocol were included as negative controls. Presence and absence of virus at Day6-post inclusion was considered the end point. Six patients were asymptomatic, 22 had upper respiratory tract infection symptoms and eight had lower respiratory tract infection symptoms. Twenty cases were treated in this study and showed a significant reduction of the viral carriage at D6-post inclusion compared to controls, and much lower average carrying duration than reported in the litterature for untreated patients. Azithromycin added to hydroxychloroquine was significantly more efficient for virus elimination. Despite its small sample size, our survey shows that hydroxychloroquine treatment is significantly associated with viral load reduction/disappearance in COVID-19 patients and its effect is reinforced by azithromycin. [ABSTRACT FROM AUTHOR]

Summary: Background: Acinetobacter baumannii has previously been detected and genotyped in human body lice. The objectives of this study were to determine the presence of this bacterium in head and body lice collected from healthy individuals in Ethiopia by molecular methods and to characterize the genotype. Methods: Human lice from locations at different altitudes in Ethiopia were screened for the presence of Acinetobacter sp by targeting the rpoB gene. Acinetobacter baumannii was detected and genotyped using recA PCR amplification. Results: A total of 115 head and 109 body lice were collected from 134 healthy individuals. Acinetobacter sp were found in 54 head (47%) and 77 body (71%) lice. The recA gene was sequenced for 60 of the Acinetobacter sp and 67% were positive for A. baumannii; genotype 1 was retrieved the most frequently. Conclusion: Our study is the first to show the presence of A. baumannii in human body lice, and also in head lice, in Ethiopia. [ABSTRACT FROM AUTHOR]