In a preliminary clinical study, we observed that the combination of hydroxychloroquine and azithromycin was effective against SARS-CoV-2 by shortening the duration of viral load in Covid-19 patients. It is of paramount importance to define when a treated patient can be considered as no longer contagious. Correlation between successful isolation of virus in cell culture and Ct value of quantitative RT-PCR targeting E gene suggests that patients with Ct above 33–34 using our RT-PCR system are not contagious and thus can be discharged from hospital care or strict confinement for non-hospitalized patients.

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Giant viruses are protist-associated viruses belonging to the proposed order Megavirales; almost all have been isolated from Acanthamoeba spp. Their isolation in humans suggests that they are part of the human virome. Using a high-throughput strategy to isolate new giant viruses from their original protozoan hosts, we obtained eight isolates of a new giant viral lineage from Vermamoeba vermiformis, the most common free-living protist found in human environments. This new lineage was proposed to be the faustovirus lineage. The prototype member, faustovirus E12, forms icosahedral virions of Ϸ200 nm that are devoid of fibrils and that encapsidate a 466-kbp genome encoding 451 predicted proteins. Of these, 164 are found in the virion. Phylogenetic analysis of the core viral genes showed that faustovirus is distantly related to the mammalian pathogen African swine fever virus, but it encodes Ϸ3 times more mosaic gene complements. About two-thirds of these genes do not show significant similarity to genes encoding any known proteins. These findings show that expanding the panel of protists to discover new giant viruses is a fruitful strategy. IMPORTANCEBy using Vermamoeba, a protist living in humans and their environment, we isolated eight strains of a new giant virus that we named faustovirus. The genomes of these strains were sequenced, and their sequences showed that faustoviruses are related to but different from the vertebrate pathogen African swine fever virus (ASFV), which belongs to the family Asfarviridae. Moreover, the faustovirus gene repertoire is Ϸ3 times larger than that of ASFV and comprises approximately two-thirds ORFans (open reading frames [ORFs] with no detectable homology to other ORFs in a database). G iant viruses were first described in 2003, with the discovery of Acanthamoeba polyphaga mimivirus (1, 2). They are protistassociated viruses that belong to a major monophyletic group of double-stranded DNA (dsDNA) viruses known as nucleocytoplasmic large DNA viruses (NCLDVs), and they have been classified under the proposed order Megavirales (3). Since the first description of Acanthamoeba polyphaga mimivirus, giant viruses have been isolated from other phagocytic protists, primarily Acanthamoeba spp. (4-6). Because these giant viruses are resistant to killing by phagocytic protists, we hypothesized that they may also reproduce in macrophages and might therefore infect humans. This proposition was validated experimentally by the isolation of mimivirus from atypical pneumonia patients and by the detection of marseilleviruses in blood donors and in human lymph nodes (7-9). Moreover, we and others identified sequences associated with giant viruses in metagenomes generated from human tissues, suggesting that giant viruses are a component of the human virome (10). Because the investigation of a virome typically starts with a filtration procedure that eliminates giant viruses (11), we developed a new culture approach that does not prevent the detection of these viruses.In the present study, we de...

Most viruses are known for the ability to cause symptomatic diseases in humans and other animals. The discovery of Acanthamoeba polyphaga mimivirus and other giant amoebal viruses revealed a considerable and previously unknown area of uncharacterized viral particles. Giant viruses have been isolated from various environmental samples collected from very distant geographic places, revealing a ubiquitous distribution. Their morphological and genomic features are fundamental elements for classifying them. Herein, we report the isolation and draft genome of Cedratvirus, a new amoebal giant virus isolated in Acanthamoeba castellanii, from an Algerian environmental sample. The viral particles are ovoid-shaped, resembling Pithovirus sibericum, but differing notably in the presence of two corks at each extremity of the virion. The draft genome of Cedratvirus—589,068 base pairs in length—is a close relative of the two previously described pithoviruses, sharing 104 and 113 genes with P. sibericum and Pithovirus massiliensis genomes, respectively. Interestingly, analysis of these viruses’ core genome reveals that only 21% of Cedratvirus genes are involved in best reciprocal hits with the two pithoviruses. Phylogeny reconstructions and comparative genomics indicate that Cedratvirus is most closely related to pithoviruses, and questions their membership in an enlarged putative Pithoviridae family.

African swine fever virus, a double-stranded DNA virus that infects pigs, is the only known member of the Asfarviridae family. Nevertheless, during our isolation and sequencing of the complete genome of faustovirus, followed by the description of kaumoebavirus, carried out over the past 2 years, we observed the emergence of previously unknown related viruses within this group of viruses. Here we describe the isolation of pacmanvirus, a fourth member in this group, which is capable of infecting Acanthamoeba castellanii. Pacmanvirus A23 has a linear compact genome of 395,405 bp, with a 33.62% GϩC content. The pacmanvirus genome harbors 465 genes, with a high coding density. An analysis of reciprocal best hits shows that 31 genes are conserved between African swine fever virus, pacmanvirus, faustovirus, and kaumoebavirus. Moreover, the major capsid protein locus of pacmanvirus appears to be different from those of kaumoebavirus and faustovirus. Overall, comparative and genomic analyses reveal the emergence of a new group or cluster of viruses encompassing African swine fever virus, faustovirus, pacmanvirus, and kaumoebavirus.IMPORTANCE Pacmanvirus is a newly discovered icosahedral double-stranded DNA virus that was isolated from an environmental sample by amoeba coculture. We describe herein its structure and replicative cycle, along with genomic analysis and genomic comparisons with previously known viruses. This virus represents the third virus, after faustovirus and kaumoebavirus, that is most closely related to classical representatives of the Asfarviridae family. These results highlight the emergence of previously unknown double-stranded DNA viruses which delineate and extend the diversity of a group around the asfarvirus members.KEYWORDS giant viruses, pacmanvirus, Asfarviridae, Acanthamoeba castellanii, NCLDV, faustovirus, kaumoebavirus, African swine fever virus T he discovery impacts of "giant viruses," such as Acanthamoeba polyphaga mimivirus (1), pandoraviruses (2), and pithoviruses (3), and their interactions with the world of protists are very common and do not need a long introduction. A large community of previously unknown viruses is emerging among the former nucleocytoplasmic large DNA viruses (NCLDV). We are witnessing a growing number of new isolates with extraordinary properties in gene content, particle resistance, and/or morphological appearance (3-7). Genome sequencing and advances in coculture isolation strategies have led to an increase in the discovery of new viruses (8,9). Some NCLDV are well studied because of their role in infecting algae, in the case of Phycodnaviridae (10), or in swine and wild boar infections, in the case of members of the Asfarviridae (11). The

Giant viruses continue to invade the world of virology, in gigantic genome sizes and various particles shapes. Strains discoveries and metagenomic studies make it possible to reveal the complexity of these microorganisms, their origins, ecosystems and putative roles. We isolated from a rat stool sample a new giant virus “Orpheovirus IHUMI-LCC2,” using Vermamoeba vermiformis as host cell. In this paper, we describe the main genomic features and replicative cycle of Orpheovirus IHUMI-LCC2. It possesses a circular genome exceeding 1.4 Megabases with 25% G+C content and ovoidal-shaped particles ranging from 900 to 1300 nm. Particles are closed by at least one thick membrane in a single ostiole-like shape in their apex. Phylogenetic analysis and the reciprocal best hit for Orpheovirus show a connection to the proposed Pithoviridae family. However, some genomic characteristics bear witness to a completely divergent evolution for Orpheovirus IHUMI-LCC2 when compared to Cedratviruses or Pithoviruses.

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.

Objectives 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). Methods 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. Results 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 %). Conclusions 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.