Direct metagenomic and amplicon-based Nanopore sequencing of French human monkeypox from clinical specimen.

We report the whole-genome sequence of monkeypox virus obtained using MinION technology (Oxford Nanopore Technologies) from a French clinical specimen during the 2022 epidemic. Amplicon-based sequencing and shotgun metagenomic approaches were directly applied to the sample.

Complete Genome Sequences of Monkeypox Virus from a French Clinical Sample and the Corresponding Isolated Strain, Obtained Using Nanopore Sequencing.

We report the whole-genome sequences of a monkeypox virus from the skin lesion of a French patient and the corresponding isolated viral strain. Both viral genomic sequences were successfully obtained by applying shotgun metagenomics using the Oxford Nanopore Technologies sequencing approach.

A Six Years (2010-2016) Longitudinal Survey of the Four Serotypes of Dengue Viruses in Lao PDR.

Dengue fever is the most prevalent arthropod-borne viral infection of humans in tropical and subtropical countries. Since 1979, dengue has been reported to be endemic in the Lao People's Democratic Republic (PDR), as in many countries in Southeast Asia, with a complex circulation of the four dengue viruses' serotypes (DENV-1 to DENV-4). By sequencing the complete envelope protein, we explored a panel of samples from five Lao Provinces (Vientiane capital, Luangprabang, Bolikhamxay, Saravane, Attapeu) to enrich knowledge about the co-circulation of DENVs in Lao PDR between 2010 and 2016.

Nanopore sequencing of a monkeypox virus strain isolated from a pustular lesion in the Central African Republic.

Monkeypox is an emerging and neglected zoonotic disease whose number of reported cases has been gradually increasing in Central Africa since 1980. This disease is caused by the monkeypox virus (MPXV), which belongs to the genus Orthopoxvirus in the family Poxviridae. Obtaining molecular data is particularly useful for establishing the relationships between the viral strains involved in outbreaks in countries affected by this disease.

Using Background Sequencing Data to Anticipate DENV-1 Circulation in the Lao PDR.

Since its first detection in 1979, dengue fever has been considered a major public health issue in the Lao People's Democratic Republic (PDR). Dengue virus (DENV) serotype 1 was the cause of an epidemic in 2010-2011. Between 2012 and 2020, major outbreaks due successively to DENV-3, DENV-4 and recently DENV-2 have been recorded.

No evidence for a pathogen associated with pulmonary MALT lymphoma: a metagenomics investigation.

Mucosa-associated lymphoid tissue (MALT) lymphoma is generally associated with chronic antigen stimulation: auto-antigens or of microbial origin. Only one study suggested association between Achromobacter xylosoxidans and pulmonary MALT lymphoma. We aimed to investigate the presence of virus or any infectious agents in pulmonary MALT lymphoma by using metagenomic next-generation sequencing (mNGS).

Rapid Genomic Characterization of SARS-CoV-2 by Direct Amplicon-Based Sequencing Through Comparison of MinION and Illumina iSeq100 System.

Global human health is increasingly challenged by emerging viral threats, especially those observed over the last 20 years with coronavirus-related human diseases, such as the Severe Acute Respiratory Syndrome (SARS) and the Middle East Respiratory Syndrome (MERS). Recently, in late December 2019, a novel , SARS-CoV-2, originating from the Chinese city of Wuhan, emerged and was then identified as the causative agent of a new severe form of pneumonia, COVID-19. Real-time genome sequencing in such viral outbreaks is a key issue to confirm identification and characterization of the involved pathogen and to help establish public health measures.

First detection and genome sequencing of SARS-CoV-2 in an infected cat in France.

After its first description in Wuhan (China), SARS-CoV-2 the agent of coronavirus disease 2019 (COVID-19) rapidly spread worldwide. Previous studies suggested that pets could be susceptible to SARS-CoV-2. Here, we investigated the putative infection by SARS-CoV-2 in 22 cats and 11 dogs from owners previously infected or suspected of being infected by SARS-CoV-2.

E3 Ligase ITCH Interacts with the Z Matrix Protein of Lassa and Mopeia Viruses and Is Required for the Release of Infectious Particles.

Lassa virus (LASV) and Mopeia virus (MOPV) are two closely related, rodent-born mammarenaviruses. LASV is the causative agent of Lassa fever, a deadly hemorrhagic fever endemic in West Africa, whereas MOPV is non-pathogenic in humans. The Z matrix protein of arenaviruses is essential to virus assembly and budding by recruiting host factors, a mechanism that remains partially defined.

Molecular characterization of measles virus strains circulating in Cameroon during the 2013-2016 epidemics.

The first genotyping data on measles virus (MeV) strains in Cameroon dates from 1994, while other studies were realized in 2001 and 2011 with the establishment of MeV virological surveillance. However, the genetic data of MeV strains circulating in Cameroon remains fragmented and concentrated in certain regions, hence the need for an update. The objective of this study was to have recent data on MeV genotypes circulating in Cameroon.

Draft Genome Sequence of a Chryseobacterium indologenes Strain Isolated from a Blood Culture of a Hospitalized Child in Antananarivo, Madagascar.

We report here the draft genome sequence of a strain, isolated from a blood culture of a 2.2-year-old child admitted to the hospital for vomiting and coughing. The genome was composed of 5,063,674 bp and had 37.

Revisiting the genetic diversity of emerging hantaviruses circulating in Europe using a pan-viral resequencing microarray.

Hantaviruses are zoonotic agents transmitted from small mammals, mainly rodents, to humans, where they provoke diseases such as Hemorrhagic fever with Renal Syndrome (HFRS) and its mild form, Nephropathia Epidemica (NE), or Hantavirus Cardio-Pulmonary Syndrome (HCPS). Hantaviruses are spread worldwide and monitoring animal reservoirs is of primary importance to control the zoonotic risk. Here, we describe the development of a pan-viral resequencing microarray (PathogenID v3.

Autophagy Promotes Infectious Particle Production of Mopeia and Lassa Viruses.

Lassa virus (LASV) and Mopeia virus (MOPV) are two closely related Old-World mammarenaviruses. LASV causes severe hemorrhagic fever with high mortality in humans, whereas no case of MOPV infection has been reported. Comparing MOPV and LASV is a powerful strategy to unravel pathogenic mechanisms that occur during the course of pathogenic arenavirus infection.

Parvovirus B19 seroprevalence, viral load, and genotype characterization in volunteer blood donors from southern Brazil.

Usually transmitted via respiratory droplets, parvovirus B19 (B19V) can also be acquired by blood transfusion especially because of viral persistence, resistance to blood treatment procedures, and high viral load during the early infection phase. This is particularly problematic in immunocompromised or anemic patients where the infection can have a severe outcome. As B19V DNA was detected in blood donations from South Brazil during a viral metagenomic survey performed by Next-Generation Sequencing, the objective of this retrospective study was to evaluate the seroprevalence, B19V DNA presence and circulating genotypes in a Hospital Blood Transfusion Service in Santa Maria city in South Brazil (Rio Grande do Sul state).

Monkeypox virus phylogenetic similarities between a human case detected in Cameroon in 2018 and the 2017-2018 outbreak in Nigeria.

A monkeypox virus was detected from a human clinical case in 2018 in Cameroon; a country where no human cases were reported since 1989. The virus exhibited close genetic relatedness with another monkeypox virus isolated in Nigeria during the 2017-2018 outbreak. Although our molecular findings argue in favor of an extension of the monkeypox outbreak from Nigeria into Cameroon, the possibility that the monkeypox virus detected could be indigenous to Cameroon cannot be ruled out.

High prevalence of cyclovirus Vietnam (CyCV-VN) in plasma samples from Madagascan healthy blood donors.

Cycloviruses, small ssDNA viruses belonging to the Circoviridae family, have been suggested as possible causes of enteric, respiratory and neurological disorders in human patients. One of these species, cyclovirus-Vietnam (CyCV-VN), initially isolated from cerebrospinal fluid samples of patients with unexplained neurological disorders, has since been reported in serum samples from chronically patients infected with HBV, HCV or HIV, in Italy. On the other hand, CyCV-VN was not detected in serum samples from healthy individuals.