Bacillus anthracis, the bacterial cause of anthrax, is a zoonosis affecting livestock and wildlife often spilling over into humans. In Vietnam, anthrax has been nationally reportable since 2015 with cases occurring annually, mostly in the northern provinces. In April 2022, an outbreak was reported in Son La province following the butchering of a water buffalo, Bubalus bubalis. A total of 137 humans from three villages were likely exposed to contaminated meat from the animal. Early epidemiological investigations suggested a single animal was involved in all exposures. Five B. anthracis isolates were recovered from human clinical cases along with one from the buffalo hide, another from associated maggots, and one from soil at the carcass site. The isolates were whole genome sequenced, allowing global, regional, and local molecular epidemiological analyses of the outbreak strains. All recovered B. anthracis belong to the A.Br.001/002 lineage based on canonical single nucleotide polymorphism analysis (canSNP). Although not previously identified in Vietnam, this lineage has been identified in the nearby countries of China, India, Indonesia, Thailand, as well as Australia. A twenty-five marker multi-locus variable number tandem repeat analysis (MLVA-25) was used to investigate the relationship between human, soil, and buffalo strains. Locally, four MLVA-25 genotypes were identified from the eight isolates. This level of genetic diversity is unusual for the limited geography and timing of cases and differs from past literature using MLVA-25. The coupled spatial and phylogenetic data suggest this outbreak originated from multiple, likely undetected, animal sources. These findings were further supported by local news reports that identified at least two additional buffalo deaths beyond the initial animal sampled in response to the human cases. Future outbreak response should include intensive surveillance for additional animal cases and additional molecular epidemiological traceback to identify pathogen sources.

The primary vector of the trypanosome parasite causing human and animal African trypanosomiasis in Uganda is the riverine tsetse fly Glossina fuscipes fuscipes (Gff). Our study improved the Gff genome assembly with whole genome 10× Chromium sequencing of a lab reared pupae, identified autosomal versus sex-chromosomal regions of the genome with ddRAD-seq data from 627 field caught Gff, and identified SNPs associated with trypanosome infection with genome-wide association (GWA) analysis in a subset of 351 flies. Results from 10× Chromium sequencing greatly improved Gff genome assembly metrics and assigned a full third of the genome to the sex chromosome. Results from ddRAD-seq suggested possible sex-chromosome aneuploidy in Gff and identified a single autosomal SNP to be highly associated with trypanosome infection. The top associated SNP was ~1200 bp upstream of the gene lecithin cholesterol acyltransferase (LCAT), an important component of the molecular pathway that initiates trypanosome lysis and protection in mammals. Results suggest that there may be naturally occurring genetic variation in Gff in genomic regions in linkage disequilibrium with LCAT that can protect against trypanosome infection, thereby paving the way for targeted research into novel vector control strategies that can promote parasite resistance in natural populations.

Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (CAS) genes make up bacteria's adaptive immune system. These genes protect bacteria from being eaten by bacteriophages. In this study, CRISPR-Cas systems were characterized using a genomic approach. For this purpose, genome sequences of Lactobacillus johnsonii strains were retrieved, and the diversity, occurrence, and evolution of the CRISPR-Cas systems were analyzed. Then, homology analyses of spacer sequences in identified CRISPR arrays were performed to analyze and characterize the diversity of target phages and plasmids. Finally, the evolutionary paths of spaceromes in each subtype of CRISPR arrays were performed using acquisition and deletion events surveyed under the selective pressure of foreign plasmids and phages. Results showed that 138 strains contain valid CRISPR-Cas structures (CRISPR loci together with the Cas genes) in their genomes, which accounted for about 17% of the L. johnsonii studied strains belonging to subtypes II-A, I-E, and I-C. Moreover, results indicated that some specific groups of plasmids were targeted with specific CRISPR array systems. Homology analysis of spacer sequences with phage genomes also revealed that spacers of strains that harbored only CRISPR-Cas subtype-II targeted a greater diversity of foreign phages. In conclusion, the current study indicates that there is great diversity between the CRISPR-Cas systems identified in L. johnsonii strains. Such diverse CRISPR-Cas systems indicate that these systems are naturally active and important in terms of adaptive immunity and evolutionary relationships.

The existence of sylvatic transmission of dengue virus in communities of neotropical bats remains uncertain. In this work we present a near-complete genome of dengue virus serotype 4 obtained from the brain sample of a bat from Platyrrhinus helleri specie collected in the Brazilian Amazon region. The presence of the virus in the brain sample may indicate a possible tropism for the central nervous system in bats, which may justify negative results in previous studies that focused on analysis of other tissues, such as liver and spleen. Besides the duration of dengue virus circulation in the Americas (circa 40 years) may be too short for an implementation of a sylvatic dengue virus cycle. Our findings suggest that continued monitoring is needed to confirm with the neotropical bats could potentially act as a natural reservoir of dengue in the region.

Given the central role of livestock in understanding the genomic epidemiology of S. aureus, the present study systematically reviewed and synthesized data on the nasal S. aureus carriage, resistance patterns to critical antimicrobial agents, virulence factors and genetic lineages among healthy livestock. Bibliographical databases were searched for published studies from May 2003 to May 2022 on nasal S. aureus carriage, their phenotypic and genetic characteristics among healthy pigs (A), sheep and goats (B), cattle (C), poultry (D), camels (E) and buffaloes (F). Special focus was given to the prevalence of nasal MRSA, MRSA-CC398, MRSA-CC9, mecC-MRSA, MSSA-CC398, and resistance to linezolid (LZDR), chloramphenicol (CLOR) and tetracycline (TETR) in S. aureus. Of the 5492 studies identified, 146 comprised groups A(83)/B(18)/C(33)/D(4)/E(5)/F(3), and were found eligible. The overall pooled nasal prevalence of MRSA in healthy livestock was 13.8% (95% CI: 13.5-14.1) among a pooled 48,154 livestock population. Specifically, the pooled prevalence in groups A to F were: 16.0% (95% CI: 15.6-16.4), 3.7% (95% CI: 2.9-4.6), 13.6% (95% CI: 12.8-14.4), 5.8% (95% CI: 5.1-6.5), 7.1% (95% CI: 6.1-10.7), and 2.8% (95% CI: 1.5-4.8), respectively. These values varied considerably by continent. Varied pooled prevalences of CC398 lineage with respect to MRSA isolates were obtained, with the highest from pigs and cattle (>70%). Moreover, other classical animal-adapted MRSA as well as MSSA-CC398-t1928 were reported. TETR-MSSA was lowest in cattle (18.9%) and highest in pigs (80.7%). LZDR-S. aureus was reported in 8 studies (mediated by optrA and cfr), mainly in pigs (n = 4), while CLOR-S. aureus was reported in 32 studies. The virulence genes luk-S/F-PV, tst, etd, sea, see were sparsely reported, and only in non-CC398-MRSA lineages. These findings highlight the need for adequate prevention against the transmission of zoonotic S. aureus lineages to humans.

In the aftermath of COVID-19, coronaviruses gained renewed attention by the scientific community. The study reports the identification and genetic characterization of a novel coronavirus in the European badger (Meles meles) obtained in the framework of passive surveillance implemented in Italian wildlife in response to the pandemic. Positive samples were characterized using next generation sequencing as well as genetic and phylogenetic analyses, aiming for taxonomic placement under ICTV guidelines of the viruses contained in each sample. Results obtained for six conserved domains within the polyprotein showed that the virus clustered as outgroup and shared <46% amino acid identity with other coronaviruses, supporting the assumption that it belongs to a new putative genus Epsiloncoronavirus. This finding highlights that mammals still hide diverse coronaviruses whose zoonotic and epizootic potential remains unknown.

BACKGROUND: United Arab Emirates, has reported the first case of COVID-19 in January 2020 and by October 2022, a total of 1 Million cases and 2348 deaths due to COVID-19 have been reported. The Abu Dhabi Public Health Center, has led a novel initiative to conduct a large scale genomic surveillance project. The aim of this surveillance project is to generate data to guide public health pandemic response decision making. METHODS: Samples mainly from the community, points of entry to the emirate and healthcare facilities were collected for surveillance using both targeted PCR and/or Genome sequence analysis. Sample criteria were defined and specific metadata were collected in parallel. Using the unique identifiers and through the available datasets, epidemiological and clinical data were integrated. RESULTS: A total of 385,190 sample undertake analysis (from January 2021 to October 2022) either genotyping and/or sequence analysis. The most frequently encountered lineages in the community and among severe cases were reported. CONCLUSIONS: Genomic surveillance is a major tool essential for guiding public health measures throughout the pandemic.

Plasmodium parasites responsible for malaria follow a complex life cycle of which half takes place inside the human host. Parasites present diverse antigens at different stages of their life cycle and interact with many surface molecules to attach to and enter host cells. The CIDRα1 domain of Plasmodium falciparum Erythrocyte Membrane Protein 1 (PfEMP1) in infected erythrocytes adheres to one such vascular receptor endothelial protein C receptor (EPCR). EPCR is implicated in the pathogenesis of severe malaria as preferential binding of CIDRα1 to endothelium results in widespread sequestration of infected erythrocytes leading to endothelium inflammation and severe disease. A single EPCR variant S219G is clinically reported to provide protection from severe malaria. In this work, we have collated all single nucleotide polymorphisms (SNPs) in EPCR from dbSNP. We structurally mapped the SNPs on the three-dimensional complex of EPCR and PfEMP1 CIDRα1. Analysis shows that most EPCR mutations lie on the receptor surface and are non-conservative. Of the 11 mutations in the CIDRα1-interaction region of EPCR, S88P, L96V/I, and R98L/H/P/C are seen with comparably higher occurrences in diverse populations. Our structural analysis details a framework of the interactions between the parasite ligand and host factor EPCR. These structural glimpses provide a blueprint for designing both field-based variant sequencing studies and vaccine development.

In 2016, the first orf virus, a double-stranded DNA (dsDNA) virus of the genus parapoxvirus, from a muskox was isolated on Victoria Island, Nunavut (NU), Canada. We used deep sequencing on DNA extracted from orf virus-positive tissues from wild muskoxen from locations on Victoria Island and the adjacent mainland. Orf virus sequence reads derived from four samples were nearly identical. The consensus sequences generated from pooled reads of MxOV comprises of a large contiguous sequence (contig) of 131,759 bp and a smaller right terminal contig of 3552 bp, containing all coding sequences identified as Parapoxvirus. Individual gene comparisons reveal that MxOV shares genetic characteristics with reference strains from both sheep and goat origin. Recombination analysis using Bootscan, MAXCHI, GENECONV, CHIMAERA, SISCAN, and RDP algorithms within the RDP4 software predicted recombination events in two virulence factors, and a large 3000 bp segment of the MxOV genome. Partial B2L nucleotide sequences from strains around the world and other North American isolates were compared to MxOV using MUSCLE alignments and RAxML phylogenetic trees. MxOV was identical to our previously characterized isolate, and shared similarity with orf virus isolated from sheep and goats. The phylogenetic grouping of partial B2L nucleotide sequences did not follow the sample geographic distribution. More full genomes of orf virus, or at least full B2L gene squences, in wildlife are needed especially in North America to better understand the epidemiology of the disease in muskoxen.

The hard tick Haemaphysalis qinghaiensis is the vector of a wide variety of infectious agents, such as spirochetes and other bacteria as well as viruses in the western plateau of China. Tick midgut is the key tissue involved in the host-pathogen-vector interface. Multiple midgut proteins are related to key functions in blood digestion, tick survival, and tick-borne pathogen transmission. However, information on the sex-specific proteins expressed in the midgut tissue of H. qinghaiensis for which the genome has not been sequenced is limited. Hence, we assembled and characterized the transcriptome of the H. qinghaiensis midgut and identified the differentially expressed genes (DEGs) in female and male ticks. The sequencing of the mRNA for this nonmodel species is essential for producing a protein database for mass spectrometry-based identification. Here, we combined high-throughput parallel sequencing and label-free quantitative proteomics analysis to extensively characterize the tick midgut using massive RNA sequencing and mass spectrometry, which allowed the detection of genes and proteins. A total of 279,186 transcripts were annotated into 125,790 coding sequences (CDSs), which were manually curated into 96 different gene families. A total of 12,837 DEGs between the two sexes were found by RNA-seq analysis. Of these, 5401 were upregulated genes, while 7436 were downregulated genes. The most common molecular functions were those related to the endocrine system, translation, signal transduction, transport, and catabolism. Meanwhile, the most common biological processes were related to cellular processes, metabolic processes, cellular anatomical entities, and cargo receptor activities. An analysis of the label-free protein quantitation dataset showed 272 upregulated proteins and 46 downregulated proteins when the fold-change was >2.0 (LC-MS/MS). Association analysis of the transcriptome and proteome with GO functional enrichment showed that the majority of the genes (proteins) were those related to catalytic activity, binding, cellular processes, metabolic processes, and responses to stimuli. This study aims to elucidate the digestive physiology of H. qinghaiensis as well as its physiological sexual dimorphism. This will allow the identification of protein candidates with physiological importance that could be used as targets to control the vector as well as the transmission of tick-borne pathogens to humans and animals.

Tibetan chicken is found in China Tibet (average altitude; ˃4500 m). However, little is known about avian leukosis virus subgroup J (ALV-J) found in Tibetan chickens. ALV-J is a typical alpharetrovirus that causes immunosuppression and myelocytomatosis and thus seriously affects the development of the poultry industry. In this study, Tibet-origin mutant ALV-J was isolated from Tibetan chickens and named RKZ-1-RKZ-5. A Myelocytomatosis outbreak occurred in a commercial Tibetan chicken farm in Shigatse of Rikaze, Tibet, China, in March 2022. About 20% of Tibetan chickens in the farm showed severe immunosuppression, and mortality increased to 5.6%. Histopathological examination showed typical myelocytomas in various tissues. Virus isolation and phylogenetic analysis demonstrated that ALV-J caused the disease. Gene-wide phylogenetic analysis showed the RKZ isolates were the original strains of the previously reported Tibetan isolates (TBC-J4 and TBC-J6) (identity; 94.5% to 94.9%). Furthermore, significant nucleotide mutations and deletions occurred in the hr1 and hr2 hypervariable regions of gp85 gene, 3'UTR, Y Box, and TATA Box of 3'LTR. Pathogenicity experiments demonstrated that the viral load, viremia, and viral shedding level were significantly higher in RKZ-1-infected chickens than in NX0101-infected chickens. Notably, RKZ-1 caused more severe cardiopulmonary damage in SPF chickens. These findings prove the origin of Tibet ALV-J and provide insights into the molecular characteristics and pathogenic ability of ALV-J in the plateau area. Therefore, this study may provide a basis for ALV-J prevention and eradication in Tibet.

Mycobacterium bovis, which belongs to the Mycobacterium tuberculosis complex, is a highly clonal pathogen. However, several lineages of M. bovis have been described worldwide and nine different clusters were identified in France. Targeted amplicon sequencing using next-generation sequencing technology of eighty-eight phylogenetically informative single nucleotide polymorphisms (SNPs) were used to infer the phylogenetic relationship of 630 strains of the National Reference Laboratory isolated between 1979 and 2018 from various animal species. This study allowed classifying 618 different genotypic profiles (combination of a spoligotype and 8 loci-MIRU-VNTR profiles) into the nine previously identified clusters. A global analysis of the entire collection of the National Reference Laboratory has made it possible to represent the evolution of clonal complexes and clusters in time and space for better assessing epidemiological changes of bovine tuberculosis in France.

Coxsackievirus A6 (CVA6) is emerging as the dominant serotype among enteroviruses (EVs) responsible for hand, foot, and mouth disease (HFMD) outbreaks in multiple countries. However, details regarding this serotype in the Philippines are limited. In this study, we investigated the epidemiological and molecular characteristics of laboratory-confirmed CVA6 HFMD cases in the Philippines between 2012 and 2017. Data collected from case report forms submitted to the National Reference Laboratory for Poliovirus and other Enteroviruses were used to determine the distribution and clinical findings of laboratory-confirmed CVA6 HFMD. Phylogenetic analyses of the complete viral protein 1 (VP1) and partial 3D polymerase (3Dpol) gene sequences were performed to determine the genotype and recombinant (RF) form of the selected samples. An increase in the detection rate of CVA6 among enterovirus-positive HFMD cases was observed from 61.9% (140/226) in 2012 to 88.1% (482/587) in 2017, with most cases coming from the Luzon island group. Among the detected cases, the majority were children, with a median age of 2 years old (interquartile range: 1.17-3.40). Respiratory-related morbidities were the commonly reported complications (7.9%; 72/907). Based on the VP1 and 3Dpol gene sequence analysis, the CVA6 strains in this study were classified as genotype D3b and RF-A group, respectively. This study elucidated that CVA6 was the most prevalent enterovirus serotype causing HFMD in the Philippines in 2012-2017, with genotype D3b/RF-A circulating within this period. This study highlights the importance of viral surveillance and molecular epidemiological analysis to broaden our understanding of HFMD in the Philippines.

Currently, tuberculosis (TB) in Japan is highly prevalent among elderly patients who were born during a time when TB was highly prevalent. Mycobacterium tuberculosis (Mtb) lineage 2 (L2) is the predominant strain in the country. Moreover, the proportion of foreign-born patients with TB has been increasing. This epidemiological situation in Japan motivated us to explore the heterogeneity in transmission dynamics among the sublineages of Mtb L2 within this aging population. For this purpose, we conducted a population-based whole genome sequencing analysis of 550 Mtb strains in Kobe, Japan, and employed pairwise single nucleotide polymorphism (SNP) distance clustering and terminal branch length (TBL) distribution analysis to assess Mtb transmission. The genomic clustering rate with a threshold of ≤5 SNPs was significantly lower in elderly patients aged 70 years or higher than in non-elderly patients. The elderly patient group showed significantly longer TBL than the non-elderly group. These results supported the notion that reactivation of distant infection is a major driving force for the high incidence of TB in elderly individuals. The age group distribution and frequency of lineages/sublineages were found to significantly differ between foreign-born and Japan-born patients. The increased proportion of foreign-born patients might have resulted in more strain diversity in Japan. The L2.2.A sublineage demonstrated a significant association with elderly patients and exhibited lower transmission rates, which indicate to be prone to reactivate from long-term latency. In contrast, L2.2.Modern, showed a strong association with younger and foreign-born patients. This sublineage showed a high genomic cluster rate, suggesting its high transmissibility. The other three major sublineages, namely L2.2.AA2, L2.2.AA3.1, and L2.2.AA3.2, exhibited a consistent increase in cluster rates across varying SNP thresholds, indicating their relatively recent emergence as endemic sublineages in Japan. In conclusion, this study highlights distinct differences in the transmission dynamics of L2 sublineages within an aging society.

Biting midges are vectors of arboviruses such as bluetongue virus, bovine ephemeral fever virus, Akabane virus, African horse sickness virus, epizootic haemorrhagic disease virus and Schmallenberg virus. Fast and accurate identification of biting midges is crucial in the study of Culicoides-borne diseases. Morphological identification of biting midges has revealed the presence of cryptic species. A total of 20 species are reported in Madagascar. In this study, we assessed wing morphometric analysis for identification of seven species namely C. dubitatus Kremer, Rebholtz-Hirtzel and Delécolle, C. enderleini Cornet and Brunhes, C. kibatiensis Goetghebuer, C. miombo Meiswinkel, C. moreli Clastrier, C. nevilli Cornet and Brunhes, and C. zuluensis de Meillon. Culicoides enderleini, C. miombo, C. moreli, C. nevilli and C. zuluensis are vectors diseases. A molecular approach, based on the cytochrome oxidase I gene (Cox1), was used for species delimitation. The molecular analysis presented seven different clades grouped two-by-two according to morphological characters. A total of 179 wing images were digitised. We found morphometric variation among seven species based on 11 landmarks and two outlines. Wing shape variation plots showed that species overlapped with species belonging to the same group. The cross-validation revealed a relatively high percentage of correct classification in most species, ranging from 91.3% to 100% for landmarks; 60% to 82.6% for outlines-1 and 77.1% to 91.3% for outlines-2. Our study suggests that wing geometric morphometric analysis is a robust tool for reliable "Moka Fohy" identification in Madagascar. This inexpensive and simple method is a precise supplement to morphological identification, with reaches the accuracy of Cox1 barcoding.

In this study, we compared the characteristics of different uropathogenic Escherichia coli phylogroups. A total of 844 E. coli isolated from urine were enrolled and the antimicrobial susceptibility of E. coli to 22 antibiotics was determined by disk diffusion test. The distribution of phylogroups and 20 virulence factor genes was determined by PCR. Phenotypes associated with bacterial virulence, including motility, biofilm formation, and the production of curli and siderophore, were examined. Phylogroup B2 was dominant in our isolates (64.8%), followed by phylogroups D (8.6%), B1 (7.8%), F (6.0%), C (4.5%), A (3.1%), untypable (2.8%), E (1.8%), and clade I (0.5%). The prevalence of multidrug-resistant strains was highest in phylogroup C (86.8%), followed by E (80.0%), F (75.0%), and D (71.2%). Moreover, 23.5% of the phylogroup F E. coli were extensively drug-resistant. Phylogroup B2 E. coli had an average of the highest virulence factor genes (10.1 genes/isolate). Compared to phylogroup B2 E. coli, phylogroups F and clade I E. coli had higher motility while phylogroup C E. coli had lower motility. >60% of phylogroups A and C E. coli showed very low curli production. In contrast, 14%, 10%, and 7%, of E. coli in phylogroups F, B2, and E, produced a very high amount of curli, respectively. Surprisingly, phylogroup A E. coli showed the highest virulence to larvae, followed by phylogroups B2 and C. In summary, we first characterized and revealed that the antimicrobial resistance, virulence gene distribution, motility, and curli production, were associated with in E. coli phylogroups.

Norovirus (NoV) is the leading pathogen responsible for global acute gastroenteritis (AGE) outbreaks and sporadic cases. NoV evolves through gene mutation and recombination, leading to the emergence of new strains capable of causing global epidemics. This study aimed to learn the epidemiological characteristics of 39 GI.6[P11] NoV outbreaks in Beijing, China, from 2016 to 2019 and to analyze the genetic diversity and phylogenetic process of GI.6[P11] strains. The Bayesian phylogenetic analysis of partial VP1 and RNA-dependent RNA polymerase (RdRp) genes showed that GI.6[P11] strains were clustered into four subclades. Eleven whole genome sequences were obtained through the amplicon sequencing with 16 pairs of newly designed primers. The phylogenetic trees based on the whole genome and ORF1, 2, and 3 showed that the clustering of the 11 strains was consistent with that of partial VP1 and RdRp genes. The Bayesian inference revealed that the most recent ancestor (TMRCA) for the four subclades of the phylogenetic tree based on the whole genome sequences was 2012.42, 2014.81, 2011.74, and 2015.53, respectively. The recombination sites of GI.6[P11] strains in Beijing were located near the ORF1/2 junction. The histo-blood group antigens (HBGA) binding sites of GI.6[P11] strains in Beijing were conserved and there were some unique amino acid mutations in non-structural proteins in the ORF1 region.

Plasmodium knowlesi is the leading cause of malaria in Malaysia. Serine Repeat Antigens (SERAs) have an essential role in the parasite life cycle. However, genetic characterization on P. knowlesi SERA3 Ag2 (PkSERA3 Ag2) is lacking. In the present study, nucleotide diversity, natural selection, and haplotypes of PkSERA3 Ag2 in clinical samples from Peninsular Malaysia and Malaysian Borneo were investigated. A total of 50 P. knowlesi clinical samples were collected from Peninsular Malaysia and Malaysian Borneo. The PkSERA3 Ag2 gene was amplified using PCR, and subsequently cloned and sequenced. Genetic diversity, haplotype, natural selection as well as genetic structure and differentiation of PkSERA3 Ag2 were analysed. In addition, in silico analyses were performed to identify repeat motifs, B-cell epitopes, and antigenicity indices of the protein. Analysis of 114 PkSERA3 Ag2 sequences revealed high nucleotide diversity of the gene in Malaysia. A codon-based Z-test indicated that the gene underwent purifying selection. Haplotype and population structure analyses identified two distinct PkSERA3 Ag2 clusters (K = 2, ΔK = 721.14) but no clear genetic distinction between PkSERA3 Ag2 from Peninsular Malaysia and Malaysian Borneo. FST index indicated moderate differentiation of the gene. In silico analyses revealed unique repeat motifs among PkSERA3 Ag2 isolates. Moreover, the amino acid sequence of PkSERA3 Ag2 exhibited potential B-cell epitopes and possessed high antigenicity indices. These findings enhance the understanding of PkSERA3 Ag2 gene as well as its antigenic properties. Further validation is necessary to ascertain the utility of PkSERA3 Ag2 as a serological marker for P. knowlesi infection.

Vibrio cholerae O1 El Tor, causative agent of the ongoing seventh cholera pandemic, is native to the aquatic environment of the Ganges Delta, Bay of Bengal (GDBB). Recent studies traced pandemic strains to the GDBB and proposed global spread of cholera had occurred via intercontinental transmission. In the research presented here, NotI-digested genomic DNA extracted from V. cholerae O1 clinical and environmental strains isolated in Bangladesh during 20042014 was analyzed by pulsed-field gel electrophoresis (PFGE). Results of cluster analysis showed 94.67% of the V. cholerae strains belonged to clade A and included the majority of clinical strains of spatio-temporal origin and representing different cholera endemic foci. The rest of the strains were estuarine, all environmental strains from Mathbaria, Bangladesh, and occurred as singletons, clustered in clades B and C, or in the small clades D and E. Cluster analysis of the Bangladeshi strains and including 157 El Tor strains from thirteen countries in Asia, Africa, and the Americas revealed 85% of the total set of strains belonged to clade A, indicating all were related, yet did not form an homogeneous cluster. Overall, 15% of the global strains comprised multiple small clades or segregated as singletons. Three sub-clades could be discerned within the major clade A, reflecting distinct lineages of V. cholerae O1 El Tor associated with cholera in Asia, Africa, and the Americas. The presence in Asia and the Americas of non-pandemic V. cholerae O1 El Tor populations differing by PFGE and from strains associated with cholera globally suggests different ecotypes are resident in distant geographies.

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.