SARS-CoV-2 Lineages and Sub-Lineages Circulating Worldwide: A Dynamic Overview

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan, China, in early December 2019 has rapidly widespread worldwide, becoming one of the major global public health issues of the last centuries. Key Messages: Over the course of the pandemic, due to the advanced whole-genome sequencing technologies, an unprecedented amount of genomes have been generated, providing invaluable insights into the ongoing evolution and epidemiology of the virus during the pandemic. Therefore, this large amount of data played an important role in the SARS-CoV-2 mitigation and control strategies. Key Messages: The active monitoring and characterization of the SARS-CoV-2 lineages circulating worldwide is useful for a more specific diagnosis, better care, and timely treatment. In this review, a concise characterization of all the lineages and sub-lineages circulating and co-circulating across the world has been presented in order to determine the magnitude of the SARS-CoV-2 threat and to better understand the virus genetic diversity and its dispersion dynamics.

Genetic diversity of Mycobacterium tuberculosis using 24-locus MIRU-VNTR typing and Spoligotyping in Upper Myanmar

INTRODUCTION

MIRU-VNTR typing and Spoligotyping are the useful molecular tools for TB epidemiology study. Information regarding genetic diversity and tuberculosis (TB) transmission in Upper Myanmar only is scares.

METHODOLOGY

We determined the genetic diversity of Mycobacterium tuberculosis (Mtb) and TB transmission from Upper Myanmar TB Reference Laboratory, Mandalay Region, including Mandalay (72), Shan (22), Magway (15), Sagaing (13), Nay Pyi Taw (8), Kachin (7), Chin (2) and Kayah (1). One hundred and forty Mtb isolates were genotyped using 24-locus MIRU-VNTR typing and spoligotyping. Lineage classification and TB transmission analysis were performed.

RESULTS

24-locus MIRU-VNTR typing identified 135 unique profiles and two clusters compared to 35 spoligotyping profiles which contained 12 clusters and 23 unique isolates, Beijing (n=100, 71.4%) was found to be prominent lineage by combine two methods. The expected proportion attributable to recent transmission based on clustering rate was 2.1%. One cluster case was more likely to be in MDR patient.

CONCLUSIONS

Our findings showed Beijing genotypes were dominant in Upper Myanmar. The usage and analysis of 24-locus MIRU-VNTR typing might prove useful for our broader understanding of TB outbreaks and epidemiology than spoligotyping. The genotypic pattern of this combined method suggests that the lower transmission rate may be due to a higher possibility of reactivation cases in Upper Myanmar.

Effect of feedback regulation on stem cell fractions in tissues and tumors: Understanding chemoresistance in cancer

While resistance mutations are often implicated in the failure of cancer therapy, lack of response also occurs without such mutants. In bladder cancer mouse xenografts, repeated chemotherapy cycles have resulted in cancer stem cell (CSC) enrichment, and consequent loss of therapy response due to the reduced susceptibility of CSCs to drugs. A particular feedback loop present in the xenografts has been shown to promote CSC enrichment in this system. Yet, many other regulatory loops might also be operational and might promote CSC enrichment. Their identification is central to improving therapy response. Here, we perform a comprehensive mathematical analysis to define what types of regulatory feedback loops can and cannot contribute to CSC enrichment, providing guidance to the experimental identification of feedback molecules. We derive a formula that reveals whether or not the cell population experiences CSC enrichment over time, based on the properties of the feedback. We find that negative feedback on the CSC division rate or positive feedback on differentiated cell death rate can lead to CSC enrichment. Further, the feedback mediators that achieve CSC enrichment can be secreted by either CSCs or by more differentiated cells. The extent of enrichment is determined by the CSC death rate, the CSC self-renewal probability, and by feedback strength. Defining these general characteristics of feedback loops can guide the experimental screening for and identification of feedback mediators that can promote CSC enrichment in bladder cancer and potentially other tumors. This can help understand and overcome the phenomenon of CSC-based therapy resistance.

Genetic diversification of acanthocephalans of the genus Floridosentis Ward 1953 (Acanthocephala: Neoechinorhynchidae), parasites of mullets from the Americas

Adult worms of the genus Floridosentis are endoparasites of marine fishes of the genus Mugil and are broadly distributed in the Americas. Currently, Floridosentis includes two species, F. mugilis, distributed in the Gulf of Mexico and along the Atlantic Ocean coast, and F. pacifica, restricted to the Pacific Ocean coast. The aim of this study was to explore the species limit of both species of the genus Floridosentis, collected in 37 localities in eight countries: Mexico, Guatemala, El Salvador, Honduras, Nicaragua, Costa Rica, Ecuador and Venezuela. We sequenced 253 specimens to build a comprehensive dataset for three genes: the cytochrome c oxidase subunit I (cox 1) from mitochondrial DNA, the internal transcribed spacers ITS1 and ITS2 including the 5.8S gene (ITS region), and the D2 + D3 domains of the large subunit (LSU) of nuclear DNA. Maximum likelihood and Bayesian analyses with the cox 1 and concatenated (cox 1 + ITS+LSU) datasets were conducted. Two species delimitation methods were implemented, the Automatic Barcode Gap Discovery (ABGD), and Bayesian species delimitation (BPP), plus a haplotype network inferred with 253 specimens, allowing us to validate two nominal species of Floridosentis., F. mugilis, plus one linage distributed in the Gulf of Mexico and along the Atlantic Ocean coast, and F. pacifica, plus two additional lineages distributed along the Pacific Ocean coast. All these lineages are shared by both species of mullet (Mugil curema and M. cephalus). The currents in the Atlantic Ocean, Pacific Ocean and Gulf of Mexico, in combination with the biology of the definitive hosts, have played a key role in the distribution of the two nominal species and of the three lineages of Floridosentis across the Americas.

Asexual organisms, identity and vertical gene transfer

This paper poses a problem for traditional phylogenetics: The identity of organisms that reproduce through fission can be understood in several different ways. This prompts questions about how to differentiate parent organisms from their offspring, making vertical gene transfer unclear. Differentiating between parents and offspring stems from what I call the identity problem. How the problem is resolved has implications for phylogenetic groupings. If the identity of a particular asexual organism persists through fission, the vertical lineage on a phylogenetic tree will split differently than if the identity of an organism does not survive the fission process.

Lineage-specific differences in lipid metabolism and its impact on clinical strains of Mycobacterium tuberculosis

Mycobacterium tuberculosis (M. tb) is the causative agent of TB and its incidences has been on the rise since 1993. Lipid metabolism is an imperative metabolic process, which grants M. tb the ability to utilize host-derived lipids as a secondary source of nutrition during infection. In addition to degrading host lipids, M. tb is proficient at using lipids, such as cholesterol, to facilitate its entry into macrophages. Mycolic acids, constituents of the mycobacterial cell wall, offer protection and aid in persistence of the bacterium. These are effectively synthesized using a complex fatty acid synthase system. Many pathogenesis studies have reported differences in lipid-metabolism of clinical strains of M. tb that belongs to diverse lineages of the Mycobacterium tuberculosis complex (MTBC). East-Asian and Euro-American lineages possess "unique" cell wall-associated lipids compared to the less transmissible Ethiopian lineage, which may offer these lineages a competitive advantage. Therefore, it is crucial to comprehend the complexities among the MTBC lineages with lipid metabolism and their impact on virulence, transmissibility and pathogenesis. Thus, this review provides an insight into lipid metabolism in various lineages of the MTBC and their impact on virulence and persistence during infection, as this may provide critical insight into developing novel therapeutics to combat TB.

IGF1R constitutive activation expands luminal progenitors and influences lineage differentiation during breast tumorigenesis

Breast tumors display tremendous heterogeneity in part due to varying molecular alterations, divergent cells of origin, and differentiation. Understanding where and how this heterogeneity develops is likely important for effective breast cancer eradication. Insulin-like growth factor (IGF) signaling is critical for normal mammary gland development and function, and has an established role in tumor development and resistance to therapy. Here we demonstrate that constitutive activation of the IGF1 receptor (IGF1R) influences lineage differentiation during mammary tumorigenesis. Transgenic IGF1R constitutive activation promotes tumors with mixed histologies, multiple cell lineages and an expanded bi-progenitor population. In these tumors, IGF1R expands the luminal-progenitor population while influencing myoepithelial differentiation. Mammary gland transplantation with IGF1R-infected mammary epithelial cells (MECs) resulted in hyperplastic, highly differentiated outgrowths and attenuated reconstitution. Restricting IGF1R constitutive activation to luminal versus myoepithelial lineage-sorted MECs resulted in ductal reconstitutions co-expressing high IGF1R levels in the opposite lineage of origin. Using in vitro models, IGF1R constitutively activated MCF10A cells showed increased mammosphere formation and CD44+/CD24-population, which was dependent upon Snail and NFκB signaling. These results suggest that IGF1R expands luminal progenitor populations while also stimulating myoepithelial cell differentiation. This ability to influence lineage differentiation may promote heterogeneous mammary tumors, and have implications for clinical treatment.

Influenza A and B in a cohort of outpatient children and adolescent with influenza like-illness during two consecutive influenza seasons

INTRODUCTION

Influenza is an important cause of morbimortality worldwide. Although people at the extremes of age have a greater risk of complications, influenza has been more frequently investigated in the elderly than in children, and inpatients than outpatients. Yearly vaccination with trivalent or quadrivalent vaccines is the main strategy to control influenza.

OBJECTIVES

Determine the clinical and molecular characteristics of influenza A and B infections in children and adolescents with influenza-like illness (ILI).

METHODS

A cohort of outpatient children and adolescents with ILI was followed for 20 months. Influenza was diagnosed with commercial multiplex PCR platforms.

RESULTS

179 patients had 277 episodes of ILI, being 79 episodes of influenza A and 20 episodes of influenza B. Influenza A and B cases were mild and had similar presentation. Phylogenetic tree of influenza B viruses showed that 91.6% belonged to the B/Yamagata lineage, which is not included in trivalent vaccines.

CONCLUSIONS

Influenza A and B are often detected in children and adolescents with ILI episodes, with similar and mild presentation in outpatients. The mismatch between the circulating influenza viruses and the trivalent vaccine offered in Brazil may have contributed to the high frequency of influenza A and B in this population.

First detection and genotypic analysis of goat enzootic nasal tumor virus 2 in Chongqing, China

Enzootic nasal adenocarcinoma (ENA) of goats, characterized by transformation of epithelial cells of the ethmoid turbinates, is caused by enzootic nasal tumor virus 2 (ENTV-2). ENTV-2 belongs to the genus Betaretrovirus and has extended its distribution globally with a high prevalence; however, the genetic diversity and genotypic distribution for ENTV-2 have not been analyzed systematically due to the limited availability of sequence data. In this study, an infection by ENTV-2 was detected by RT-PCR in Chongqing in July 2018, and the complete sequence of one strain (CQ1) was determined. Phylogenetic analysis indicated a high degree of genetic heterogeneity among ENTV-2 sequences, with the existence of two main lineages. Lineage 1 and 2 were composed of ENTV-2 from China and the UK, respectively. Although CQ1 was closely related to recent ENTV-2 strains collected in the neighboring provinces of Chongqing (Shaanxi and Sichuan), it formed a separate sublineage of lineage 1 (sublineage 1.3). This report will enhance our understanding of the epidemiology of ENTV-2 in China.

G and P genotype profiles of rotavirus A field strains circulating in beef and dairy cattle herds in Brazil, 2006-2015

The aim of this retrospective study was to use RT-PCR and nucleotide sequencing analysis to determine the G (VP7 gene) and P (VP4 gene) genotypes of 155 Brazilian bovine rotavirus A (RVA) wild-type strains detected in diarrheic calves from all Brazilian geographical regions from 2006 to 2015. The RVA strains evaluated belonged to the G6, G10, P[5], and P[11] genotypes. The G6P[5] genotype was prevalent (65.5%; P < 0.05) in beef, and the G10P[11] (38.4%) and G6P[11] (30.8%) genotypes were more prevalent in dairy cattle herds. The Midwest was the region with the highest number of genotyped RVA strains, where the genotypes G6, P[5], and P[11] were identified. Genotype combination G6-IV/P[5]-IX, prevalent in beef herds, and G6-III/P[11]-III or G10-IV/P[11]-III, prevalent in dairy herds, were detected. In addition, for the first time in Brazil, we detected the P[5] and P[11] genotype RVA strains that belong to lineage II and VII, respectively.

A next generation sequencing approach for targeted Varroa destructor (Acari: Varroidae) mitochondrial DNA analysis based on honey derived environmental DNA

Honey contains DNA from many different organisms that are part of hive micro-environmental niches and honey bee pathospheres. In this study, we recovered and sequenced mite mitochondrial DNA (mtDNA) from honey from different locations around the world (Europe, Asia, Africa, North and South America). DNA extracted from 17 honey samples was amplified with eight primer pairs targeting three mite mtDNA genes, obtaining 88 amplicons that were sequenced with an Ion Torrent sequencing platform. A bioinformatic pipeline compared produced reads with Varroa spp. mtDNA sequence entries available in GenBank and assigned them to different mitotypes. In all honey samples, the highest percentage of reads was attributed to the K1 lineage, including a few variants derived from it, in addition to J1 reads observed in the two South American samples and C1-1 reads obtained from the Chinese honey. This study opens new possibilities to analyse mite lineages and variants and monitor their geographical and temporal distribution, simplifying surveillance against this damaging honey bee parasite.

Emergence of new genotypes and lineages of dengue viruses during the 2012-15 epidemics in southern India

OBJECTIVES

To genotypically characterize dengue virus (DENV) isolates among dengue-infected children from 2012-13/2014-15 outbreaks in southern India.

METHODS

Children hospitalized with suspected dengue were tested for dengue RT-PCR targeting Capsid-preMembrane (C-prM) and Envelope (Env) regions. Following virologic confirmation (n=612), a representative selection of DENV isolates (n=99) were sequenced for C-prM, aligned using ClustalW and subjected to phylogenetic analysis by maximum-likelihood method in MEGA6.

RESULTS

In 2012-13 (n=113), DENV-3 (44, 38.9%) and DENV-2 (43, 38.1%) predominated; DENV-1 (22, 19.5%) and DENV-4 (1, 0.9%) were less common. The pattern changed in 2014-15 (n=499), when DENV-1 (329, 65.7%) predominated, followed by DENV-2 (97, 21.2%), DENV-3 (36, 6.7%) and DENV-4 (10, 2.0%). Multiple-serotype co-infections occurred in 2.7% and 5.4% in 2012-13 and 2014-15, respectively. Genotype III (GIII) of DENV-1 predominated (85.7%) in 2012-13, ceding to GI predominance (80.8%) in 2014-15. Among DENV-2, 71.9% (23/32) showed distinct clustering suggesting a new lineage, 'GIVc'. All tested DENV-4 were GIC, whose clustering pattern showed the emergence of two distinct clades.

CONCLUSIONS

New genotypic/lineage variations in DENV-1 and DENV-2 may have influenced the magnitude and severity of dengue epidemics in southern India during this period. These findings emphasize the role of active surveillance of DENV serotypes/genotypes in aiding outbreak control and vaccine studies.

Characterization of human parainfluenza virus-3 circulating in Israel, 2012-2015

BACKGROUND

Human parainfluenza virus 3 (hPIV-3) causes respiratory tract infection.

OBJECTIVES

The objective of this study was to describe the epidemiology of hPIV-3 infection among hospitalized patients and characterize the circulating strains.

STUDY DESIGN

A cross-sectional study was conducted using respiratory samples of 15,946 hospitalized patients with respiratory symptoms in 2012-2015 in Israel. All samples were subjected to q-PCR and q-RT-PCR to determine the presence of hPIV-3 and other respiratory viruses. Samples positive for hPIV-3 were subjected to molecular typing and phylogenetic analysis.

RESULTS

Overall, 547 samples 3.4% (95% CI 3.2-3.7) were positive for hPIV-3. Of these 87 (15.9%) were mixed infections; 41.4% with adenovirus, 40.2% with RSV (40.2%) and 19.5% influenza A viruses. The prevalence of hPIV-3 was highest (5.1%) in children aged 0-4 years. Hospitalization in oncology department was associated with increased likelihood of hPIV-3 infection: adjusted odds ratio [aOR] 2.29 (95% confidence intervals [CI] 1.78-2.96), as well as hospitalization in organ transplantation department: aOR 3.65 (95% CI 2.80-4.76). The predominant lineages were C3c (62.3%) and C1b (24.6%), followed by sub-lineages C5 (8.7%) and C3b (2.9%). A new sub-lineage emerged in our analysis, named C1d, which was 17 (1.5%) nucleotide different from C1a, 25 (2.2%) nucleotide different from C1b and 24 (2.1%) nucleotide different from C1c.

DISCUSSION

Young children and immunocompromised patients are likely the risk groups for severe respiratory infections with hPIV-3. Strains belonging to lineages C3c and C1b, which are present worldwide, should be targeted in vaccine development. The emergence of new lineage might have public health implications and on vaccine development.

Phylogenetic analysis of the wild-type strains of canine distemper virus circulating in the United States

Background

Canine distemper (CD) is a highly contagious, systemic, viral disease of dogs seen worldwide. Despite intensive vaccination in developed countries, recent reports suggest both the re-emergence and increased activity of Canine distemper virus (CDV) worldwide, including the United States. CDV is an RNA virus of the genus Morbillivirus within the family Paramyxoviridae. Viral genomic RNA encodes six structural proteins. Of the six structural proteins, the hemagglutinin (H) gene has the greatest genetic variation and is therefore a suitable target for molecular epidemiological studies. The majority of neutralizing epitopes are found on the H protein, making this gene also important for evaluation of changes over time that may result in antigenic differences among strains. The aim of this study was to determine the phylogenetic relationship of CDV strains circulating in the US.

Methods

Fifty-nine positive canine distemper virus samples collected from dogs from different regions and states from 2014 to 2017 were sequenced with a targeted next-generation sequencing (NGS) method. The sequences of the H, F, and P genes and the matrix-fusion (M-F) intergenic region of the amplified CDVs were analyzed individually.

Results

Sequence analysis of the H gene revealed that there are at least 3 different lineages of CDV currently circulating in the US. These lineages include America-3 (Edomex), America-4, and a clade that was previously reported in association with an outbreak in Wyoming, which was linked to a domestic dog-breeding facility in Kansas in 2010. These lineages differ from the historically identified lineages in the US, including America-1, which contains the majority of the vaccine strains. Genetic differences may result in significant changes to the neutralizing epitopes that consequently may lead to vaccine failure. Phylogenetic analyses of the nucleotide sequences obtained in this study of the F and P genes and the M-F intergenic region with sequences from the GenBank database produced similar findings to the H gene analysis.

Conclusions

The CDV lineages currently circulating in the US differ from the historically identified lineages America-1. Continuous surveillance is required for monitoring circulating CDV strains in the US, to prevent potential vaccine breakthrough events.

Electronic supplementary material

The online version of this article (10.1186/s12985-018-1027-2) contains supplementary material, which is available to authorized users.

Toxoplasma gondii Lineages Circulating in Slaughtered Industrial Pigs and Potential Risk for Consumers

Toxoplasma gondii is a cosmopolitan zoonotic protozoan parasite, and the consumption of raw or undercooked pig meat is one of the most important sources of T. gondii infection. Three predominant lineages, types I, II, and III, are widespread in Europe. Although still poorly understood, a relationship between each type and the severity of illness represents a public health issue. To gain further knowledge of the genotypes in circulation and of the potential risk for consumers, one heart sample and one diaphragm sample (206 total) were taken from each of 103 pig carcasses at an abattoir in Italy. Then, we used 529-bp repetitive element PCR and a B1 real-time PCR high-resolution melting assay coupled with sequencing to detect and genotype T. gondii isolates. T. gondii DNA was detected in 14 pigs (13.6%, 95% confidence interval = 7 to 20.2%), and types I (3.9%), II (5.8%), and III (3.9%) were identified. We found that heart tissue had a significantly higher PCR positivity rate for T. gondii than did diaphragm tissue. This is Europe's largest study on genotyping of T. gondii from pigs, and it demonstrates that all three main lineages are present in carcasses of industrially reared pigs in Italy. There is a potential risk to consumers of infection with any or all of the three lineages, and the related clinical consequences should be taken into account. This study suggests that monitoring of T. gondii types in meat is essential, especially in meat that is traditionally eaten raw or that is minimally processed.

Characteristics of methicillin-resistant Staphylococcus aureus in patients on admission to a teaching hospital in Rio de Janeiro, Brazil

BACKGROUND

Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) are associated with greater mortality and morbidity; however, risk factors for community-acquired infections caused by MRSA have not been established. Therefore, community patients who are admitted to hospitals without the necessary contact precautions and are infected with community-acquired lineages eventually cause these lineages to spread to these settings. The aim of this study was to detect community-acquired lineages of MRSA in patients on admission to a Brazilian teaching hospital.

METHODS

The antimicrobial susceptibility of the MRSA isolates from nasal swabs was evaluated as was the molecular characteristics of the staphylococcal cassette chromosome mec (SCCmec). The clonality was determined using pulsed-field gel electrophoresis and multilocus sequence type analysis.

RESULTS

A total of 702 patients were evaluated between March 2012 and March 2013; 180 (25%) of them were colonized by S aureus, and 21 (3%) were MRSA. The SCCmec IV/USA1100/sequence type (ST) 30 was the predominant MRSA lineage (42.8%), followed by SCCmec IV/USA800/ST5 (23.8%).

CONCLUSIONS

The occurrence of MRSA colonization was very low, and only 1 patient from cardiac surgery developed an infection, which was caused by an SCCmec II/USA100/ST5 isolate. Screening for MRSA colonization on admission does not seem to be productive; however, for populations submitted to specific surgeries, active surveillance should be implemented.

New genetic lineage within the Siberian subtype of tick-borne encephalitis virus found in Western Siberia, Russia

Tick-borne encephalitis virus (TBEV), a member of the Flaviviridae family, is a causative agent of a severe neurological disease. There are three main TBEV subtypes: the European (TBEV-Eu), Far Eastern (TBEV-FE), and Siberian (TBEV-Sib). Currently, three lineages within TBEV-Sib have been recorded. In this study, the genetic and biological characteristics of a new original strain, TBEV-2871, isolated in the Novosibirsk province of Western Siberia, Russia were investigated. The strain has low neuroinvasiveness in mice. Phylogenetic analysis demonstrated that TBEV-2871 belongs to TBEV-Sib, but does not cluster with any of the TBEV-Sib lineages. The TBEV-2871 strain has 88-89% nucleotide sequence identity with the other TBEV-Sib strains, 84-86% nucleotide sequence identity with the TBEV-FE and TBEV-Eu subtypes and is genetically close to the subtype division border. The TBEV-2871 polyprotein sequence includes 43 unique amino acid substitutions, 30 of which are recorded at positions that are conserved among all TBEV subtypes. Strain TBEV-2871 and two similar but not identical isolates found in Kemerovo province, Western Siberia are separated into a new lineage tentatively named Obskaya after the name of Ob riber, in the vicinity of which the TBEV-2871 was first found. A molecular evolution investigation demonstrated that within TBEV-Sib, the Obskaya lineage likely separated 1535years ago, which is even earlier than the Baltic lineage.

Occurrence of Toxoplasma gondii in Carcasses of Pigs Reared in Intensive Systems in Northern Italy

To evaluate the occurrence of Toxoplasma gondii and to genetically characterize its isolates in carcasses of industrial fattening pigs, blood, diaphragm, and heart samples were collected from 375 carcasses of pigs slaughtered to be processed for Parma ham production. Pigs had been bred on approved farms (n = 75) located in the so-called Food Valley in Italy. Sera were examined for immunoglobulin G antibodies to T. gondii by modified agglutination test (MAT). Both heart and diaphragm samples from seropositive carcasses were processed for the presence of T. gondii DNA (B1 locus) by real-time PCR and high resolution melting (HRM) assay. Anti-Toxoplasma antibodies were detected in 2.1% of pig carcasses, with titers from 1:10 to 1:320. T. gondii DNA was detected in all (eight) seropositive carcasses and in 11 (5 heart and 6 diaphragm samples) of 16 samples; that is, it was detected in heart tissue in two subjects, in diaphragm tissue in three subjects, and in both muscle tissues in three subjects. Toxoplasma genotypes were determined in seven of eight carcasses: type III was identified in four carcasses, type II in two, and both III and II in one carcass. The serological findings and the molecular detection of T. gondii strains suggest that cured meat products obtained from industrially bred pigs may be potential sources of toxoplasmosis for humans. Our results provide novel, important information regarding the seroprevalence and molecular prevalence of T. gondii in intensively reared pigs within this specific region of Italy, particularly because Parma ham from this region is known and consumed worldwide. On-farm preventive measures combined with slaughterhouse monitoring of carcasses of pigs bred for cured meat production should never be overlooked to prevent the introduction of T. gondii into the food chain and to ensure safety for consumers of these products.

Evolutionary history and spatiotemporal dynamics of DENV-1 genotype V in the Americas

The genotype V has been the most prevalent dengue virus type 1 (DENV-1) clade circulating in the Americas over the last 40years. In this study, we investigate the spatiotemporal pattern of emergence and dissemination of DENV-1 lineages in the continent. We applied phylogenetic and phylogeographic approaches to a comprehensive data set of 836 DENV-1 E gene sequences of the genotype V isolated from 46 different countries around the world over a period of 50years (1962 to 2014). Our study reveals that genetic diversity of DENV-1 genotype V in the Americas resulted from two independent introductions of this genotype from India. The first genotype V strain was most probably introduced into the Lesser Antilles at around the early 1970s and this Caribbean region becomes the source population of several DENV-1 lineages that spread in the Americas during the 1970s and 1980s. Most of those lineages appear to become extinct during the 1990s, except one that persisted in Venezuela and later spread to other American countries, dominating the DENV-1 epidemics in the region from the early 2000s onwards. The second genotype V strain of Indian origin was also most probably introduced into the Lesser Antilles at around the early 1980s. This lineage remained almost undetected for nearly 15years, until it was introduced in Northern Brazil around the middle 1990s and later spread to other country regions. These results demonstrate that different geographic regions have played a role in maintaining and spreading the DENV-1 genotype V in the Americas over time. DENV-1 genotype V lineages have originated, spread and died out in the Americas with very different dynamics and the phenomenon of lineage replacement across successive DENV-1 epidemic outbreaks was a common characteristic in most American countries.

Zika Virus Strains Potentially Display Different Infectious Profiles in Human Neural Cells

The recent Zika virus (ZIKV) epidemic has highlighted the poor knowledge on its physiopathology. Recent studies showed that ZIKV of the Asian lineage, responsible for this international outbreak, causes neuropathology in vitro and in vivo. However, two African lineages exist and the virus is currently found circulating in Africa. The original African strain was also suggested to be neurovirulent but its laboratory usage has been criticized due to its multiple passages. In this study, we compared the French Polynesian (Asian) ZIKV strain to an African strain isolated in Central African Republic and show a difference in infectivity and cellular response between both strains in human neural stem cells and astrocytes. Consistently, this African strain led to a higher infection rate and viral production, as well as stronger cell death and anti-viral response. Our results highlight the need to better characterize the physiopathology and predict neurological impairment associated with African ZIKV.

A multiplex PCR for detection of Listeria monocytogenes and its lineages

A novel multiplex PCR assay was developed to identify genus Listeria, and discriminate Listeria monocytogenes and its major lineages (LI, LII, LIII). This assay is a rapid and inexpensive subtyping method for screening and characterization of L. monocytogenes.

Real time PCR assay for detection of all known lineages of West Nile virus

West Nile virus (WNV) is one of the most widespread arbovirus and a large variety of WNV strains and lineages have been described. The molecular methods for the diagnosis of WNV target mainly lineages 1 and 2, which have caused outbreaks in humans, equines and birds. But the last few years new and putative WNV lineages of unknown pathogenicity have been described. Here we describe a new sensitive and specific real-time PCR assay for the detection and quantification of all the WNV lineages described until now. Primers and probe were designed in the 3'-untranslated region (3'-UTR) of the WNV genome and were designed to match all sequenced WNV strains perfectly. The sensitivity of the assay ranged from 1,5 to 15 copies per reaction depending on the WNV lineage tested. The method was validated for WNV diagnosis using different viral strains, human samples (cerebrospinal fluid, biopsies, serum and plasma) and mosquito pools. The assay did not amplify any other phylogenetically or symptomatically related viruses. All of the above make it a very suitable tool for the diagnosis of WNV and for surveillance studies.

Analysis of an echovirus 18 outbreak in Thuringia, Germany: insights into the molecular epidemiology and evolution of several enterovirus species B members

In October and November 2010, six children and one woman were presented with symptoms of aseptic meningitis in Jena, Thuringia, Germany. Enterovirus RNA was detected in the cerebrospinal fluid of all patients by RT-PCR, and preliminary molecular typing revealed echovirus 18 (E-18) as causative agent. Virus isolates were obtained from stool samples of three patients and several contact persons. Again, most isolates were typed as E-18. In addition, coxsackievirus B5 (CV-B5) and echovirus 25 (E-25) were found to co-circulate. As only few complete E-18 sequences are available in GenBank, the entire genomes of these isolates were determined using direct RNA-sequencing technology. We did not find evidence for recombination between E-18, E-25 or CV-B5 during the outbreak. Viral protein 1 gene sequences and the cognate 3D polymerase gene sequences of each isolate and GenBank sequences were analysed in order to define type-specific recombination groups (recogroups).

Phylodynamics of DENV-1 reveals the spatiotemporal co-circulation of two distinct lineages in 2013 and multiple introductions of dengue virus in Goiás, Brazil

Dengue virus type 1 (DENV-1) was the first serotype introduced in Brazil, during in the 1980s. Since then, this virus has spread in the Brazilian territory, causing several outbreaks. In 2013 the highest number of dengue cases was notified, when compared to the previous years in Brazil, and the state of Goiás reported over 160 thousand cases. In this study, we aimed to present the Phylodynamics of DENV-1 isolates from the state of Goiás, Brazil, during 2013 outbreak, based on the envelope gene (E) sequences. Phylogenetic analysis revealed that Brazilian DENV-1 isolates are grouped together with viruses from genotype V in two distinct lineages (lineage I and lineage II) reflecting co-circulation. Phylogeographic analyses showed that these lineages were introduced in different moments in Goiás, Brazil, using distinct routes, likely originated from the Caribbean. Lineage I was first introduced coming from Rio de Janeiro (2007-2012), followed by the introduction from Argentina (2010-2013). Lineage II was introduced in a single moment from Rio de Janeiro and this clade has existed since 2007-2010. The different viral introduction events demonstrate the viral dispersion process with neighboring regions, which is essential for the maintenance of outbreaks and introduction of new emerging viruses. In conclusion, obtained data reveals the importance of continuous molecular surveillance of this virus in different regions, providing a better understanding of DENV-1 circulation, considering the evolutionary and virus spread patterns.

"Population structure of drug-susceptible,-resistant and ESBL-producing Escherichia coli from community-acquired urinary tract"

Background

Escherichia coli is the most common cause of urinary tract infection (UTI). The pathogenic isolates are becoming increasingly resistant to antibiotics; with a worldwide dissemination of resistant sequence types (ST). We characterized three different uropathogenic E. coli populations, from non-hospitalized patients to describe the genetic kinship between resistant and susceptible isolates. We studied the populations by use of multi-locus sequence typing (MLST) and abbreviated-multi locus variable number of tandem repeat analysis (a-MLVA). Urine samples submitted for testing, by general practitioners, were identified at Dept. of Clinical Microbiology at Hvidovre Hospital, Denmark, from Oct. 2011 to July 2012. We included 94 fully susceptible, 94 resistant (non-ESBL) and 98 Extended Spectrum Beta-lactamases- (ESBL)-producing E. coli isolates.

Results

The ESBL population was dominated vastly by ST131 (51 %), ST38 (9 %) and ST69 (6 %). In the resistant group ST69 (18 %), ST73 (11 %) and ST131 (15 %) were the largest clusters. In the susceptible population more STs and a-MLVA codes were identified compared to the other groups and ST73 and ST95 were found as the only clusters with 16 % and 6 %, respectively. Ninety-eight per cent of the ESBL-producing E. coli isolates were CTX-M-producers.

Conclusion

ST131 dominated the population of community-associated uropathogenic ESBL-producing E. coli, but was less frequent among non-ESBL-producing E. coli. The fully susceptible E. coli population was a much more diverse group than the resistant and ESBL-producing E. coli populations. Overall, these findings suggest that dominant ESBL-producing lineages are derived from UPEC lineages already established in the general UPEC population.

Electronic supplementary material

The online version of this article (doi:10.1186/s12866-016-0681-z) contains supplementary material, which is available to authorized users.