North American Isolates Research Articles

A new subtype of serovar 6, K6b:O3, of Actinobacillus pleuropneumoniae based on genotypic analysis

We have analyzed the capsule (CPS) and the lipopolysaccharide O-Antigen (O-Ag) biosynthesis loci of fifteen field isolates of Actinobacillus pleuropneumoniae, including eleven North American and four Japanese ones, reactive to antisera against serovars 3, 6, 8 and/or 15. Ten North American isolates amplified a serovar 6-indicative fragment derived from the capsular loci, whereas one North American isolate and all four Japanese isolates amplified the serovar 6-indicative fragment as well as the serovar 3-indicative fragment. The five isolates producing a 3/6 banding pattern contain a type I CPS locus, named K6b, similar to serovar 6, but with differences in the cpxABCD and cpsABC gene sequences and the length of intergenic regions (modF-cpxA, and cpsC-cpsD). The main difference found between the K6 and K6b cps genes is a loss of function of a 113 AA UDP-glycosyltransferase found in type 6b due to the amino acid substitutions in the C-terminal domain of Cps6bA. Additionally, the isolates harbor a LPS O-Ag locus highly identical to those of field and reference strains of serovars 3, 8, 15, 17 and 19 but different from that of serovar 6. Taken together, our results indicate the existence of a subtype of A. pleuropneumoniae, serovar 6, that we called “K6b:O3′′, and we propose isolate EH1248 as the reference strain.

Dear Malaria: Deer Have Malaria! Prevalence ofPlasmodium odocoilei Infection in White-tailed deer in Pennsylvania

Abstract Background To combat antimalarial treatment resistance, better understanding of malaria pathogenesis is needed, but existing animal model have various limitations. Notably, prevailing murine models require laboratory infection of non-natural host species. In 2016, the parasite Plasmodium odocoilei was identified in white-tailed deer (Odocoileus virginianus). This was the first non-human mammalian malaria parasite identified in North America, representing a novel naturally occurring model system that allows for integrated examination of host, vector, and systems parasite biology. In addition, sickle hemoglobinopathy is exceptionally common among white-tailed deer, occurring in up to 60% of apparently healthy animals. In humans, the prevalence of sickle hemoglobinopathy in individuals with ancestry from malaria-endemic regions is due to the protective effects of sickle trait against severe malaria. Thus, the white-tailed deer-P. odocoilei system represents the only known naturally occurring model of the association between malaria parasite biology and sickle cell disease. Pennsylvania white-tailed deer have not previously been surveyed for infection. In this study, we determined P. odocoilei prevalence in a sample of 170 Pennsylvania white-tailed deer. Methods We amplified the CytB gene of P. odocoilei by nested PCR from DNA extracted from homogenized white-tailed deer tongue tissue obtained from the PennVet Wildlife Futures Program. We confirmed samples screening positive on gel electrophoresis via unprimed sequencing (Plasmidsaurus, USA) and NCBI-BLAST analysis. Results We estimate the prevalence of P. odocoilei infection in Pennsylvania white-tailed deer to be 0.6% (1 of 170 samples). Sequencing of the positive sample revealed a 621-bp sequence with close sequence identity to previous North American isolates of P. odocoilei (query cover 91-100%, percent identity 99.34-100.00%). Biobank metadata showed the positive sample originated from a roadkilled yearling male picked up at GPS coordinates (40.8423, -79.0409) on August 15, 2022. Conclusion P. odocoilei is endemic to Pennsylvania white-tailed deer. Our future directions include screening of additional samples, determination of host hemoglobin allele frequencies, detailed parasite genetic studies, and entomologic studies to elucidate vector biology. In addition, granular sample metadata collected by the PennVet Wildlife Futures Program will allow us to analyze the effects of geographic, demographic, and temporal variables on epidemiology. In sum, our survey data empowers future Pennsylvania-based studies to take advantage of the only known naturally occurring animal model of sickling and its association with protozoan infection.

Comparative evaluation of three real-time polymerase chain reaction assays to detect Myxobolus cerebralis.

We sought to evaluate accurate and reproducible detection of Myxobolus cerebralis (Mc), the causative agent of whirling disease, by using nested polymerase chain reaction (nPCR) and three previously established real-time quantitative PCR (qPCR) assays: K18S (Kelley 18S), C18S (Cavender 18S), and Hsp70 (heat shock protein 70). We used a "fit for purpose" approach combined with intra- and interlaboratory testing to identify a molecular testing method that would be equivalent to the currently accepted nPCR procedure for Mc. Assay performance was compared using a combination of intra- and interlaboratory testing that used synthetic gBlocks along with naturally and experimentally infected fish tissue. North American isolates representing geographically distinct locations were also tested using all three assays. The K18S and C18S assays exhibited high assay sensitivity, intra- and interlaboratory repeatability of sample replicates, and reproducible identification of all test samples across multiple laboratories. In contrast, the Hsp70 assay failed to detect several positive samples at low DNA concentrations during intra- and interlaboratory testing. The K18S assay was the only procedure that demonstrated perfect detection accuracy when testing geographically distinct Mc isolates. Results demonstrated the K18S assay is robust under variable test conditions, is more accurate than the C18S and Hsp70 assays, and provides detection capabilities equivalent to those of the currently accepted nPCR confirmation assay "gold standard" that is described in the American Fisheries Society-Fish Health Section (AFS-FHS) Blue Book. The "fit for purpose" approach and preliminary completion of the World Organization for Animal Health validation pathway demonstrate that the K18S assay provides an alternate method for Mc testing. This work provides the foundation for acceptance of the K18S assay into the AFS-FHS Blue Book as a standardized test procedure for Mc.

Population structure and ongoing microevolution of the emerging multidrug-resistant Salmonella Typhimurium ST213

Salmonella enterica serovar Typhimurium ST213 is an emergent multidrug-resistant sequence type associated with the food chain, and gastrointestinal and invasive infections in North America. Here, we applied genomic and phenotypic analyses to illustrate the diversity and evolution of sequence type ST213. The population structure and evolutionary history of ST213 strains, particularly the North American isolates (NA-ST213) distinguish them from other S. Typhimurium sequence types, including European ST213 strains. NA-ST213 isolates were distributed in four co-circulating lineages with distinct multidrug resistance profiles and unique phage and CRISPR spacers patterns that could have shaped their local microevolution. Compared to the SL1344 reference strain, NA-ST213 demonstrated reduced adherence and internalization in cultured eukaryotic cell lines but exhibited more efficient replication and intracellular survival. This study underscores the relevance of studying an emergent S. Typhimurium sequence type and the events leading to its diversification beyond the well-characterized reference strains and worldwide predominant sequence types. However, it must also serve as a cautionary tale of the potential health risk the NA-ST213 may represent; particularly when there is a close relationship with pandemic sequence types such as the monophasic ST34.

Highly pathogenic avian influenza virus H5N1 clade 2.3.4.4b from Peru forms a monophyletic group with Chilean isolates in South America

Highly pathogenic avian Influenza virus (HPAIV) has spread in an unprecedented extent globally in recent years. Despite the large reports of cases in Asia, Europe, and North America, little is known about its circulation in South America. Here, we describe the isolation, and whole genome characterization of HPAIV obtained from sampling 26 wild bird species in Peru, representing one of the largest studies in our region following the latest HPAIV introduction in South America. Out of 147 samples analyzed, 22 were positive for detection of avian influenza virus using a qRT-PCR-based assay. Following inoculation into embryonated chicken eggs, fourteen viral isolates were obtained from which nine isolates were selected for genome characterization, based on their host relevance. Our results identified the presence of HPAIV H5N1 subtype in a highly diverse wild bird species. Phylogenetic analysis revealed that these isolates correspond to the clade 2.3.4.4b, sharing a common ancestor with North American isolates and forming a monophyletic group along with isolates from Chile. Altogether, changes at the amino acid levels compared to their closest relatives indicates the virus is evolving locally, highlighting the need for constant genomic surveillance. This data evidence the chances for spillover events increases as the virus spreads into large populations of immunologically naïve avian species and adding conditions for cross species transmission.

Evolution and Current Status of Influenza A Virus in Chile: A Review.

The influenza A virus (IAV) poses a significant global threat to public health and food security. Particularly concerning is the avian influenza virus (AIV) subtype H5N1, which has spread from Europe to North and Central/South America. This review presents recent developments in IAV evolution in birds, mammals, and humans in Chile. Chile's encounter with IAV began in 2002, with the highly pathogenic avian influenza (HPAI) H7N3 virus, derived from a unique South American low pathogenic avian influenza (LPAI) virus. In 2016-2017, LPAI H7N6 caused outbreaks in turkey, linked to wild birds in Chile and Bolivia. The pandemic influenza A (H1N1) 2009 (H1N1pdm09) virus in 2009 decreased egg production in turkeys. Since 2012, diverse IAV subtypes have emerged in backyard poultry and pigs. Reassortant AIVs, incorporating genes from both North and South American isolates, have been found in wild birds since 2007. Notably, from December 2022, HPAI H5N1 was detected in wild birds, sea lions, and a human, along Chile's north coast. It was introduced through Atlantic migratory flyways from North America. These findings emphasize the need for enhanced biosecurity on poultry farms and ongoing genomic surveillance to understand and manage AIVs in both wild and domestic bird populations in Chile.

First Report of Powdery Mildew Caused by Golovinomyces ambrosiae on Solanum carolinense in Korea.

Solanum carolinense L. (Solanaceae) is a perennial herbaceous plant native to the southeastern United States. The plant has been invasive in Europe, Australia, and Asia. It was accidentally introduced to Korea in the 1960s (Oh et al. 2002) and is now widely naturalized mostly in the southern area of the Korean peninsula. Since 2002, it has been designated as one of 'harmful non-indigenous plants' by the Korean Ministry of Environment due to its adverse effects on native plants. In September 2014, several S. carolinense plants were found infested with a powdery mildew disease in Busan, which was the first for Korea. Later in 2020-2022, hundreds of plants were continuously observed with an approximately 50% disease incidence in Jeonju, Korea. Symptoms first appeared as circular to irregular white patches, which subsequently coalesced to develop into abundant hyphal growth on both sides of the leaves. Representative voucher specimens were deposited in the Korea University herbarium (KUS-F28240 and F32541). Hyphal appressoria were nipple-shaped. Conidiophores were cylindrical, 110 to 190 × 10 to 12 µm, and produced 2 to 5 immature conidia in chains with a sinuate outline. Foot-cells of conidiophores were straight, cylindrical, and 58 to 90 μm long, followed by 2 to 3 cells. Conidia were ellipsoid to barrel-shaped, 29 to 36 × 15 to 20 μm (l/w 1.6 to 2.0), and devoid of distinct fibrosin bodies. Germ tubes were at the perihilar position of the conidia. Sexual stage was not developed. These morphological characteristics are consistent with those of Golovinomyces ambrosiae (Schwein.) U. Braun & R.T.A. (Braun and Cook 2012). Sequences of the internal transcribed spacer (ITS) region and large subunit (LSU) gene of rDNA were determined using primer pairs ITS1/PM6 and PM3/TW14, respectively (Bradshaw and Tobin 2020). A comparison of the resulting sequences using the BLASTn algorithm showed 100% identity with reference sequences of G. ambrosiae (MT355556, AB769425) and G. spadiceus (MN365027) for ITS and LSU in NCBI. Obtained sequences were deposited in GenBank (Accession Nos: OP585651-OP585654). A Maximum parsimony tree was constructed based on ITS+LSU dataset consisting of 23 sequences. Our sequences were clustered with sequences of G. ambrosiae, G. latisporus and G. cichoracearum, and supported with 100% BS value. A pathogenicity test was performed by gently dusting conidia onto leaves of five healthy potted plants. Five non-inoculated plants served as controls. Powdery mildew colonies developed on all inoculated plants after 5 days, whereas the control plants remained symptomless. The fungus present on the inoculated leaves was morphologically identical to that observed on the originally diseased leaves, which supports Koch's postulate. Previously, Erysiphe cichoracearum (syn. of G. cichoracearum) was recorded on this plant in theUSA (Farr and Rossman 2022). Since G. cichoracearum has been divided into several distinct species (Takamatsu et al. 2013, Qiu et al. 2020), the current taxonomic position of the North American isolate is unknown. In Korea, G. ambrosiae was reported on several asteraceous hosts such as Bellis perennis, Brachyscome multifida, Helianthus annuus, H. salicifolius, and Verbena bonariensis (Farr and Rossman 2022). To our knowledge, this is the first report of powdery mildew on this plant outside the USA. According to our field observations, powdery mildew infestation had little effect on plant growth and vigor.

Genetic variation and population differentiation in North American, central Asian and European isolates of Venturia inaequalis

AbstractVenturia inaequalis, the causal fungal pathogen of apple scab, has evolved with its Malus hosts during apple domestication. This co‐evolution has resulted in a genetic structure in V. inaequalis populations from Europe and central Asia based on host species and geographic isolation. However, it is not yet clear if geographic isolation has led to population differentiation in North American isolates. We resequenced the genomes of 54 V. inaequalis isolates from North America and analysed them with publicly available genome sequences of 90 European and central Asian isolates for variant discovery and population structure. A total of 204,566 high‐quality single‐nucleotide polymorphisms (SNPs) were identified and used to assess population genetic structure and genomic diversity across 123 Venturia spp. isolates from around the world. Population genetic analysis identified four clusters based on Malus and non‐Malus hosts and Venturia species; this differentiation was supported by genetic diversity parameters including FST, Nei's π and Tajima's D. Genetic structure analysis did not reveal a distinct subpopulation of North American V. inaequalis isolates within the global isolates. Additionally, structure was not observed in V. inaequalis isolates collected on M. × domestica between North America and Europe. These observations indicate that geographical isolation has not contributed to the population differentiation between North America and Europe/central Asia. These results will enhance our understanding of the evolution of V. inaequalis, the emergence of virulent isolates and their implications for managing apple scab effectively.

Unique genomic sequences in a novel Mycobacterium avium subsp. hominissuis lineage enable fine scale transmission route tracing during pig movement

Mycobacterium avium subsp. hominissuis (MAH) is one of the most prevalent mycobacteria causing non-tuberculous mycobacterial disease in humans and animals. Of note, MAH is a major cause of mycobacterial granulomatous mesenteric lymphadenitis outbreaks in pig populations. To determine the precise source of infection of MAH in a pig farm and to clarify the epidemiological relationship among pig, human and environmental MAH lineages, we collected 50 MAH isolates from pigs reared in Japan and determined draft genome sequences of 30 isolates. A variable number of tandem repeat analysis revealed that most pig MAH isolates in Japan were closely related to North American, European and Russian human isolates but not to those from East Asian human and their residential environments. Historical recombination analysis revealed that most pig isolates could be classified into SC2/4 and SC3, which contain MAH isolated from pig, European human and environmental isolates. Half of the isolates in SC2/4 had many recombination events with MAH lineages isolated from humans in East Asia. To our surprise, four isolates belonged to a new lineage (SC5) in the global MAH population. Members of SC5 had few footprints of inter-lineage recombination in the genome, and carried 80 unique genes, most of which were located on lineage specific-genomic islands. Using unique genetic features, we were able to trace the putative transmission route via their host pigs. Together, we clarify the possibility of species-specificity of MAH in addition to local adaptation. Our results highlight two transmission routes of MAH, one exposure on pig farms from the environment and the other via pig movement. Moreover, our study also warns that the evolution of MAH in pigs is influenced by MAH from patients and their residential environments, even if the MAH are genetically distinct.

Next-generation sequencing approach to investigate genome variability of Parapoxvirus in Canadian muskoxen (Ovibos moschatus).

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 131,759bp and a smaller right terminal contig of 3552bp, 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 3000bp 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.

Elucidating the life cycle of opossum parasites: DNA sequences reveal the involvement of planorbid snails as intermediate hosts of Rhopalias spp. (Trematoda: Echinostomatidae) in Brazil.

Echinostomatid digeneans belonging to the genus Rhopalias are intestinal trematodes found mainly in opossums in the New World. The genus comprises seven species, but their life cycles and intermediate hosts have been unknown until now. During our long-term study carried out in freshwater habitats within the state of Minas Gerais, Southeast Brazil, echinostomatid cercariae lacking collar spines were found in planorbid snails Biomphalaria glabrata, Biomphalaria straminea, Drepanotrema lucidum and Gundlachia ticaga in six different batches of snail samples collected between 2010 and 2019. Morphologically, the larvae reported herein are morphologically consistent with each other and characterized by the presence of 2-3 large ovoid or spherical corpuscles in each main duct of the excretory system, resembling to Cercaria macrogranulosa previously described from the same region of Brazil. Partial sequences of the ITS (ITS1-5.8S-ITS2) region and 28S gene of the nuclear ribosomal RNA operon, and partial sequences of mitochondrial nad1 and cox1 genes were obtained and compared with the data available for members of the family Echinostomatidae. Nuclear markers indicate that all samples of cercariae evaluated in the present study can be assigned to Rhopalias, but distinct from North American isolates of Rhopalias macracanthus, Rhopalias coronatus and Rhopalias oochi (divergence 0.2-1.2% in 28S and 0.8-4.7% in ITS). The lack of differences verified in both 28S and ITS in 5 out 6 studied samples suggested that they belong to the same species. However, nad1 sequences revealed that our cercariae correspond to three distinct species of Rhopalias (interspecific divergence: 7.7-9.9%), named here as Rhopalias sp. 1, found in B. straminea and G. ticaga, Rhopalias sp. 2 found in B. glabrata and D. lucidum, and Rhopalias sp. 3 also found in D. lucidum. They also differ by 10.8-17.2% from a North American isolate of R. macracanthus sequenced in this study. The cox1 sequences obtained for Rhopalias sp. 1 and Rhopalias sp. 2 (but not Rhopalias sp. 3) reveal that they are distinct from North American isolates of R. macracanthus (genetic divergence 16.3-16.5% and 15.6-15.7%, respectively), R. coronatus (9.2-9.3% and 9.3-9.5%) and Rhopalias oochi (9.0% and 9.5-10.1%). Encysted metacercariae with general morphology similar to that of the body of cercariae were found in tadpoles of Rhinella sp. from the same stream where snails harbored Rhopalias sp. 2, suggesting that the amphibians could act as second intermediate hosts of species of Rhopalias. Data obtained provide the first insights into the life cycle of this unusual echinostomatid genus.

Phylogenetic analysis and genotyping of Iranian infectious haematopoietic necrosis virus (IHNV) of rainbow trout (Oncorhynchus mykiss) based on the glycoprotein gene.

Infectious haematopoietic necrosis (IHN) is known as one of the most contagious systemic viral diseases in salmonids which can lead to significant mortality rates and negative impacts on the salmonid farming industry. Infectious haematopoietic necrosis virus (IHNV) was first detected in rainbow trout (Oncorhynchus mykiss) farms in Iran in 2003. We conducted the present study to determine the detection of IHN genotypes in rainbow trout (O. mykiss) in farms in the central parts of Iran, using molecular and phylogenetic techniques. Samples were collected from fries exhibiting clinical signs such as darkening of the skin, abdominal swelling, and loss of appetite. Phylogenetic analysis was performed by the neighbour-joining method, using MEGA 5.1 software. For phylogenetic analysis and genotyping of IHNV from central parts of Iran, the sequences of the glycoprotein gene were determined for two Iranian isolates (Jahad-UT1 and Jahad-UT2). Phylogenetic analysis revealed that the detected strains (Jahad-UT1 and Jahad-UT2 isolates) are closely related (97.23%-100%) to European isolates within genogroup 'E'. This finding indicates that Jahad-UT1 and Jahad-UT2 isolates have been widely transferred to Iran from European countries. Moreover, the nucleotide diversity of these Iranian isolates showed a close relationship with the North American and Asian isolates, although the Iranian isolates were collected from a smaller geographical area and within a shorter time period between 2014 and 2015.

A new species of Versteria (Cestoda: Taeniidae) parasitizing Galictis cuja (Carnivora: Mustelidae) from Patagonia, Argentina: Morphological and molecular characterization.

Via morphological and molecular analysis, we describe a new species of taeniid from Patagonia (Argentina): Versteria cuja n. sp., parasitizing the Lesser grison Galictis cuja (Molina) (Carnivora: Mustelidae). This is the first report of a species of Versteria in Argentina and for a native mustelid. The new species (the third in the genus Versteria) is proposed using an integrative taxonomic approach, based on traditional morphology (distinctive morphological and morphometric diagnostic characters), genetic distances and phylogeny based on molecular data, the distinct geographical distribution, and the different definitive host species. Versteria cuja n. sp. mainly differs from Versteria mustelae (Gmelin, 1790) (from Europe) in the number of testes (54–85 vs. 83–127 in V. mustelae), the rostellum size (39–75 vs. 85–180 μm in V. mustelae), the genital atrium size (170–420 vs. 68-91 μm in V. mustelae) and in the hooks’ shape. It also differs from the African species Versteria brachyacantha (Baer and Fain, 1951) by having smaller measurements regarding the main diagnostic characters, i.e. size of scolex, rostellum and suckers, number, size and shape of rostellar hooks, number of testes, and by having smooth cirrus (vs. cirrus covered with hair-like bristles in V. brachyacantha). Phylogenetical analysis using cox1 showed our specimens clustering with North American isolates of Versteria sp. in a well-supported American clade (mean genetic divergence 0.024), separated from another clade composed of different isolates of V. mustelae (0.093). The close relationship between the new species and the North American species, known as “zoonotic” Versteria sp., and responsible for fatal infections by metacestodes in free-ranging wildlife (rodents), captive primates and immunosuppressed people, lead us to think that the zoonotic potential of Versteria cuja n. sp. should not be discarded.

Piroplasmid infection is not associated with clinicopathological and laboratory abnormalities in cats from Midwestern Brazil.

Feline piroplasmids include the genera Babesia spp., Cytauxzoon spp., and Theileria spp. In Brazil, there are few reports regarding these hemoprotozoans; however, clinicopathological and molecular data are scarce. This study aimed to characterize the clinical relevance of these parasites through hematological, biochemical, and molecular approaches. For this purpose, 166 cats from Brasilia, Federal District, Midwestern Brazil, were screened using a quantitative polymerase chain reaction (qPCR) for piroplasmids based on the LSU4 mitochondrial gene, which resulted in an overall prevalence of 36/166 (21.7%). Twelve of 166 samples (7.2%) were positive for C. felis, while 19/166 (11.4%) were positive for Babesia vogeli. No samples tested positive for Theileria spp. Babesia vogeli and Cytauxzoon spp. LSU4 sequences showed identities of 97-100% and 99.3%, respectively, to US isolates. The hematological and biochemical findings did not differ significantly between the cats that tested positive and negative for piroplasmids. Although the lack of abnormalities in clinical and laboratory parameters does not eliminate the possibility that these cats were sick and recovered, it may suggest that the Brazilian strain of Cytauxzoon spp. is not as pathogenic as that from the USA, despite the high molecular identity with North American isolates.

Molecular Epidemiology of Turkey Coronaviruses in Poland.

The only knowledge of the molecular structure of European turkey coronaviruses (TCoVs) comes from France. These viruses have a quite distinct S gene from North American isolates. The aim of the study was to estimate the prevalence of TCoV strains in a Polish turkey farm during a twelve-year period, between 2008 and 2019, and to characterize their full-length S gene. Out of the 648 flocks tested, 65 (10.0%, 95% CI: 7.9–12.6) were positive for TCoV and 16 of them were molecularly characterized. Phylogenetic analysis showed that these strains belonged to two clusters, one formed by the early isolates identified at the beginning of the TCoV monitoring (from 2009 to 2010), and the other, which was formed by more recent strains from 2014 to 2019. Our analysis of the changes observed in the deduced amino acids of the S1 protein suggests the existence of three variable regions. Moreover, although the selection pressure analysis showed that the TCoV strains were evolving under negative selection, some sites of the S1 subunit were positively selected, and most of them were located within the proposed variable regions. Our sequence analysis also showed one TCoV strain had recombined with another one in the S1 gene. The presented investigation on the molecular feature of the S gene of TCoVs circulating in the turkey population in Poland contributes interesting data to the current state of knowledge.

Phylogenetic Structure and Comparative Genomics of Multi-National Invasive Haemophilus influenzae Serotype a Isolates.

Recent reports have indicated a rise of invasive disease caused by Haemophilus influenzae serotype a (Hia) in North America and some European countries. The whole-genome sequences for a total of 410 invasive Hia isolates were obtained from 12 countries spanning the years of 1998 to 2019 and underwent phylogenetic and comparative genomic analysis in order to characterize the major strains causing disease and the genetic variation present among factors contributing to virulence and antimicrobial resistance. Among 410 isolate sequences received, 408 passed our quality control and underwent genomic analysis. Phylogenetic analysis revealed that the Hia isolates formed four genetically distinct clades: clade 1 (n = 336), clade 2 (n = 13), clade 3 (n = 3) and clade 4 (n = 56). A low diversity subclade 1.1 was found in clade 1 and contained almost exclusively North American isolates. The predominant sequence types in the Hia collection were ST-56 (n = 125), ST-23 (n = 98) and ST-576 (n = 51), which belonged to clade 1, and ST-62 (n = 54), which belonged to clade 4. Clades 1 and 4 contained predominantly North American isolates, and clades 2 and 3 predominantly contained European isolates. Evidence of the presence of capsule duplication was detected in clade 1 and 2 isolates. Seven of the virulence genes involved in endotoxin biosynthesis were absent from all Hia isolates. In general, the presence of known factors contributing to β-lactam antibiotic resistance was low among Hia isolates. Further tests for virulence and antibiotic susceptibility would be required to determine the impact of these variations among the isolates.

Comparative analysis of Streptococcus suis genomes identifies novel candidate virulence-associated genes in North American isolates

Streptococcus suis is a significant economic and welfare concern in the swine industry. Pan-genome analysis provides an in-silico approach for the discovery of genes involved in pathogenesis in bacterial pathogens. In this study, we performed pan-genome analysis of 208 S. suis isolates classified into the pathogenic, possibly opportunistic, and commensal pathotypes to identify novel candidate virulence-associated genes (VAGs) of S. suis. Using chi-square tests and LASSO regression models, three accessory pan-genes corresponding to S. suis strain P1/7 markers SSU_RS09525, SSU_RS09155, and SSU_RS03100 (>95% identity) were identified as having a significant association with the pathogenic pathotype. The proposed novel SSU_RS09525 + /SSU_RS09155 + /SSU_RS03100 + genotype identified 96% of the pathogenic pathotype strains, suggesting a novel genotyping scheme for predicting the pathogenicity of S. suis isolates in North America. In addition, mobile genetic elements carrying antimicrobial resistance genes (ARGs) and VAGs were identified but did not appear to play a major role in the spread of ARGs and VAGs.

Multiplexed SSR marker analysis of Diplocarpon coronariae reveals clonality within samples from Middle Europe and genetic distance from Asian and North American isolates

BackgroundApple blotch (AB) caused by Diplocarpon coronariae (Dc) has been established in Europe since 2010. AB is a serious apple disease, mostly in low input orchards and in cider production areas in Northern Italy, Switzerland, Austria and Germany. However, the epidemiology and population genetic structure of this pathogen is unknown.MethodsWe developed twelve Dc-specific microsatellite markers and screened DNA of both pure fungal isolates and infected apple leaves. The marker data of 313 European samples of Dc were compared to Dc isolates from Asia (n = 7) and the USA (n = 3).ResultsWe found 31 distinct multilocus genotypes (MLGs) in European samples, and seven additional MLGs in the Asian and USA samples. The European samples had the typical genetic signature of a recently introduced species including high clonality, a low number of private alleles and one dominant MLG across all the sampling sites. All European MLGs were genetically distant from those MLGs of Asian and USA origin. Based on the lack of linkage disequilibrium observed, there is evidence that Dc undergoes regular cycles of sexual recombination in the European population, although the sexual stage (apothecia) has not been observed in Europe.ConclusionsThe twelve newly developed SSR markers reported here provide a useful tool to characterize the population genetic diversity and structure of Dc in Europe. Our study supports the hypothesis that Dc is a recently introduced pathogen in Europe, but of currently unknown origin. Dc has a large effective population size during field epidemics, so we believe that the pathogen has substantial evolutionary potential. Application of the SSR markers to large-scale and diverse Dc samples will help to better understand the epidemiology of AB, which has become a global apple disease, and will help guide effective mitigation strategies based on disease management and resistance breeding.

Tracing genetic signatures of bat-to-human coronaviruses and early transmission of North American SARS-CoV-2.

Highly pathogenic coronaviruses, including SARS‐CoV‐2, SARS‐CoV and MERS‐CoV, are thought to be transmitted from bats to humans, but the viral genetic signatures that contribute to bat‐to‐human transmission remain largely obscure. In this study, we identified an identical ribosomal frameshift motif among the three bat–human pairs of viruses and strong purifying selection after jumping from bats to humans. This represents genetic signatures of coronaviruses that are related to bat‐to‐human transmission. To further trace the early human‐to‐human transmission of SARS‐CoV‐2 in North America, a geographically stratified genome‐wide association study (North American isolates and the remaining isolates) and a retrospective study were conducted. We determined that the single nucleotide polymorphisms (SNPs) 1,059.C > T and 25,563.G > T were significantly associated with approximately half of the North American SARS‐CoV‐2 isolates that accumulated largely during March 2020. Retrospectively tracing isolates with these two SNPs was used to reconstruct the early, reliable transmission history of North American SARS‐CoV‐2, and European isolates (February 26, 2020) showed transmission 3 days earlier than North American isolates and 17 days earlier than Asian isolates. Collectively, we identified the genetic signatures of the three pairs of coronaviruses and reconstructed an early transmission history of North American SARS‐CoV‐2. We envision that these genetic signatures are possibly diagnosable and predic markers for public health surveillance.

Ecology of avian influenza viruses in migratory birds wintering within the Yangtze River wetlands

Migratory birds are considered natural reservoirs of avian influenza A viruses (AIVs). To further our viral ecology knowledge and understand the subsequent risk posed by wild birds, we conducted a 4-year surveillance study of AIVs in the bird wintering wetlands of the Yangtze River, China. We collected over 8000 samples and isolated 122 AIV strains. Analyses were then carried out with 108 novel sequenced genomes and data were deposited in GISAID and other public databases. The results showed that the Yangtze River wintering wetlands functioned as a mixing ground, where various subtypes of AIVs were detected harboring a high diversity of nucleotide sequences; moreover, a portion of AIV gene segments were persistent inter-seasonally. Phylogenetic incongruence presented complex reassortment events and distinct patterns among various subtypes. In addition, we observed that viral gene segments in wintering wetlands were closely related to known North American isolates, indicating that intercontinental gene flow occurred. Notably, highly pathogenic H5 and low pathogenic H9 viruses, which usually circulate in poultry, were found to have crossed the poultry/wild bird interface, with the viruses introduced to wintering birds. Overall, this study represented the largest AIV surveillance effort of wild birds within the Yangtze River wintering wetlands. Surveillance data highlighted the important role of wintering wild birds in the ecology of AIVs and may enable future early warnings of novel AIV emergence.