Genetic characterisation of the influenza viruses circulating in Bulgaria during the 2019-2020 winter season

Influenza viruses have a high potential for genetic changes. The objectives of this study were to analyse influenza virus circulation in Bulgaria during the 2019/2020 season, to perform a phylogenetic and molecular analyses of the haemagglutinin (HA) and neuraminidase (NA) sequences of representative influenza strains, and to identify amino acid substitutions compared to the current vaccine strains. Seasonal influenza viruses A(H3N2), A(H1N1)pdm09 and B/Victoria-lineage were detected using a real-time RT-PCR in 323 (23.3%), 149 (10.7%) and 138 (9.9%) out of 1387 patient samples studied, respectively. The HA genes of A(H3N2) viruses analysed belonged to clades 3C.3a (21 strains) and 3C.2a (5 strains): subclades 3C.2a1b + T131K, 3C.2a1b + T135K-B and 3C.2a1b + T135K-A. The clade 3C.3a and subclade 3C.2a1b viruses carried 5 and 14-17 substitutions in HA, as well as 3 and 9 substitutions in NA, respectively, in comparison with the A/Kansas/14/2017 vaccine virus, including some substitutions in the HA antigenic sites A, B, C and E. All 21 A(H1N1)pdm09 viruses sequenced fell into 6B.1A5A subclade. Amino acid sequence analysis revealed the presence of 7-11 substitutions in HA, compared to the A/Brisbane/02/2018 vaccine virus, three of which occurred in antigenic site Sb, along with 6-9 changes at positions in NA. All 10 B/Victoria-lineage viruses sequenced belonged to clade 1A with a triple deletion in HA1 (genetic group 1A(Δ3)B) and carried 7 and 3 substitutions in HA and NA, respectively, with respect to the B/Colorado/06/2017 vaccine virus. The results of this study confirm the rapid evolution of influenza viruses and the need for continuous antigenic and genetic surveillance.

Molecular detection of Strongyloides sp. in Australian Thoroughbred foals

Background

Strongyloides westeri is found in the small intestine of young horses, mainly in foals up to about 16 weeks of age. The main source of infection for foals is through transmammary transmission, and foals can develop acute diarrhoea, weakness, dermatitis and respiratory signs. The epidemiology of S. westeri in Australia is largely unknown. Further, molecular techniques have never been employed for detection of S. westeri in horses. This pilot study aimed to assess the utility of a molecular phylogenetic method for the detection of S. westeri in the faeces of foals.

Methods

Faecal samples were collected from a foal of less than 2 months of age, and eggs of Strongyloides sp. were detected using the modified McMaster technique. DNA was extracted from purified eggs, and a partial fragment of the small subunit of the nuclear ribosomal DNA (18S) was characterised using polymerase chain reaction, DNA sequencing and phylogenetic methods.

Results

Microscopic examination of faeces revealed small ellipsoidal eggs typical of Strongyloides sp. The 18S sequence generated by PCR in this study revealed 98.4% identity with that of a reference sequence of S. westeri available from GenBank. Phylogenetic analyses revealed a polyphyletic clustering of S. westeri sequences.

Conclusion

This is the first study reporting the detection of DNA of Strongyloides sp. in faeces of a foal using a molecular phylogenetic approach targeting the variable region of 18S rDNA. It is anticipated that this study will allow future molecular epidemiological studies on S. westeri in horses.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-021-04966-1.

Review on the molecular study of the Diplozoidae: analyses of currently available genetic data, what it tells us, and where to go from here

The use of molecular tools in the study of parasite taxonomy and systematics have become a substantial and crucial component of parasitology. Having genetic characterisation at the disposal of researchers has produced mostly useful, and arguably more objective conclusions. However, there are several groups for which limited genetic information is available and, coupled with the lack of standardised protocols, renders molecular study of these groups challenging. The Diplozoidae are fascinating and unique monogeneans parasitizing mainly freshwater cyprinid fishes in Europe, Asia and Africa. This group was studied from a molecular aspect since the turn of the century and as such, limitations and variability concerning the use of these techniques have not been clearly defined. In this review, all literature and molecular information, primarily from online databases such as GenBank, were compiled and scrupulously analysed for the Diplozoidae. This was done to review the information, detect possible pitfalls, and provide a "checkpoint" for future molecular studies of the family. Hindrances detected are the availability of sequence data for only a limited number of species, frequently limited to a single sequence per species, and the heavy reliance on one non-coding ribosomal marker (ITS2 rDNA) which is difficult to align objectively and displays massive divergences between taxa. Challenging species identification and limited understanding of diplozoid species diversity and plasticity are also likely restricting factors, all of which hamper the accurate taxonomic and phylogenetic study of this group. Thus, a more integrated taxonomic approach through the inclusion of additional markers, application of more rigorous morphological assessment, more structured barcoding techniques, alongside thorough capturing of species descriptions including genetypes, genophore vouchers and reference collections in open sources are encouraged. The pitfalls highlighted are not singular to the Diplozoidae, and the study of other groups may benefit from the points raised here as well.

Genetic diversity and relationships among three Southern African Nguni cattle populations

The Nguni cattle breed has distinct populations that are adapted to the different ecological zones of Southern Africa. This study was carried out to assess genetic diversity and establish the relationships among South African (SA), Mozambican (Landim), and Swazi Nguni cattle populations, using 25 microsatellite markers. Genotypic data were generated from deoxyribonucleic acid (DNA) samples of 90 unrelated individuals of the three cattle populations, collected from government conservations and stud herds. DNA profiles of five local beef breeds were used as the reference populations. Most of the 25 microsatellite markers were highly polymorphic across the studied populations, with an overall polymorphic information content (PIC) mean of 0.676. Genetic diversity within populations was high with expected heterozygosity varying from 0.705 ± 0.024 (Landim) to 0.748 ± 0.021 (SA Nguni) and mean number of alleles being highest in the SA Nguni (7.52 ± 0.42). Average observed heterozygosity (0.597 ± 0.046) compared to the expected heterozygosity (0.719 ± 0.022) was lowest for the Swazi Nguni, which also had a high number of Hardy-Weinberg Equilibrium (HWE) deviated loci (13), confirming the relatively high level of inbreeding (0.158 ± 0.058) in that population. Analysis of molecular variance revealed only 9.61% of the total variation between the populations and 90.39% within populations. A short genetic distance (0.299) was observed between Landim and Swazi Nguni, with the SA Nguni (> 0.500) being the most genetically distant population. The distant relationship between SA Nguni and the other two Nguni cattle populations was further confirmed by a principal coordinates analysis. The three Nguni populations clustered independently from each other, despite some evidence of admixture. Therefore, it can be concluded that SA Nguni, Landim, and Swazi Nguni populations in Southern Africa exhibit high levels of genetic diversity and are genetically distant; with the two latter populations being less genetically apart. These results present useful information for the development of strategies for regional management of animal genetic resources, through conservation and sustainable utilisation.

An integrative taxonomic assessment of Procamallanus (Spirocamallanus) huacraensis (Nematoda: Camallanidae), infecting the freshwater catfish Trichomycterus spegazzinii (Siluriformes: Trichomycteridae) in Argentina

Procamallanus (Spirocamallanus) huacraensis infecting the catfish Trichomycterus spegazzinii from Escoipe River, Salta province (Argentina), is redescribed and genetically characterised for the first time, based on three genetic markers (nuclear 18S and 28S rRNA; cytochrome c oxidase subunit I [cox1] mtDNA). The phylogeny of Camallanidae was also discussed. Morphological evaluation of P. (S.) huacraensis using light and scanning electron microscopy revealed the previously undescribed features: location of deirids, accurate morphology of larvae (L1) and ovijector in females, as well as phasmids in males. Differences were found comparing the newly collected material and the type specimens, probably because the original description lacked detailing. Unfortunately, type specimens of P. (S.) huacraensis were no available for loan. The results of morphological and genetic analyses supported the validity of P. (S.) huacraensis. Inconsistencies regarding the taxonomic identification of species of Camallanidae in GenBank database were noted. Based on the current genetic database of Camallanidae, phylogenetic reconstructions using the 18S rRNA sequences were most consistent, due to the inclusion of higher number of taxa. Procamallanus (S.) huacraensis appeared as sister group of P. (S.) rarus, also isolated from a catfish in a neighbouring region. The order and habitat of hosts were also similar within some well-supported parasite lineages, but without common geographic origin. However, it is still premature to make definitive affirmations regarding the role of such features in the phylogenetic patterns of Camallanidae, given the scarcity of genetic data. The phylogenetic reconstructions also confirmed the artificiality of the morphology-based systematics of the family.

The high genetic similarity between rhinoviruses and enteroviruses remains as a pitfall for molecular diagnostic tools: A three-year overview

BACKGROUND

Enteroviruses (EVs) and rhinoviruses (RVs) belong to the Enterovirus genus within the Picornaviridae family, and show genetic similarities. These viruses are related to mild diseases, but EVs infections can sometimes lead to more severe complications. Current diagnostic molecular techniques should discriminate between the four EV and the three RV species that infect humans. The aim was to revise the EV and RV PCR-confirmed specimens by sequencing for genetic characterisation.

MATERIAL AND METHODS

Respiratory tract specimens were collected from patients with suspicion of respiratory infection. Respiratory viruses' laboratory-confirmation was performed by commercial multiplex real-time RT-PCR assays. Genetic characterisation of all EV and in a selection of RV was performed based on the phylogenetic analyses of partial VP1 and VP4/2 sequences, respectively.

RESULTS

From 19,957 tested specimens, 309 (1.5%) were EV-positive, 2546 (12%) were RV-positive, and 233 (1%) were EV/RV co-detections. The phylogenetic analyses revealed that: among single EV detections, 177/309 (57%) were characterised as EV, 2/309 (1%) as RV, and 130/309 (42%) could not be typed; among single 1771 RV detections (Ct < 35), 1651/1771 (93%) were characterised as RV, 3/1771 (0.3%) as EV and 117/1771 (6.7%) could not be typed. Among EV/RV co-detections, 62/233 (27%) were characterised as EV, 130/233 (56%) as RV and 41/233 (18%) could not be typed.

CONCLUSIONS

A diagnostic method well considered for routine laboratory-confirmation of respiratory viruses should discriminate EV and RV targets. RVs are usually associated with mild respiratory disease, but the potential relatedness of EVs to neurological complications makes their monitoring mandatory. Therefore, an accurate detection and differentiation should be required in commercial diagnostic solutions.

Whole genome characterisation of quail deltacoronavirus detected in Poland

Quail deltacoronavirus (QdCoV) described for the first time in the United Arab Emirates in 2018 belongs to the same deltacoronavirus species as viruses discovered in swine and tree sparrows. The full-length genome of QdCoV detected in quails with enteritis in Poland has similar organization as Middle Eastern viruses although there is no NSP7c gene. The overall degree of nucleotide sequence identity was 92.4-92.6% between Polish PL/G032/2015 and Middle Eastern UAE-HKU30 QdCoV isolates. The sequences of the individual genes show similar nucleotide identities in the range of 91.4-94.7% with the exception of the S gene with lower identity of 85.6-85.7%. The most variable part of the S gene is its fragment encoding the N-terminal domain of the S protein which is responsible for receptor binding. The amino acid homology in this region between PL/G032/2015 and UAE-HKU30 QdCoVs was 74.5-74.7%. In contrast, the C-terminal domain of the S protein which is responsible for membrane fusion had an amino acid homology of 96.9%. In the phylogenetic tree, PL/G032/2015 branched separately but clustered with the UAE-HKU30 QdCoV isolates. These data suggest that PL/G032/2015 could be a new genetic/serologic variant of QdCoV.

Morphological and molecular characterisation of Eimeria vison-like oocysts (Apicomplexa:Eimeriidae) in farmed mink (Neovison vison) in Denmark

A survey was conducted on 30 Danish mink farms from April to October 2016 to determine the prevalence and species of Eimeria in Danish farmed mink. In total, 2.6% of mink faecal samples (108/4140) were positive for Eimeria vison-like oocysts by microscopy, with 24.8% (78/315) of mink being positive at least once during the study period. Morphological analysis of sporulated oocysts (n = 20) identified Eimeria vison-like oocysts measuring 21.0 × 13.8 μm with a length/width (L/W) ratio of 1.5. Phylogenetic analysis of 18S rRNA sequences (1221 bp) from three positive mink indicated that Eimeria vison-like shared the highest genetic similarity to Eimeria sp. ex Apodemus agrarius from a Striped field mouse (A. agrarius) from the Czech Republic (99.6%). Analysis of a shorter region of 18S (531 bp) revealed that the E. vison-like genotype sequences grouped in the same clade and shared 97.7% similarity with E. furonis. At the cytochrome c oxidase subunit I (COI) locus, mink-derived sequences were not available from GenBank and phylogenetic analysis placed the novel E. vison-like in a clade with E. cf. ictidea (99.4% similarity) from a black footed ferret (Mustela nigripes) from Canada.

Detection and genetic characterisation of porcine circovirus 3 from pigs in Sweden

Porcine circovirus 3 (PCV3) is a newly detected circovirus belonging to the family Circoviridae with a circular ssDNA genome of 2000 bp that encodes two proteins-the replicase protein and the capsid protein. PCV3 was discovered for the first time in the US in 2016. After this initial discovery, PCV3 was detected in other parts of the world such as in China, South Korea, Italy and Poland. In this study, 49 tissue samples from Swedish pig herds were screened for PCV3 using PCR and 10 samples were positive and one was uncertain. The entire PCV3 genome and a mini PCV-like virus (MPCLV) were obtained from one of these samples. These two viruses showed a high sequence identity to PCV3 viruses from other countries as well as to MPCLV from the US. However, the sequence identity to PCV1 and 2 was only 31-48% on amino acid level. This is the first detection and complete genetic characterisation of PCV3 in Swedish pigs. It is also interesting to note that one of the positive samples was collected in 1993, showing that PCV3 has been present for a long time.