Complete genome sequence of a novel secovirid infecting cassava in the Americas

We report the complete genome sequence of a field isolate of a novel bipartite secovirid infecting cassava in Colombia, provisionally named "cassava torrado-like virus" (CsTLV). The genome sequence was obtained using Oxford Nanopore Technology, and the 5’ ends were confirmed by RACE. The RNA1 is 7252 nucleotides (nt) long, encoding a polyprotein of 2336 amino acids (aa) containing the typical “replication block”, conserved torradovirus motifs, and a Maf/Ham1 domain, which is not commonly found in viral genomes. The RNA2 is 4469 nt long and contains two overlapping ORFs encoding proteins of 226 and 1179 aa, showing the characteristic genome arrangement of members of the genus Torradovirus.

Antitrypanosomal activity of hydromethanol extract of leaves of Cymbopogon citratus and seeds of Lepidium sativum: in-vivo mice model

Background Trypanosomiasis is one of the neglected tropical diseases of both humans and animals which decreases their productivity and causes death in the worst scenario. Unavailability of vaccines, the low therapeutic index of trypanocidal drugs, and the development of resistance lead to the need for research focused on developing alternative treatment options especially from medicinal plants. The present study was aimed to investigate antitrypanosomal activities of leaves of Cymbopogon citratus and seeds of Lepidium sativum in in-vivo mice model. Methods The plant extracts were prepared by maceration using 80% methanol and reconstituted with 10% dimethyl sulfoxide (DMSO) to have the desired concentration. The test doses were adjusted to 100, 200 and 400 mg/kg based on the toxicity profile. The plants extracts were administered to the respective groups of mice after the 12th day of field isolate T. congolense inoculation for seven consecutive days. The level of parasitemia, bodyweight, packed cell volume (PCV), and differential white blood cell counts were measured. Results The in -vivo test results revealed that both plant extracts had dose-dependent antitrypanosomal activity. Both crude extracts showed a significant reduction in parasite load (P < 0.05), increased or prevent the fall of PCV value (P < 0.05), decreased lymphocytosis and increased neutrophil counts (p < 0.05) and improved bodyweight but significant bodyweight increment (P < 0.05) was observed only in C. citratus treated mice compared to the negative and positive controls. Conclusion The present study concluded that the crude extracts of leaves of C. citratus and seeds of L. sativum had antitrypanosomal effects. Both plants extracts reduced parasitemia level, prevented anemia and improved bodyweight of treated mice. Comparative results from all tested parameters showed that the best activities were observed with C. citratus treated groups of mice.

Efficacy of a Modified Live Virus Vaccine against Porcine Reproductive and Respiratory Syndrome Virus 1 (PRRSV-1) Administered to 1-Day-Old Piglets in Front of Heterologous PRRSV-1 Challenge

PRRSV is one of the most important viruses in the global swine industry and is often controlled by the use of modified live virus (MLV) vaccines. This study assessed the impact of a PRRSV-1 MLV vaccine applied to 1-day-old piglets challenged on day 28 of life with a PRRSV-1 field isolate (AUT15-33). Twenty-one piglets were vaccinated within 24 h of birth (T02), whereas 20 piglets were left unvaccinated (T01). Necropsy was performed two weeks post-challenge. Comparing the two groups, T02 piglets showed significantly higher (p = 0.017) average daily weight gain. In addition, significantly lower (p < 0.0001) PRRSV RNA loads were measured in serum of T02 piglets at all investigated time points. All T01 piglets were viremic and shed virus in nasal swabs, whereas only 71.4 % and 38.1 % of the T02 group were viremic or shed virus, respectively. Piglets from T02 had significantly higher numbers (p < 0.0001) of IFN-γ producing lymphocytes compared to T01. At necropsy, differences in gross and histologic lung lesions were statistically significant (p = 0.012 and p < 0.0001, respectively) between the two groups. Hence, this MLV vaccine administered to 1-day-old piglets was able to protect piglets against PRRSV infection at weaning.

First report of Phytophthora nicotianae causing stem canker of Catalpa bungei (Chinese catalpa) in China

Chinese catalpa, Catalpa bungei C.A. Mey is native to China and has been widely cultivated as an important tree species for timber and ornamental purposes (Tao et al. 2019). The properties and high durability of the wood can resist the damage caused by microorganisms and insects (Xiao Y et al. 2019). In September 2020, stem cankers were observed in 5-year-old and 3-year-old C. bungei in a pilot experiment field covering 16-hectare area in Shuyang city (Jiangsu province, China) and in a nursery in Binhai city (Jiangsu Province, China), respectively. The disease incidence in both locations was about 1% to 3%. The typical disease symptoms include small to large, dark-brown and irregular-sunken canker around and along the stem under 2 meters from the stem base. The phloem and xylem of the symptomatic stem were dark brown and the xylem had larger necrosis than the phloem. The cross section of the diseased stem was partially died. The symptomatic stem were collected in both locations for pathogen isolation. In total, seven purified isolates from the diseased samples were obtained using potato dextrose agar (PDA) following standard isolation protocol (Huang et al. 2019). In order to determine the pathogenicity, 3-year-old Chinese catalpa seedlings were artificially inoculated with each of the seven isolates in April 2021. After removing the bark of the stem by a sterilized punch (diameter 6mm), an agar plug (diameter 6mm) pre-colonized by the isolate was inoculated to the stem and the inoculation point was sealed with parafilm. The agar plug without pre-colonization was used as control. Six tree seedlings were inoculated for each isolate. Ten days after inoculation, only the treatment with isolate QS.1 showed obvious discoloration around the inoculation point. One month after inoculation, the canker around the inoculation point was formed (3.4 cm ± 1.0 cm) and spread to the xylem, similar to the symptoms observed in the field. Isolate QS.1 was re-isolated successfully from the inoculated stem based on morphological characters, confirming the Koch's postulates and QS.1 as the causal pathogen. The isolate QS.1 formed white colonies with abundant aerial mycelia on V8 juice agar and produced a large amount of persistent and papillary ovoid sporangia with size of 22 ~ 45μm (average 31μm) × 18 ~ 39μm (average 23μm) in 10% aqueous solution of V8. The spore was spherical with thick-wall and diameter of 24 ± 3.9μm. The morphology of QS.1 is similar to that of Phytophthora nicotianae. The genomic DNA of representative isolate QS.1 was extracted from mycelium by a modified CTAB method (Murray et al. 1980). The rDNA internal transcribed spacer (ITS) region, β-tubulin and EF1-α genes were amplified and sequenced with primers ITS1/ITS4 (White et al. 1990), BTub_F1/TUBUR1 (L. et al. 2004) and EF1A_for/EF1A_rev (Blair et al. 2008), respectively. The BLAST results of these sequences (Accession No. MZ646302, MZ672116, and MZ675589, respectively) showed 99%, 100% and 100% identity with sequences of P. nicotianae (Accession No. KJ494902, KY205750, and MH359041), respectively. Based on the morphological characteristics and DNA analysis, isolate QS.1 was identified as P. nicotianae. To our best knowledge, this is the first report of P. nicotianae causing stem canker on Chinese Catalpa. This disease may pose potential threat on Catalpa due to the increase in Catalpa planting for economic and ecological purposes in China.

In vitro culture of freshly isolated Trypanosoma brucei brucei bloodstream forms results in gene copy-number changes

Most researchers who study unicellular eukaryotes work with an extremely limited number of laboratory-adapted isolates that were obtained from the field decades ago, but the effects of passage in laboratory rodents, and adaptation to in vitro culture, have been little studied. For example, the vast majority of studies of Trypanosoma brucei biology have concentrated on just two strains, Lister 427 and EATRO1125, which were taken from the field over half a century ago and have since have undergone innumerable passages in rodents and culture. We here describe two new Trypanosoma brucei brucei strains. MAK65 and MAK98, which have undergone only 3 rodent passages since isolation from Ugandan cattle. High-coverage sequencing revealed that adaptation of the parasites to culture was accompanied by changes in gene copy numbers. T. brucei has so far been considered to be uniformly diploid, but we also found trisomy of chromosome 5 not only in one Lister 427 culture, but also in the MAK98 field isolate. Trisomy of chromosome 6, and increased copies of other chromosome segments, were also seen in established cultured lines. The two new T. brucei strains should be useful to researchers interested in trypanosome differentiation and pathogenicity. Initial results suggested that the two strains have differing infection patterns in rodents. MAK65 is uniformly diploid and grew more reproducibly in bloodstream-form culture than MAK98.

BIODIVERSITY OF MOLD FUNGI IN THE AREAS OF THE CITY OF CHEBOKSARY

A study of 12 soil samples in the summer period in the districts of the city of Cheboksary was conducted. The aim of the research was to conduct a mycological analysis of the soil and isolate particularly dangerous micromycetes in the urban environment. Soil samples were taken from the Moskovsky, Kalininsky, Leninsky districts of Cheboksary and Marposadsky highway. The pH of the soil environment of the city of Cheboksary was: Embankment of the Moskovsky district – 7.67, Kirovsky – 7.23; Leninsky – 7.28; Marposadskoe highway – 7.51. In mycological analysis of soil samples on agarized media of Chapek, the highest concentration of micromycetes was recorded in soil samples from the Moskovsky district on the Embankment, where the concentration of fungi of the genus Aspergillus fumigates was 27 %, fungi of the genus Fusarium sporotrichioides and Fusarium graminearum was 15 %. The soil of the Leninsky district was dominated by fungi of the genus Penicillium, their concentration was 23 %, Aspergillus flavus – 18 %. Isolates of fungi of the genus Penicillium spp. were isolated in the soil of the Kalininsky district, and their concentration was – 7 %, Aspergillus flavus – 21 %. The soil from the Marpasad highway was dominated by fungi of the genus Mucor sp. Testing on Paramecium caudatum infusoria showed that the field isolate of Aspergillus fumigates had toxic properties, the evaluation criterion for biotesting was 38 %. Aspergillus flavus showed a 78 % survival rate when tested on infusoria.

Comparative study between lumpy skin disease virus and sheep pox virus vaccines against recent field isolate of lumpy skin disease virus

Lumpy Skin Disease (LSD) is a vector born disease of cattle, caused by Lumpy Skin Disease Virus (LSDV), there is antigenic relationship between LSDV, Sheeppox virus (SPPV) and Goat pox virus GTPV within a genus Capripoxvirus, accordingly it can be used homologous or heterologous Capripoxvirus strains for vaccination of cattle against LSD. This study compare the efficacy of live attenuated Neethling LSDV vaccine and live attenuated Romanian SSPV Vaccine against recent circulating LSDV field isolate. The evaluation was done in calves as the main host of LSD, through using three different batches for each vaccine type. Experimental calf groups were vaccinated with vaccines batches, and after 21 days serum samples were collected for evaluation of humoral immune response by using SNT and commercial ELISA technique, then the vaccinated calves were challenged by virulent LSDV field isolate. The results of SNT for vaccinated calves by LSDV vaccines indicated mean neutralizing antibody titer 1.2, 1.6 and1.5 log10 for the batches 1, 2 and 3 respectively, while vaccinated calves by SPPV vaccines indicated 1.05, 1.05 and 1.5 log10 for the batches 1,2 and 3 respectively; the ELISA mean sample to positive (S/P) percentage for the vaccine batches 1, 2 and 3 of LSDV were 40, 45 and 42% respectively and for SPPV vaccine batches 1,2 and 3 were 35, 37 and 40 % respectively, the challenge test indicated mean difference titer for the groups of calves vaccinated with LSDV vaccine were 4.2, 4.5 and 3.8 log10 and for groups vaccinated with SPPV vaccine were 2.6, 2 and 2.65 log10 respectively, it was concluded that potential using of Neethling LSDV vaccine against LSD is superior for combating and prevention of the lumpy skin disease.

Genetic Variability of PRRSV Vaccine Strains Used in the National Eradication Programme, Hungary

Porcine reproductive and respiratory syndrome (PRRS) is a globally spread, highly infectious viral disease. Live, attenuated vaccines against PRRS virus (PRRSV) decrease virus excretion and evoke protective immunity reducing the economic damage caused by the disease. In a longitudinal molecular epidemiological study accompanying ongoing national eradication programme we evaluated the suitability of PRRSV ORF5 and ORF7 sequences to identify possible field strains of vaccine-origin. In total, 2342 ORF5 sequences and 478 ORF7 sequences were analysed. Vaccine strains were identified by sequence identity values and phylogenetic network analysis. Strains that shared greater than 98% nucleotide identity within ORF5 and/or ORF7 were considered to have originated from vaccine. A total of 882 (37.6%) ORF5 and 88 (18.4%) ORF7 sequences met these criteria. In detail, 618, 179 and 35 ORF5 and 51, 29 and 8 ORF7 sequences were related to Porcilis PRRS vaccine, Unistrain PRRS vaccine, and ReproCyc PRRS EU vaccine, respectively. Data showed that the Porcilis vaccine was genetically more stable. Whereas, the variability of the Unistrain and the ReproCyc strains was significantly higher. Given that ORF7 shares, in some instances, complete identity between a particular vaccine strain and some historic variants of field PRRSV strains, care must be taken when evaluating vaccine relatedness of a field isolate based on the ORF7. On the contrary, ORF5 sequences were more suitable to predict the vaccine origin making a distinction more robustly between field and vaccine strains. We conclude that ORF5 based molecular epidemiological studies support more efficiently the ongoing PRRS eradication programmes. The conclusions presented in this large-scale PRRS molecular epidemiological study provides a framework for future eradication programmes planned in other countries.

Generation of Tetracycline and Rifamycin Resistant Chlamydia Suis Recombinants

The Chlamydiaceae are a family of obligate intracellular, gram-negative bacteria known to readily exchange DNA by homologous recombination upon co-culture in vitro, allowing the transfer of antibiotic resistance residing on the chlamydial chromosome. Among all the obligate intracellular bacteria, only Chlamydia (C.) suis naturally integrated a tetracycline resistance gene into its chromosome. Therefore, in order to further investigate the readiness of Chlamydia to exchange DNA and especially antibiotic resistance, C. suis is an excellent model to advance existing co-culture protocols allowing the identification of factors crucial to promote homologous recombination in vitro. With this strategy, we co-cultured tetracycline-resistant with rifamycin group-resistant C. suis, which resulted in an allover recombination efficiency of 28%. We found that simultaneous selection is crucial to increase the number of recombinants, that sub-inhibitory concentrations of tetracycline inhibit rather than promote the selection of double-resistant recombinants, and identified a recombination-deficient C. suis field isolate, strain SWA-110 (1-28b). While tetracycline resistance was detected in field isolates, rifampicin/rifamycin resistance (RifR) had to be induced in vitro. Here, we describe the protocol with which RifR C. suis strains were generated and confirmed. Subsequent whole-genome sequencing then revealed that G530E and D461A mutations in rpoB, a gene encoding for the β-subunit of the bacterial RNA polymerase (RNAP), was likely responsible for rifampicin and rifamycin resistance, respectively. Finally, whole-genome sequencing of recombinants obtained by co-culture revealed that recombinants picked from the same plate may be sibling clones and confirmed C. suis genome plasticity by revealing variable, apparently non-specific areas of recombination.