Understanding the Genetic Diversity of Picobirnavirus: A Classification Update Based on Phylogenetic and Pairwise Sequence Comparison Approaches

Picobirnaviruses (PBVs) are small, double stranded RNA viruses with an ability to infect a myriad of hosts and possessing a high degree of genetic diversity. PBVs are currently classified into two genogroups based upon classification of a 200 nt sequence of RdRp. We demonstrate here that this phylogenetic marker is saturated, affected by homoplasy, and has high phylogenetic noise, resulting in 34% unsolved topologies. By contrast, full-length RdRp sequences provide reliable topologies that allow ancestralism of members to be correctly inferred. MAFFT alignment and maximum likelihood trees were established as the optimal methods to determine phylogenetic relationships, providing complete resolution of PBV RdRp and capsid taxa, each into three monophyletic groupings. Pairwise distance calculations revealed these lineages represent three species. For RdRp, the application of cutoffs determined by theoretical taxonomic distributions indicates that there are five genotypes in species 1, eight genotypes in species 2, and three genotypes in species 3. Capsids were also divided into three species, but sequences did not segregate into statistically supported subdivisions, indicating that diversity is lower than RdRp. We thus propose the adoption of a new nomenclature to indicate the species of each segment (e.g., PBV-C1R2).

Multilocus gene analysis reveals the presence of two phytoplasma groups in Impatiens balsamina showing flat stem and phyllody

Rose balsam (Impatiens balsamina) is an important ornamental species grown worldwide for its attractive flowers and also having medicinal properties. Flat stem, little leaf, and phyllody symptoms were observed in I. balsamina nurseries in Uttar Pradesh and Tripura states of India during surveys from 2018 to 2020, with an incidence from 6 to 27%. Amplicons of ~ 1.2 kb were amplified in all the tested symptomatic samples of I. balsamina using universal phytoplasma primer pairs from different surveyed locations, but not from the asymptomatic plants. Pairwise sequence comparison, phylogeny, and virtual RFLP analysis of 16S rRNA gene sequences identified the phytoplasmas as 16SrI-B subgroup strain from Tripura (Lembucherra) and 16SrII-D subgroup strain from Uttar Pradesh (Gorakhpur and Faizabad). Phytoplasma presence and identity was further confirmed by amplifying secA, rp, secY, and tuf genes. This is the first report of 16SrI-B and 16SrII-D phytoplasmas detection in I. balsamina in the world.

Comparison of viromes in vaginal secretion from pregnant women with and without vaginitis

Background Although some studies have investigated the bacterial community in vaginal tract of pregnant women, there are few reports about the viral community (virome) in this type of microenvironment. Methods To investigate the composition of virome in vaginal secretion samples, 40 vaginal secretion samples from pregnant women with vaginitis and 20 vaginal secretion samples from pregnant women without vaginitis, pooled into 4 and 2 sample pools, respectively, were subjected to viral metagenomic analysis. Results Results indicated virus sequences showing similarity to human papillomavirus (HPV), anellovirus, and norovirus were recovered from this cohort of pregnant women. Further analysis indicated that 15 different defined types and one unclassified type of HPV were detected from pregnant women with vaginitis while only 3 defined types of HPV were detected in pregnant women without vaginitis. Five different groups of viruses from the family Anelloviridae were present in pregnant women with but none of them were detected in pregnant women without vaginitis. Norovirus was detected in 3 out of the 4 sample pools from pregnant women with vaginitis but none in the pregnant women without vaginitis. Twelve complete genomes belonging to 10 different types of HPV, and 5 novel anllovirus genomes belonging 2 different genera in Anelloviridae were acquired from these libraries, based on which phylogenetical analysis and pairwise sequence comparison were performed. Phageome in these samples was also briefly characterized and compared between two groups. Conclusion Our data suggested that virome might play an important role in the progression of vaginitis in pregnant women.

GH101 FAMILY OF GLYCOSIDE HYDROLASES: SUBFAMILY STRUCTURE AND EVOLUTIONARY CONNECTIONS WITH OTHER FAMILIES

The GH101 family is composed of endo-α-N-acetylgalactosaminidases and their homologues. Pairwise sequence comparison and phylogenetic analysis allowed us to distinguish five to six subfamilies in this family. Diverse domain structures were found among the family members. Usually they have five irreplaceable and some optional domains. Iterative screening of the protein database revealed an evolutionary relationship of the GH101 catalytic domain with glycoside hydrolase domains from GH13, GH31, and GH70 families. Among other homologous proteins we have found representatives of COG1649, as well as members of four new families of predicted glycoside hydrolases (GHL1-GHL4).