Genetic Characterization and Recombinant History of a Novel Emerging HIV-1 Second-Generation Circulating Recombinant Form (CRF120_0107) Identified Among Sexually Transmitted Infections in Shenzhen, China

Under the background of the main epidemic HIV strains (CRF01_AE and CRF07_BC) co-circulation in China, more HIV second-generation recombinant (SGR) strains with CRF01_AE and CRF07_BC as the backbone are emerging. In this study, we analyzed the characteristics and evolutionary history of a newly emerging HIV-1 CRF120_0107 composed of CRF01_AE and CRF07_BC based on the near full-length genome (NFLG) in Shenzhen, Guangdong Province, China. NFLG phylogenetic analysis revealed that these sequences formed a distinct monophyletic branch with a high bootstrap value (>90%), distantly related to all known HIV-1 genotypes. Recombination analysis showed that CRF120_0107 was composed of the predominant HIV-1 strains in China: CRF01_AE and CRF07_BC. Further subregional phylogenetic analysis was performed that possible parental lineages of CRF07_BC segments (Ⅰ, Ⅲ, and Ⅴ) belonged to the CRF07_BC men who have sex with men cluster (MSM cluster), other CRF01_AE segments also mainly belonged to MSM Cluster (such as CRF01_AE Cluster 5). Bayesian analysis results inferred that CRF120_0107 placed its emergence in Shenzhen approximately between 2009-2011. The appearance of CRF120_0107 further highlights that more and more HIV-1 SGR strains containing CRF01_AE and CRF07_BC will be more generated frequently and will most likely be more conducive to accelerating the spread of HIV in China. This highlighted it is necessary to monitor MSM high-risk individuals with HIV-1 CRF01_AE and CRF07_BC dual infection to prevent the generation of CRF01_AE/CRF07_BC recombinant strains, thus reducing the possibility of HIV-1 genotype resistance and the complexity of treatment in China.

The Emergence of the New P.4 Lineage of SARS-CoV-2 With Spike L452R Mutation in Brazil

The emergence of several SARS-CoV-2 lineages presenting adaptive mutations is a matter of concern worldwide due to their potential ability to increase transmission and/or evade the immune response. While performing epidemiological and genomic surveillance of SARS-CoV-2 in samples from Porto Ferreira—São Paulo—Brazil, we identified sequences classified by pangolin as B.1.1.28 harboring Spike L452R mutation, in the RBD region. Phylogenetic analysis revealed that these sequences grouped into a monophyletic branch, with others from Brazil, mainly from the state of São Paulo. The sequences had a set of 15 clade defining amino acid mutations, of which six were in the Spike protein. A new lineage was proposed to Pango and it was accepted and designated P.4. In samples from the city of Porto Ferreira, P.4 lineage has been increasing in frequency since it was first detected in March 2021, corresponding to 34.7% of the samples sequenced in June, the second in prevalence after P.1. Also, it is circulating in 30 cities from the state of São Paulo, and it was also detected in one sample from the state of Sergipe and two from the state of Rio de Janeiro. Further studies are needed to understand whether P.4 should be considered a new threat.

Identification of Two Similar Novel HIV-1 Recombinant Forms (CRF01_AE/CRF07_BC) among Intravenous Drug Users in Guangxi, China

New kinds of HIV-1 circulating recombinant forms (CRFs) and unique recombinant forms (URFs) earn a great prevalence in China nowadays. In this study, we identified 2 similar URFs (2016GXNNIDU037 and 2019QZLSIDU253) both isolated from intravenous drug users (IDUs) in Guangxi, China. Phylogenetic analysis of the near full-length genome (NFLG) revealed 2 URFs both clustered with CRF01_AE but setting up a monophyletic branch, supporting a high bootstrap value. Bootscan analysis and subregional recombinant analysis found that the NFLG of 2016GXNNIDU037 and 2019QZLSIDU253 were both composed of CRF01_AE and CRF07_BC, with 3 CRF07_BC mosaic segments inserted into CRF01_AE backbones. The CRF01_AE segments of the 2 URFs clustered with a previously reported cluster 2 lineage of CRF01_AE. The 5 recombinant breakpoints of the 2 URFs were quite similar. Distinct from CRF01_AE/CRF07_BC URFs reported before, 2016GXNNIDU037 and 2019QZLSIDU253 are new evidence of a high genetic variety of HIV-1 in Guangxi, which may pose new challenges to HIV-1 prevention and molecular epidemiological surveillance in China.

Genetic variation and structure of complete chloroplast genome in alien monoecious and dioecious Amaranthus weeds

Amaranthus is a complex taxon with economic importance as well as harmful weeds. We studied the genetic variation and structure of the chloroplast genomes of 22 samples from 17 species of three subgenera. It was found that the length of the chloroplast genome of Amaranthus varied from 149,949 bp of A. polygonoides to 150,757 bp of A. albus. The frequencies of SNPs and InDels in chloroplast genomes were 1.79 % and 2.86 %, and the variation mainly occurred in the non-coding regions. The longest InDel was 387 bp, which occurred on ycf2, followed by 384 bp InDel on psbM-trnD. Two InDels in ndhE-I on the SSC make the three subgenera clearly distinguished. In LSC, SSC and IRs regions, there were four 30 bp forward and reverse repeats, and the repeats in SSC and LSC were in nearly opposite positions in circular genome structure, and almost divided the circular genome into symmetrical structures. In the topological tree constructed by chloroplast genome, species in subgen. Amaranthus and subgen. Acnida form monophyletic branches separately and cluster together. A. albus, A. blitoides and A. polygonoides were separated from subgen. Albersia, and the rest of subgen. Albersia were clustered into a monophyletic branch. The rpoC2, ycf1, ndhF-rpl32 were good at distinguishing most amaranths. The trnk-UUU-atpF, trnT-UGU-atpB, psbE-clpP, rpl14-rps19, and ndhF-D can distinguish several similar species. In general, the chloroplast genome is of certain value for the identification of the similar species of Amaranthus, which provides more evidence for clarifying the phylogenetic relationships within the genus.

Molecular barcoding of marine ornamental fish from the southern coast of West Java validates conventional identification

Conventional identification of marine ornamental fish has faced difficulties due to similar color patterns of closed related species, or juvenile individuals have different color patterns from adult individuals. Molecular barcoding using the cytochrome c oxidase I (COI) gene provides a reliable tool for unmasking such difficulties. This study aimed to barcode marine ornamental fish from the southern coast of West Java. Fragment of the COI gene was sequenced from 54 morphotypes. In this study, we determined the taxonomic status of the samples based on a 5% genetic divergence, with the parameter including sequence percent identity, genetic distance, and length of monophyletic branch in a phylogenetic tree. The result showed that most samples had a high percentage of sequence identities, low genetic distances, and short chapters in monophyletic clades, but the remaining were not. Those data indicated that most samples could be identified at species-level without doubt and support conventional identification. Barcoding success is also depending on the availability of conspecific sequences in the databases. This study concluded that molecular barcoding could strengthen and validate traditional identification.

Gymnopilus minisporus sp. nov., a new species and a new record of the European species G. hybridus from northeast China

During our field work in northeast China, two species of Gymnopilus, Gymnopilus minisporus sp. nov. and Gymnopilus hybridus, were identified and described based on morphological characteristics and phylogenetic analyses. The main distinguishing characteristic of G. minisporus is the conspicuously small basidiospores. The phylogenetic tree based on internal transcribed spacers of rDNA sequences using Bayesian and Maximum Likelihood methods showed that G. minisporus has an independent monophyletic lineage, and G. hybridus from China and Sweden grouped in a monophyletic branch.

Comamonas zonglianii sp. nov., isolated from phenol-contaminated soil

A bacterial strain, designated BF-3T, was isolated from phenol-contaminated soil and investigated using a polyphasic taxonomic approach. Cells were Gram-reaction-negative, non-sporulating, non-motile, short rods. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain BF-3T formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Comamonas; it showed highest sequence similarities to Comamonas aquatica LMG 2370T (96.8 %), C. nitrativorans DSM 13191T (96.4 %), C. odontotermitis LMG 23579T (96.4 %), C. kerstersii LMG 3475T (96.3 %), C. koreensis KCTC 12005T (96.1 %) and C. terrigena LMG 1253T (96.0 %). The major cellular fatty acids were C16 : 0, C18 : 1/C18 : 1 ω7c, C17 : 0 cyclo and summed feature 3 (C16 : 1 ω7c and/or iso-C15 : 0 2-OH). Based on the phylogenetic analysis, DNA–DNA hybridization, whole-cell fatty acid composition and biochemical characteristics, strain BF-3T was clearly distinct from type strains of other recognized species of the genus Comamonas and, as such, represents a novel species of the genus Comamonas, for which the name Comamonas zonglianii sp. nov. is proposed. The type strain is BF-3T (=CCTCC AB 209170T =DSM 22523T).

Oceanicola marinus sp. nov., a marine alphaproteobacterium isolated from seawater collected off Taiwan

A short-rod-shaped, Gram-negative, non-motile bacterial strain, designated AZO-CT, was isolated from a sample of seawater collected from the Eluanbi coast of Pingtung County in southern Taiwan and was characterized by using a polyphasic approach. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strain formed a monophyletic branch at the periphery of the evolutionary radiation occupied by the genus Oceanicola in the order Rhodobacterales of the Alphaproteobacteria. The closest neighbours were Oceanicola batsensis HTCC2597T (95.6 % similarity), Oceanicola nanhaiensis SS011B1-20T (94.5 %) and Oceanicola granulosus HTCC2516T (94.0 %). The predominant fatty acid was 18 : 1ω7c (49.1 %), and significant amounts of 19 : 0 cyclo (24.6 %) and 16 : 0 (14.7 %) were present. The DNA–DNA relatedness of the strain with respect to recognized species of the genus Oceanicola was less than 70 %. The isolate was also distinguishable from members of the genus Oceanicola on the basis of phenotypic and biochemical characteristics. It is evident from the genotypic, chemotaxonomic and phenotypic data, therefore, that strain AZO-CT represents a novel species of the genus Oceanicola, for which the name Oceanicola marinus sp. nov. is proposed. The type strain is AZO-CT (=LMG 23705T=BCRC 17591T).