Jingyun Li

Our understanding of the molecular mechanisms by which DNA meiotic recombination occurs has significantly increased in the past decades. A more representative molecular model has also undergone repeated revisions and upgrades with the continuous expansion of experimental data. Considering several apparent issues in the field, we intend to make necessary upgrades to previous models and reanalyze those data, exploring structural details and molecular mechanisms of DNA meiotic recombination. Eligible studies were identified from PubMed/Medline (up to June 2024). Key related publications and experimental data were retrieved from eligible studies, displaying five major issues. Meanwhile, the biophysical modeling method was used to establish an enlacement model. Then, the model was used to wholly reanalyze the collected data. An updated molecular model was supplemented. In the current model, a copy choice mechanism can initiate DNA meiotic recombination. The copy choice is based on a branched structure of DNA, which results from relative motion between homologous single strands. The reanalysis of previous experimental data based on this model can lead to new interpretations that can better address the discrepancies between previous experimental observations and theoretical models, including (1) the intertwinement model having embodied the particular characteristics of the SDSA model; (2) hDNA arising from JM resolution rather than being followed by a JM; (3) strand specificity of hDNA mismatch repair seeming to be an illusion and copy choice more likely to be the actual state; (4) parity in resolution patterns of a dHJ leading to parity of gene conversion; (5) the cooperation of multiple HJs readily generating a high correlation between gene conversion and crossover; and (6) transpositional recombination and site-specific recombination seeming to have a common pathway to meiotic recombination. The results indicate that both revisions and reanalysis are necessary. The novel interpretations would be critical to the understanding of the mechanisms of DNA recombination as well as its role in DNA repair. Additionally, the work could have implications for how the field views the importance of factors such as Spo11 or the mechanisms that drive meiotic pairing.

Shenzhen City is a rapidly growing area with a large number of floating populations, thus making it difficult to control HIV. Serial cross-sectional studies are helpful for the prediction of epidemiological tendency. In this study, two parallel cross-sectional studies were compared to explore changes in HIV epidemiology in Shenzhen, China. Two hundred and fifty newly reported HIV-positive cases were randomly selected in Shenzhen City in 2013 and 2015. Socio-demographical information was collected with informed consent. Full-length gag and partial pol genes were amplified using nested RT-PCR followed by sequencing and phylogenetic analysis. The genotypes of anti-HIV drug resistance were also analyzed. The characteristics of the HIV epidemics of 2013 and 2015 were compared to identify patterns. The proportion of single, young MSMs dramatically increased in 2015 compared to 2013. Many subtypes, including CRF07_BC (36.4%), CRF01_AE (34.1%), CRF55_01B (10.2%), B (6.4%), CRF08_BC (3.4%), CRF59_01B (0.9%), C (0.7%), D (0.2%), CRF68_01B (0.2%), CRF67_01B (0.2%), and unique recombinant forms (URFs, 7.3%), were identified. Close phylogenetic relationships between strains prevalent in Shenzhen and other areas of China was observed. No epidemic cluster confined to single, young MSMs was identified. 0.4 and 2.8% of the strains contained transmitted drug-resistant mutations in 2013 and 2015, respectively. Although the interval period is short, changes in HIV epidemiology in Shenzhen City are distinct. Frequent surveillance of HIV epidemics in Shenzhen City is thus necessary. Single, young MSMs have become a high-risk population for HIV infection and should be considered as focus population for HIV prevention and behavior intervention in Shenzhen City.

Hepatitis B virus is a hepatotropic DNA virus that reproduces via an RNA intermediate. It can lead to an increased risk of serious liver diseases such as hepatocellular carcinoma and is a serious threat to public health. Currently, the HBV are designated based on greater than 8% nucleotide variation along the whole genome. The recombination of HBV is very common, a large majority of which are recombinants between 2 genotypes. The current work aims to characterize a suspected recombinant involving 3 genotypes. Fifty-seven HBV full-genome sequences were obtained from 57 patients co-infected with HBV and HIV-1 by amplification coupled with sequencing. JpHMM and RDP4 were used to perform recombination analysis respectively. The recombination results of a suspected 3-genotypic recombinant were further confirmed by both maximum likelihood phylogenetic tree and Mrbayes tree. JpHMM recombination analysis clearly indicated one 3-genotypic HBV recombinant composing of B/C/D. The genotype assignments are supported by significant posterior probabilities. The subsequent phylogenetic analysis of sub-regions derived from inferred breakpoints led to a disagreement on the assignment of D segment. Investigating the conflict, further exploration by RDP4 and phylogenies revealed that the jpHMM-derived 3-genotypic recombinant is actually a B/C genotypic recombinant with C fragment spanning 1899 to 2295 (jpHMM) or 1821 to 2199 (RDP4). The whole analysis indicated that (i) determination of small genomic regions should be performed with more caution, (ii) combinations of various recombination detection approaches conduce to obtain impartial results, and (iii) a unified system of nomenclature of HBV genotypes is necessary.

As the most dominant HIV-1 strain in China, CRF01_AE needs to have its evolutionary and demographic history documented. In this study, we provide phylogenetic analysis of all CRF01_AE pol sequences identified in mainland China. CRF01_AE sequences were collected from the Los Alamos HIV Sequence Database and the local Chinese provincial centers of disease control and prevention. Phylogenetic trees were constructed to identify major epidemic clusters. Bayesian coalescent-based method was used to reconstruct the time scale and demographic history. There were 2965 CRF01_AE sequences from 24 Chinese provinces that were collected, and 5 major epidemic clusters containing 85% of the total CRF01_AE sequences were identified. Every cluster contains sequences from more than 10 provinces with 1 or 2 dominant transmission routes. One cluster arose in the 1990s and 4 clusters arose in the 2000s. Cluster I is in the decline stage, while the other clusters are in the stable stage. Obvious lineage can be observed among sequences from the same transmission route but not the same area. Two large clusters in high-level prevalence were found in MSM (Men who have sex with men), which highlighted that more emphasis should be placed on MSM for HIV control in mainland China.

Most HIV subtypes prevalent in China can be found in Shenzhen, including CRF07_BC, CRF01_AE, CRF08_BC, CRF55_01B, and subtype B. Multiple subtypes spreading in the same population always lead to the emergence of unique recombinant strains. Here, we report two unique recombinant forms (SZ44LS7251 and SZ95LS8027) of HIV-1 identified in a heterosexual population. Recombinant analyses were fulfilled based on the near full-length genomes. Both strains comprise subtypes B, C, and CRF01_AE. Phylogenetic analysis reveals that SZ44LS7251 is the second generation recombination originated from CRF55_01B andCRF07_BC, whereas SZ95LS8027 comprises CRF01_AE and CRF07_BC.The emergence of second generation recombination of HIV with complicated genomic structures supposed that high ratio of super infections or coinfections might happen in the Shenzhen area.

The widespread use of antiretroviral therapies has led to considerable concerns about the prevalence of drug-resistant, as transmission of drug-resistant (TDR) strains poses a challenge for the control of the HIV-1 epidemic. We conducted an epidemiological study enrolling treatment-naïve HIV-1-positive subjects at the Peking Union Medical College Hospital since 1991. Drug resistance was determined by submitting the sequences to the Stanford University Network HIV-1 database. Of 521 participants, 478 samples were amplified and sequenced successfully. HIV Transmitted drug resistance prevalence in China was determined to be 6.7 %. We did not find significant differences in the TDR rate by demographic characteristics. No significant time trend in the prevalence of overall TDR was observed (p > 0.05). We identified an intermediate prevalence of transmitted drug resistance (TDR), exhibiting a stable time trend. These findings enhance our understanding of HIV-1 drug resistance prevalence and time trend, and provide some guidelines for the comprehensive public health strategy of TDR prevention.

With increasing data on HIV-1, a more relevant molecular model describing mechanism details of HIV-1 genetic recombination usually requires upgrades. Currently an incomplete structural understanding of the copy choice mechanism along with several other issues in the field that lack elucidation led us to perform an analysis of the correlation between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarity to further explore structural mechanisms. Near full length sequences of URFs from Asia, Europe, and Africa (one sequence/patient), and representative sequences of worldwide CRFs were retrieved from the Los Alamos HIV database. Their recombination patterns were analyzed by jpHMM in detail. Then the relationships between breakpoint distributions and (1) the probability of base pairing, and (2) intersubtype genetic similarities were investigated. Pearson correlation test showed that all URF groups and the CRF group exhibit the same breakpoint distribution pattern. Additionally, the Wilcoxon two-sample test indicated a significant and inexplicable limitation of recombination in regions with high pairing probability. These regions have been found to be strongly conserved across distinct biological states (i.e., strong intersubtype similarity), and genetic similarity has been determined to be a very important factor promoting recombination. Thus, the results revealed an unexpected disagreement between intersubtype similarity and breakpoint distribution, which were further confirmed by genetic similarity analysis. Our analysis reveals a critical conflict between results from natural HIV-1 isolates and those from HIV-1-based assay vectors in which genetic similarity has been shown to be a very critical factor promoting recombination. These results indicate the region with high-pairing probabilities may be a more fundamental factor affecting HIV-1 recombination than sequence similarity in natural HIV-1 infections. Our findings will be relevant in furthering the understanding of HIV-1 recombination mechanisms.

Recombination contributes substantially to the genetic diversity of HIV-1. Recently, many kinds of circulating recombinant forms (CRFs) and unique recombinant forms (URFs) were identified in China, especially in areas with multiple subtypes of HIV-1 circulating. Yunnan, which borders the ‘‘Golden triangle’’ region of South China, is an epicenter of HIV-1 infections in China. Multiple subtypes, including subtype B, CRF01_AE, CRF07_BC and CRF08_BC were found epidemic in the area. Many URFs composed of subtype B and C genomes were identified in Yunnan, however CRF01_AE/B recombinant is relatively rare. In this study, we identified a novel recombinant form of CRF01_AE/B, which was isolated from heterosexual transmitted individual. The genomic structure of the strain is distinctly different from any previously reported URFs. 3 CRF01_AE segments were inserted into subtype B backbone genome. In last few years, many kinds of URFs and CRFs have emerged and spread quickly in China, which implies that co-infection or super-infection of more than one HIV-1 subtype might be common in China, especially in Yunnan. Therefore, more work is needed to monitor the appearance of URFs and survey the epidemiologic significance of the new recombination.

This study was designed to identify common HIV-1 mutation complexes affecting the slope of inhibition curve, and to propose a new parameter incorporating both the IC50 and the slope to evaluate phenotypic resistance. Utilizing site-directed mutagenesis, we constructed 22 HIV-1 common mutation complexes. IC50 and slope of 10 representative approved drugs and a novel agent against these mutations were measured to determine the resistance phenotypes. The values of new parameter incorporating both the IC50 and the slope of the inhibition curve were calculated, and the correlations between parameters were assessed. Depending on the class of drug, there were intrinsic differences in how the resistance mutations affected the drug parameters. All of the mutations resulted in large increases in the IC50s of nucleoside reverse transcriptase inhibitors. The effects of the mutations on the slope were the most apparent when examining their effects on the inhibition of non-nucleoside reverse transcriptase inhibitors and protease inhibitors. For example, some mutations, such as V82A, had no effect on IC50, but reduced the slope. We proposed a new concept, termed IIP_atoxic, on the basis of IC50, slope and the maximum limiting concentrations of the drug. The IIP_atoxic values of 10 approved drugs and 1 novel agent were calculated, and were closely related to the IIP_max values (r > 0.95, p < 0.001). This study confirms that resistance mutations cannot be accurately assessed by IC50 alone, because it tends to underestimate the degree of resistance. The slope parameter is of very importance in the measurement of drug resistance and the effect can be applied to more complex patterns of resistance. This is the most apparent when testing the effects of the mutations on protease inhibitors activity. We also propose a new index, IIP_atoxic, which incorporates both the IC50 and the slope. This new index could complement current IIP indices, thereby enabling predict the efficacy of pre-clinical drugs for which human pharmacokinetic is not available.

In this study, the prevalence of HIV-1 CRF01_AE intrasubtype recombinants in China is estimated and their contributions to the epidemic are explored. Available HIV-1 complete genomes of CRF01_AE were retrieved from the HIV database. The two alignments were evaluated with RDP3. Recombinants were defined as cases in which the recombination signal was supported by at least 3 methods with P-values of ≤0.05 after Bonferroni correction for multiple comparisons implemented in RDP3. Phylogenetic analysis was performed to further investigate the role of intrasubtype recombinants in epidemics. Here, 124 out of the 339 sequences from around the world (36.6 %) showed significant evidence of recombination. Here, 84 of these recombinants were from China, accounting for 54.9 % of local total sequences (84 out of 153). The results indicated non-negligible levels of intrasubtype recombination. Subsequent phylogenetic analysis indicated that a considerable proportion of CRF01_AE strains in China originated from circulating intrasubtype recombinant forms. Three large, well-supported intrasubtype recombinants clusters were identified here. Through a survey of risk factors and sampling cities and provinces, cluster I and cluster II were found to be prevalent primarily among men who have sex with men in major northern cities. Cluster III was prevalent among heterosexuals and intravenous drug users in southern and southwestern provinces. The current work highlighted the remarkable prevalence of intrasubtype recombination within the CRF01_AE epidemic and emphasized the value of intrasubtype recombinants, which came to circulate in the same manner as intersubtype recombinants.