Classification of NIPG.

<p>(A) Distribution of NIPG within each study participant. Purple: hypermutation; Green: Gag deletion; Red: intact near-full length, replication-deficient due to nonsense mutations or INDELs; Blue: undefined non-Gag deletion; Orange: defined non-Gag deletion; empty circle: not evaluable. (B) Distribution of NIPG across study participants after Gag and near-full length sequencing. <i>NIPG</i>: <i>non-induced proviral genomes</i>.</p

Urogenital <i>Chlamydia trachomatis</i> multilocus sequence types and genovar distribution in chlamydia infected patients in a multi-ethnic region of Saratov, Russia

<div><p>Background</p><p>This is the first report to characterize the prevalence and genovar distribution of genital chlamydial infections among random heterosexual patients in the multi-ethnic Saratov Region, located in Southeast Russia.</p><p>Methods</p><p>Sixty-one clinical samples (cervical or urethral swabs) collected from a random cohort of 856 patients (7.1%) were <i>C</i>. <i>trachomatis</i> (CT) positive in commercial nucleic acid amplification tests (NAATs) and duplex TaqMan PCRs.</p><p>Results</p><p>Sequence analysis of the VDII region of the <i>ompA</i> gene revealed seven genovars of <i>C</i>. <i>trachomatis</i> in PCR-positive patients. The overall genovars were distributed as E (41.9%), G (21.6%), F (13.5%), K (9.5%), D (6.8%), J (4.1%), and H (2.7%). CT-positive samples were from males (n = 12, 19.7%), females (n = 42, 68.8%), and anonymous (n = 7, 11.5%) patients, with an age range of 19 to 45 years (average 26.4), including 12 different ethnic groups representative of this region. Most patients were infected with a single genovar (82%), while 18% were co-infected with either two or three genovars. The 1156 bp-fragment of the <i>ompA</i> gene was sequenced in 46 samples to determine single nucleotide polymorphisms (SNP) among isolates. SNP-based subtyping and phylogenetic reconstruction revealed the presence of 13 variants of the <i>ompA</i> gene, such as E (E1, E2, E6), G (G1, G2, G3, G5), F1, K, D (D1, Da2), J1, and H2. Differing genovar distribution was identified among urban (E>G>F) and rural (E>K) populations, and in Slavic (E>G>D) and non-Slavic (E>G>K) ethnic groups. Multilocus sequence typing (MLST) determined five sequences types (STs), such as ST4 (56%, 95% confidence interval, CI, 70.0 to 41.3), ST6 (10%, 95% CI 21.8 to 3.3), ST9 (22%, 95% CI 35.9 to 11.5), ST10 (2%, 95% CI 10.7 to 0.05) and ST38 (10%, 95% CI 21.8 to 3.3). Thus, the most common STs were ST4 and ST9.</p><p>Conclusion</p><p><i>C</i>. <i>trachomatis</i> is a significant cause of morbidity among random heterosexual patients with genital chlamydial infections in the Saratov Region. Further studies should extend this investigation by describing trends in a larger population, both inside and outside of the Saratov Region to clarify some aspects for the actual application of <i>C</i>. <i>trachomatis</i> genotype analysis for disease control.</p></div

Characteristics of the study population.

<p>Characteristics of the study population.</p

HIV DNA concentrations from cultured resting CD4+ T cell QVOA wells with and without NIPG.

<p>“N” represents the number of QVOA culture wells.</p

HIV-specific antibody responses of plasma samples.

<p>HIV-specific antibody responses of plasma samples.</p

Deletions in NIPG with defined junctions.

<p>Letters and numbers correspond to participant identifiers listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0170548#pone.0170548.t001" target="_blank">Table 1</a>. A) Sequences are aligned to HXB2. Sequenced positions appear as a black polygon. Gray thin lines indicate deleted regions of genomes. B) Regions with relatively high coverage were extracted for phylogenetic analysis. Location shown is according to HXB2 numbering. Colors correspond to nucleotides on the left. Sequences designated with a red dot were not used in subsequent analysis due to missing sequence segments. C) Phylogenetic analysis of sequences rooted using HXB2 and aligned to positions 3350–4327 and 9105–9597.</p

Phylogenetic tree demonstrating the relationship of Saratov <i>ompA</i> sequences to references strains from Table 1.

<p>Thick branches, subtending all large clades, represent 100% bootstrap support. The scale at the bottom represents one substitution per site.</p

Clonal grouping of sequence types (STs) of <i>C</i>. <i>trachomatis</i> strains found in our study (marked with gray ovals).

<p>The division into Group I (A) and Group III (B) was based on the EBURST analysis with other STs of these clonal complexes obtained from PubMLST/Chlamydiales database.</p

Phylogenetic analyses of concatenated sequences of 7 housekeeping gene fragments of representative <i>C</i>. <i>trachomatis</i> strains.

<p><b>Concatenated sequences were aligned and analyzed in MEGA 7</b>. Phylogenetic tree was constructed using the UMPGA hierarchical clustering method model. Relevant STs & genotypes including in the clustering analyses are presented in Tables <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195386#pone.0195386.t001" target="_blank">1</a> & <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0195386#pone.0195386.t002" target="_blank">2</a>, respectively.</p

The <i>ompA</i> and seven housekeeping genes MLST sequence types of Saratov and reference strains of <i>C</i>. <i>trachomatis</i> obtained from the PubMLST database (https://pubmlst.org).

<p>The <i>ompA</i> and seven housekeeping genes MLST sequence types of Saratov and reference strains of <i>C</i>. <i>trachomatis</i> obtained from the PubMLST database (<a href="https://pubmlst.org" target="_blank">https://pubmlst.org</a>).</p