All consensus env nucleic acid sequences were aligned with molecular evolutionary genetic analysis, using MEGA7 software www. The human immunodeficiency virus type 1 K Phylogenetic trees were constructed in MEGA7 using the maximum likelihood algorithm, and their reliability was estimated from 1, bootstrap replicates.
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The extent of the HIV TC was classified as unique 1 member , small 2—4 members , or large 5—60 members in the transmission chain. We used Dendroscope version 3. We used bivariate and multivariate analyses to determine the independence of associations between exposed variables epidemiologic and clinical factors and outcome clustering. Categorical variables were compared using a chi-square or Fisher's exact test, and continuous variables were compared using a two-sample Student's t -test or Wilcoxon rank sum test.
The determination of agreement between env gpV3 sequence clusterings determining with a partial env fragment as a gold standard to correctly identify individuals in a cluster tree was assessed using Cohen's kappa coefficient. The estimated parameters were sensitivity, specificity, positive predictive value, and negative predictive value. All work was conducted in accordance with the Declaration of Helsinki in terms of informed consent. All samples were anonymized before we accessed them for this study. No nominal information was used for analysis or data management. In addition, depending on the length the HIV-1 envelope sequence to be amplified, this procedure is known to be challenging.
Flowchart of HIV-1 envelope sequences used in this study.
The demographic characteristics are described in Table 1. The mean HIV-1 viral load in total population was 4. Of the individuals, The mean age of recently infected individuals was Table presents the repartition of demographic, epidemiologic, clinical, and risk factors of the study population by infection status recent or chronic. From the sequences analyzed, 4 were excluded because of insufficient env length.
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Finally, 98 sequences with satisfactory and similar lengths were included in the phylogenetic analysis. Of these 98 sequences, The HIV-1 subtype B envelope sequence represented The non-B HIV-1 subtypes, which represented 7. The cluster tree contains sequences from HIVinfected individuals, including 98 from the study cohort and 3 reference sequences introduced in the analyses as controls AF These clusters are labeled from Clust1 to Clust16 and are depicted using different colors.
The cohort-derived clusters are shown in blue for subtype B Clust1 to Clust15, except Clust4 and orange for subtype D Clust The control sequence names are shown in red Clust4. Sequences that did not form a cluster are shown in black. Color images are available online. The inclusion or noninclusion in clusters for acutely and chronically HIVinfected individual envelope sequences was statistically significant using the chi-square test as follows: odds ratio OR : 0.
The env loop 3 sequence-based clustering reproduced Five clusters labeled Clust3, 5, 11, 13, and 14 , shown in Figure 2 , were not observed when using the env V3 sequence-based clustering Fig. However, it identified an additional cluster Clust6 Fig. The cluster tree contains sequences from HIVinfected individual's env -V3 sequences, including 98 from the study cohort and 3 reference sequences introduced in the analyses as controls AF Each tip represents an individual patient.
These clusters are labeled from Clust1 to Clust11 and are depicted using different colors. Clusters including sequence names are shown in blue for subtype B Clust2 to Clust11 and orange for subtype D Clust1. The control sequence names are shown in red. Sequences that did not cluster are shown in black. An additional cluster C6 was identified only with env -V3 loop sequence-based clustering, shown in Figure 4.
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Tanglegrams of rooted phylogenetic trees and networks comparing the HIV-1 envelope gp loop 3 a with the HIV-1 partial envelope length b sequence-based clustering. The linked clusters and sequences between the two trees are connected by a gray line. Table 2. The sensitivity and specificity were In addition, the positive predictive value and negative predictive value were CI, confidence interval; n , number of clusters identified by env gp V3 loop-derived sequences; N , number of clusters identified by the gold standard.
This unexpected result represented less than the number of clusters identified by V3 loop-derived sequences alone, estimated to be The distribution of the HIV-1 TCs by epidemiologic, clinical, and risk factors of acquisition is presented in Table 3. Table 3. Bold values illustrate the number of recent versus chronic HIV-1 infection sequences include or non-include in HIV-1 transmission clusters. Table presents the summary statistics of the demographic, epidemiologic, clinical, and risk factors of HIVinfected individuals associated with inclusion in or not in clusters. The mean age of HIVinfected individuals included in clusters was Table 4.
For multivariate analysis, HIV-1 subtype B vs. Ref: variable of comparison. The statistically significant variables were indicated by their p values.
HIV-1 envelope sequence inference was used to reveal HIV-1 transmission clustering network among newly diagnosed individuals in in Quebec, Canada. We used the envelope loop 3 V3 fragment as comparison because it is the most conserved of the HIV-1 env hypervariable regions, and its sequences are frequently used to predict coreceptor tropism 44—50 and may be available for intention-to-treat analysis using entry inhibitors in clinics.
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This observation underlies and confirms that the length of HIV-1 genome sequences analyzed inflects on TC determination. The three regions decreased the sensitivity associated with the use of a larger fragment comprising two constant regions and the V3 loop. It may be that not all have a good degree of conservation of the nucleotide sequences.
However, the small number of env sequence data sets used in this study did not yield formal conclusions.
Further studies including a large env sequence data set and the combination of different env segments can help confirm the present result. We have proceeded to new phylogenetic analyses concerning the gp C2V3C3 clustering and reached the same conclusions. We will consider in the future a large sequence data set and may evaluate different segments of the envelope sequence. However, in screening for public health surveillance purposes, it may be useful as V3 loop sequencing techniques are routinely performed in clinical laboratories to inform virus tropism and the use of CCR5 inhibitors in treatment.
A recent study has shown that the V3 loop is one of most predictable segments of the HIV-1 envelope and that using its sequences contributes to estimating the recency of an infection. If sequencing is performed on a regular basis, it may help track the early founder of nascent clusters before the growth that will be identified in the following periods and help adapt prevention strategies for at-risk populations.
Considering CDC Guide, June , the identification of most linked sequences over a short period of time could possibly indicate that transmission occurs rapidly within a group. Using a small cutoff value may underestimate cluster sizes and, on the contrary, using a large cutoff value may overestimate them.
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Therefore, the cutoff value has to be well defined 5 , 8 , 21 , 56 , 57 according to the study by Novitsky et al. Further studies that may also evaluate the performance of using the near full-length HIV-1 genome and its three regions GAG , Pol , and Env adjusted by subtypes as independent tools for determining HIV-1 TCs are also encouraged using large sequence data sets. Compared with earlier studies conducted by Brenner et al. Lubelchek et al. These findings contrast those of the present study, where no large cluster has been identified.
The present study aimed to track the nascent or forming clusters in real time to help adapt early prevention strategies that may limit the formation of large clusters. This observation is in agreement with results presented by Brenner et al. Individuals younger than This finding also reflects the most prevalent subtype circulating in Quebec. The objective of the present study was to evaluate tools to detect newly HIV-infected individuals who have the potential to transmit and sustain HIV epidemics as early as possible.
Newly HIV-infected individuals are generally unaware of their infection status 66 , 67 and therefore can contribute to the spread of infection. The timing of viral load assessment after diagnostic testing might also be a factor. This finding reflects the demographics of the HIV epidemic of Quebec, where black people are not overrepresented.
The short-term assessment of early cluster building may help improve quick responses to prevent HIV transmission by identifying the nascent or forming clusters and populations at high risk. HIV subtype B-infected individuals and individuals younger than The HIV-1 partial env fragment length-derived sequences were able to detect clusters of transmission contributing to the persistence of the HIV epidemic in Quebec.
Although less sensitive than the sequencing of partial env fragments, the V3-derived sequences were able to identify HIV TCs with moderate agreement.
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The latter tools V3 sequence may be useful for short-term assessment of nascent HIV-1 transmission clustering in support of the existing methods in screening purposes. We are grateful to all the technicians of the molecular biology, serodiagnosis, and virology departments at the provincial Public Health Reference Laboratory LSPQ , Montreal, Canada, for their technical support. We thank Dr. Art FY.