Journal:

Article Title: The Explosive Human Immunodeficiency Virus Type 1 Epidemic among Injecting Drug Users of Kathmandu, Nepal, Is Caused by a Subtype C Virus of Restricted Genetic Diversity

doi:

Figure Lengend Snippet: Flow diagram outlining the method used to preserve, transport, and amplify HIV-1 RNA. Three oligonucleotide primers were included in the RT-PCR step to allow for the sequence variation in all HIV-1 subtypes. The final PCR step (with M13-tailed primers) generates products of sufficient quantity for direct automated DNA sequencing.

Article Snippet: A total of 46 IDU were examined (42 males and 4 females; average age, 27 years), 35 of whom had previously been found seropositive by an HIV-1 enzyme-linked immunosorbent assay (ELISA) (United Biomedical Incorporated, Hauppauge, N.Y.), 2 of whom had previously been found HIV-1 seronegative by the same method, and 9 of whom had not yet been tested.

Techniques: Reverse Transcription Polymerase Chain Reaction, Sequencing, DNA Sequencing

Journal:

Article Title: The Explosive Human Immunodeficiency Virus Type 1 Epidemic among Injecting Drug Users of Kathmandu, Nepal, Is Caused by a Subtype C Virus of Restricted Genetic Diversity

doi:

Figure Lengend Snippet: Alignment of the predicted amino acid sequence of the HIV-1 envelope V3–V4 region from 36 Nepalese IDU. The two variable regions are boxed at the terminal cysteine residues. The consensus sequence is shown, and residues agreeing with the consensus are indicated by periods. Conservation of the GPGQ motif in the tetrameric V3 loop (indicated by a brace) is almost total. The most substantial variation occurs in V4, with numerous deletions (indicated by dashes), insertions, and mutations. Sample 99NP15 contains a 186-bp deletion encompassing almost the entire V4 region and was excluded from some of the following analyses.

Article Snippet: A total of 46 IDU were examined (42 males and 4 females; average age, 27 years), 35 of whom had previously been found seropositive by an HIV-1 enzyme-linked immunosorbent assay (ELISA) (United Biomedical Incorporated, Hauppauge, N.Y.), 2 of whom had previously been found HIV-1 seronegative by the same method, and 9 of whom had not yet been tested.

Techniques: Sequencing

Journal:

Article Title: The Explosive Human Immunodeficiency Virus Type 1 Epidemic among Injecting Drug Users of Kathmandu, Nepal, Is Caused by a Subtype C Virus of Restricted Genetic Diversity

doi:

Figure Lengend Snippet: Phylogenetic analysis of sequences from the HIV-1 envelope C3–V4 region (pNL43 nt 7023 to 7477) from 35 Nepalese IDU and 23 reference HIV-1 subtype C isolates from India and Africa. The country of isolate origin is indicated by I (Indian) or A (African). The phylogenetic tree was constructed by using an ML algorithm. The stability of the tree topology was verified by construction of a NJ tree by using the same alignment. This NJ tree was tested by using bootstrapping, and the percentage of bootstrap trees (from 100 data sets) for which the sequences at one end of the branch are a monophyletic group is indicated. The Nepalese sequences form two clusters that are distinct from other reported subtype C sequences (clusters 1 and 2). Cluster 1 is closest to a group of Indian isolates, whereas the nearest neighbor to cluster 2 is the African isolate ZAM18. The nucleotide alignment used to generate this analysis may be found at the R. B. Oelrichs website (http://www .burnet.edu.au/oelrichs/align1.htm). For sequences of Indian isolates, see reference 19 for 11246, 21068, 301904, 301905, and 301999; reference 9 for D747X; and reference 33 for IND3, IND7, and IND8. The sequences of African isolates BW01B03, BW0402, BW0504, BW1106, BW1210, BW15C05, BW16B01, and BW17B03 were obtained from GenBank (V. Novitsky unpublished data), and those of other African isolates may be found in the references cited, as follows: BU9102 (28); DJ259, UG268, ZAM18, and ZAM20 (20); and MW960 (11).

Article Snippet: A total of 46 IDU were examined (42 males and 4 females; average age, 27 years), 35 of whom had previously been found seropositive by an HIV-1 enzyme-linked immunosorbent assay (ELISA) (United Biomedical Incorporated, Hauppauge, N.Y.), 2 of whom had previously been found HIV-1 seronegative by the same method, and 9 of whom had not yet been tested.

Techniques: Construct

Journal:

Article Title: The Explosive Human Immunodeficiency Virus Type 1 Epidemic among Injecting Drug Users of Kathmandu, Nepal, Is Caused by a Subtype C Virus of Restricted Genetic Diversity

doi:

Figure Lengend Snippet: Phylogenetic analysis of sequences from the HIV-1 envelope C3–V4 region (pNL43 nt 7023 to 7477) from the 35 Nepalese IDU HIV-1 subtype C isolates alone. An ML tree is shown with significant NJ bootstrap values (from 100 data sets) by the relevant nodes. The major and minor clusters (clusters 1 and 2, respectively) observed in Fig. ​Fig.33 are preserved. Within cluster 1, two additional monophyletic groups (clusters 1A and 1B) are supported by highly significant bootstrap values. The nucleotide alignment used to generate this analysis may be found at the R. B. Oelrichs website (http://www.burnet.edu.au/oelrichs/align2.htm).

Article Snippet: A total of 46 IDU were examined (42 males and 4 females; average age, 27 years), 35 of whom had previously been found seropositive by an HIV-1 enzyme-linked immunosorbent assay (ELISA) (United Biomedical Incorporated, Hauppauge, N.Y.), 2 of whom had previously been found HIV-1 seronegative by the same method, and 9 of whom had not yet been tested.

Techniques:

Journal:

Article Title: The Explosive Human Immunodeficiency Virus Type 1 Epidemic among Injecting Drug Users of Kathmandu, Nepal, Is Caused by a Subtype C Virus of Restricted Genetic Diversity

doi:

Figure Lengend Snippet: Plots of the distribution of pairwise genetic distances in the entire alignment of 35 Nepalese IDU HIV-1 cDNA sequences (pNL43 nt 7025 to 7477) and in four subalignments covering the 5′ flanking region (pNL43 nt 7025 to 7099), the V3 region (pNL43 nt 7100 to 7207), the 3′ flanking region (pNL43 nt 7208 to 7366), and the V4 region (pNL43 nt 7367 to 7468). The number of distance values within a given percentage range (y axis) is plotted against an increasing percentage range, from 0 to 1% to 44 to 45% (x axis). The mean genetic distance, standard deviation, and range are given. The entire alignment shows moderate genetic diversity (average, 5.8%) and evidence of positive selection pressure (Ks:Ka = 0.86; P < 0.001). The V4 region contributes most highly to genetic diversity, with the largest mean genetic distance and the broadest range of values. The 3′ flanking region also contributes substantially to diversity and experiences the strongest evolutionary pressure (Ks:Ka = 0.74; P < 0.001).

Article Snippet: A total of 46 IDU were examined (42 males and 4 females; average age, 27 years), 35 of whom had previously been found seropositive by an HIV-1 enzyme-linked immunosorbent assay (ELISA) (United Biomedical Incorporated, Hauppauge, N.Y.), 2 of whom had previously been found HIV-1 seronegative by the same method, and 9 of whom had not yet been tested.

Techniques: Standard Deviation, Selection