Rapid and simple characterization of in vivo HIV-1 sequences using solid-phase direct sequencing

Area of Science:

• Virology
• Molecular Biology
• Genetics

Background:

• Understanding the genetic diversity and origin of Human Immunodeficiency Virus type 1 (HIV-1) is crucial for epidemiological and pathogenic studies.
• Accurate and efficient sequencing methods are essential for analyzing in vivo viral genetic material.

Purpose of the Study:

• To evaluate solid-phase direct sequencing as a method for obtaining in vivo HIV-1 p25/p7 gene segment sequences.
• To compare the consistency of solid-phase direct sequencing with traditional double-strand sequencing methods.
• To analyze the genetic diversity and origins of HIV-1 strains circulating in Finland.

Main Methods:

• Solid-phase direct sequencing was employed to analyze polymerase chain reaction (PCR)-amplified HIV-1 p25/p7 gene segments.
• Comparison of solid-phase sequencing with double-strand sequencing of gel-purified amplification products.
• Analysis of HIV-1 sequences amplified from both cell lysates and purified DNA templates.

Main Results:

• Solid-phase direct sequencing yielded more consistent results compared to double-strand sequencing.
• HIV-1 sequences were successfully amplified from both cell lysates and purified DNA.
• Analysis of 7,780 bp from 41 samples revealed sequence motifs linking them to Euroamerican and African HIV-1 groups, with a predominance of Euroamerican types in Finland.

Conclusions:

• Solid-phase direct sequencing is a reliable and consistent method for in vivo HIV-1 sequence data acquisition.
• The study identified a diverse range of HIV-1 strains in Finland, predominantly of Euroamerican origin.
• Solid-phase direct sequencing is a valuable tool for future epidemiological and pathogenic investigations of HIV-1 infections.