Analysis of HIV type 1 reverse transcriptase: comparing sequences of viral isolates with mutational data

Area of Science:

• Virology
• Molecular Biology
• Genetics

Background:

• High mutation rates during human immunodeficiency virus type 1 (HIV-1) replication lead to many defective, non-infectious virions and proviruses.
• The Los Alamos HIV-1 sequence database contains extensive sequence data, but the infectious nature of most entries is unconfirmed.
• Determining the infectivity of viral sequences is crucial for accurate research and therapeutic development.

Purpose of the Study:

• To evaluate the infectivity of HIV-1 sequences in the Los Alamos database.
• To develop a method for predicting whether HIV-1 sequences are derived from infectious clones.

Main Methods:

• Conducted saturation mutagenesis on a 109-amino acid region of HIV-1 reverse transcriptase, assaying 366 single-amino acid substitutions.
• Analyzed sequences from the Los Alamos HIV-1 sequence database.
• Compared sequence data with known effects of amino acid substitutions on reverse transcriptase activity.

Main Results:

• No sequences from confirmed stable infectious clones exhibited substitutions that inactivate reverse transcriptase.
• Identified numerous sequences in the database with inactivating reverse transcriptase substitutions.
• These findings suggest that sequences with inactivating mutations are unlikely to originate from infectious clones.

Conclusions:

• The presence of inactivating mutations in reverse transcriptase can serve as a reliable indicator of non-infectious HIV-1 sequences.
• This approach can help filter and validate viral sequences for research purposes.
• The methodology may be applicable to assessing the sequences of other viruses.