"HIV" sequences might found in the human genome?

Guest Post by Miguel Romero

I was recently alerted to the work of Miguel Romero, in response to my post What is one thing you’d like to see RFKJ do?

Mr. Romero—who holds not only an MSc and two Master’s degrees in Engineering, but is also currently a medical student—has kindly agreed to allow me to repost his comments here and with the exception of this introduction, all credit goes to him. I think you will find his work fascinating. In particular, Mr. Romero has found numerous “HIV” associated genetic sequences in places it might be surprising to find them, including a 135 base pair sequence in none other than James Watson’s human genome, and of certain “HIV” genes in malignancies unrelated to “HIV.” I’m not sure what these findings will imply moving forward—we’ll just have to see.

It should be pointed out that some “HIV” proteins share characteristics with other retroviruses (it is unclear whether these include HERVs, but I suspect they might). Additionally, I should add that HIV is known for its high genetic diversity—being referred to as a “quasi species”—with, and this is a mainstream view, a myriad of subtypes and variants circulating within and between individuals. This is also complicated by the fact that RNA itself inserts itself into the human genome, as we have discussed many times.

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Here is Mr. Romero’s biography:

Miguel Romero holds a MEng in Computer Engineering from the Universitat Oberta de Catalunya (UOC), Barcelona. He also earned a MEng in Telecommunications Engineering through a joint program between UOC and Universitat Ramon Llull (URL), with the degree awarded by both institutions. He completed a Postgraduate Diploma in Bioinformatics at UOC, followed by an MSc in Bioinformatics and Biostatistics jointly awarded by UOC and the University of Barcelona (UB). He is currently pursuing a degree in Medicine at the University of Castilla-La Mancha (UCLM), Spain.

His interest in HIV research emerged unexpectedly during postgraduate studies in Bioinformatics. While working on his final postgraduate project, by chance he discovered small length HIV sequences in many unexpected places. These were present in many datasets from unrelated organisms, including bacteria, the human genome, and even plants. He put these down to contamination. This serendipitous finding sparked a deep scientific interest in virology, genomic data curation, and the implications of cross-species contamination in biomedical research.

Here are his findings, in his own words:

I am a graduate in Bioinformatics and Biostatistics in Open University from Catalonia– Barcelona University Spain. Since 2014 I have discovered many HIV genetic sequences in sources unrelated to HIV infection. The details and citations are listed below. For various reasons I concluded they were probably contaminations. However, I was not entirely convinced because I failed to find HIV DNA in “control” RNA viruses. The HIV contaminations are widespread. This raises the possibility that some positive HIV PCR tests are also contaminations. Since HIV DNA is believed unique to HIV, and exclusive to HIV positive individuals, I wonder if Mr. Robert Kennedy Jr. may be in a position to look into this further.

1. A heterogeneous collection of dozens of HIV genetic sequences documented in animal and plant taxa, and inanimate sources, such as wastewater and seawater (metagenomes). See tables and 58 links in Reference 1.

2. In November 2014 I reported the presence of a 135 bp nucleotide HIV-1 sequence in the genome of Dr. James Watson. This sequence aligns with the 7464-7598 region of the HIV-1 env (gp120/160) gene. Additional BLASTN testing revealed high identity sequences between Dr. Watson's genome and the HIV-1 LTRs (long terminal repeats), p17 and p51 (reverse transcriptase) genes.

Note: Nature has recently removed my comments [2].

3. In 2010 Professor Svante Pääbo sequenced the genome of a 38,000-year-old fossil Homo sapiens neanderthalens. Pääbo was fastidious in avoiding contamination between Homo sapiens and Neanderthal DNA. In 2022 a BLASTN search revealed DNA homologous to the DNA of HIV-1 proteins p10, p51 and p66. TBLASTN, a sensitive bioinformatic tool for searching similarities at the protein level, returned amino acid sequences with high identity to the p7, p24, p41, p51, p66 and p160 HIV-1 proteins.

4. In response to a BMJ News Item on the plight of women with ovarian cancer I reported work published 25 years ago by the U.S. scientist Dr. Eva Rakowicz- Szulczynska. In several papers she reported the presence of HIV env gene sequences in a number of malignancies. These included breast and ovarian cancers. The sequences were not present in adjacent, cancer free tissue excised from the same operative specimens as the cancers. On several occasions I unsuccessfully attempted to interest the scientific community in investigating these data further. I thought they may serve as a liquid biopsy for the early diagnosis of these neoplasms. Especially the blight of ovarian cancer, “the most fatal of all gynecologic malignancies”. Perhaps Mr. Kennedy has physicians or scientists at the NIH who will be interested in pursuing this possibility [4].

References

1. Romero Fernández-Bravo M. Contamination of genomic databases by HIV-1 and its possible consequences. A study in Bioinformatics. 2014. LINK

2. Romero Fernández-Bravo M. Readers comment on genome of Dr. James Watson. Nature 2014; 452: 872-6. Romero’s comment LINK This second link contains the instructions relevant to confirming the HIV-1 sequence in Dr. Watson’s genome. It requires minimal knowledge of bioinformatics.

3. Comment on Neanderthal Nobel Prize to Paleogenetics Rockstar Svante Pääbo Evokes Memories of Being Drawn to Science. LINK

4. Romero Fernández-Bravo M. Less than half of women are diagnosed with ovarian cancer within a month of seeing a doctor, finds survey. Comment at BMJ. 2018. LINK

Miguel Ángel Romero

2nd March 2025

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Thank you again to Mr. Romero for sharing his work; please let me know what you think in the comments.