CDC Flu PCR Primers Match Human DNA Across the Genome: New BLAST Data

Are we detecting viruses or ourselves?

The CDC’s ‘Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay’ is a real-time reverse-transcription polymerase chain reaction (rRT-PCR) laboratory test used to detect influenza A, influenza B, and SARS-CoV-2 in upper or lower respiratory samples.

Mainstream health authorities use PCR tests to quantify how many infection cases there are.

Case numbers are used to declare pandemics and justify pandemic response measures like lockdowns, masking, social distancing, and vaccination campaigns.

But what if these tests aren’t detecting viruses?

What if they’re detecting human DNA?

That would mean the primary justification for pandemic declarations is built on signals that may not represent viral infection at all, but amplified fragments of the human genome—calling into question the scientific basis for case counts, emergency powers, and every downstream policy decision tied to them.

Scrutiny of the PCR test is warranted, given the high likelihood of an incoming bird flu pandemic and the international coordination documented on this website.

A new BLAST analysis of the CDC’s Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay reveals that every variant of the influenza A forward primer, reverse primer (across all ambiguity resolutions), and probe independently produces dozens to over 100 significant partial matches—often perfect over 15–18 bp core segments—scattered across nearly every human chromosome, establishing widespread human genomic homology.

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CDC’s Flu PCR Test

A positive PCR test result requires genetic material in the specimen to match three genetic sequences: a forward primer sequence, a reverse primer sequence, and a target probe sequence.

(While those bindings must align in the correct orientation, spacing, and combination to produce a detectable amplicon and fluorescent signal under the test’s specific conditions, the current project only focuses on genetic alignment between the PCR test primers/probe and the human genome.)

The U.S. Centers for Disease Control and Prevention (CDC) shares the primer and probe sequences for its ‘Influenza SARS-CoV-2 (Flu SC2) Multiplex Assay,’ shown below with red boxes indicating the influenza A forward primer, reverse primer, and probe.

You can see in the above screenshot that portions of the forward and reverse primers have a “Y” and “V” in some places instead of the standard A, C, G, or T nucleotide letters for DNA.

The Y and V are IUPAC ambiguity codes that allow the primers to bind to more than one possible genetic sequence in a sample, greatly increasing the range of DNA sequences the primers can bind to.

This creates more paths to reach a positive PCR result.

Moreover, primers can bind to sample DNA even when the sequences don’t match perfectly, again multiplying the number of paths to a positive PCR result.

Y can be a C or T.

V can be an A, C, or G.

We tested each variation below.

BLAST Results

Using the government’s BLAST (Basic Local Alignment Search Tool) software, we tested whether any of these three PCR sequences used to count influenza A infections match any human genome sequences.

Forward Primer Results

Y = C

When we substituted the CDC’s forward primer Y ambiguity code for C, the results reveal that the forward primer sequence produces numerous significant alignments distributed across nearly every human chromosome, including chromosomes 1 through 12, 14 through 21, X, and several alternate locus scaffolds and genomic patches.

The highest-scoring matches achieve scores of 32.8 bits with 95–100% identity and E-values of 2.4, primarily on chromosomes 5 and 10, while most other alignments show 94–100% identity over 15–23 bases, with many shorter segments matching perfectly.

Overall, more than 100 significant hits were identified genome-wide.

These findings indicate that the forward primer (when Y=C) is not unique to a single locus but corresponds to a common motif or highly similar repetitive sequence present in multiple regions throughout the human genome.

Y = T

When we substituted the CDC’s forward primer Y ambiguity code for T, the results reveal that the primer sequence produces numerous significant alignments distributed across most human chromosomes, including chromosomes 1 through 13, 15 through 20, X, and several genomic patches or scaffolds.

The highest-scoring match achieves a score of 36.5 bits with 95.45% identity and an E-value of 0.20 on chromosome 20, while most other alignments show 90–100% identity over 15–23 bases, with many shorter segments matching near-perfectly.

Overall, dozens of significant hits were identified genome-wide, with multiple matching regions per chromosome (e.g., up to 8 on chromosome 1).

These findings indicate that the forward primer sequence (when Y=T) is not unique to a single locus but corresponds to a common motif or highly similar repetitive element present in various regions throughout the human genome.

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Reverse Primer Results

Y = C, V = A

When we substituted the CDC’s reverse primer Y ambiguity code for C and ambiguity code V for A, the results reveal that the primer sequence produces significant alignments distributed across several human chromosomes, including chromosomes 1 through 11, 14, 18, 20, 21, and X.

The highest-scoring match achieves a score of 32.8 bits with 95% identity over 96% query coverage and an E-value of 2.4 on chromosome 9, while most other alignments show 87–100% identity over 15–20 bases, with many shorter segments matching perfectly.

Overall, around 30–40 significant hits were identified genome-wide, with multiple matching regions per chromosome (e.g., up to 6 on chromosome 9).

These findings indicate that the forward sequence (when Y = C, V = A) is not unique to a single locus but corresponds to a common motif or highly similar repetitive element present in various regions throughout the human genome.

Y = C, V = C

When we substituted the CDC’s reverse primer Y ambiguity code for C and ambiguity code V for C, the results revealed significant alignments on several human chromosomes, including chromosomes 2, 3, 4, 6, 7, 12, 13, 14, and 19, with one additional lower-identity hit on chromosome 9.

All top matches have scores of 28.3–29.2 bits and E-values of 29, consisting primarily of perfect 15/15-bp matches (100% identity) or near-perfect longer segments (e.g., 17/18 at 94% on chromosome 2 and 18/20 at 90% on chromosome 9).

Overall, approximately 11 significant hits were identified across these chromosomes, with chromosome 7 showing two separate matches.

These findings indicate that the reverse primer sequence (when Y = C, V = C) is not unique to a single locus but shares a highly conserved 15-bp core motif that appears in multiple regions throughout the human genome, with surrounding bases showing minor variation.

Y = C, V = G

When we substituted the CDC’s reverse primer Y ambiguity code for C and ambiguity code V for G, the results reveal significant alignments distributed across multiple human chromosomes, including chromosomes 1 through 3, 5 through 9, 11, 13, 14, 18, 20, 21, and X.

The highest-scoring matches achieve scores of 30.1 bits with 100% identity over 70–96% query coverage and E-values of 8.4 (e.g., on chromosomes 1, 5, 11, and 18), while most other alignments show 90–100% identity over 15–20 bases, with many shorter segments matching perfectly.

Overall, around 30–40 significant hits were identified genome-wide, with multiple matching regions per chromosome (e.g., up to 6 on chromosome 1).

These findings indicate that the reverse primer sequence (when Y = C, V = G) is not unique to a single locus but corresponds to a common motif or highly similar repetitive element present in various regions throughout the human genome.

Y = T, V = A

When we substituted the CDC’s reverse primer Y ambiguity code for T and ambiguity code V for A, the results reveal that the sequence produces numerous significant alignments distributed across most human chromosomes, including chromosomes 1 through 7, 9 through 12, 14, 17, 18, 20, X, and Y, as well as several genomic patches and scaffolds.

The highest-scoring matches achieve scores of 32.8 bits with 95% identity over 87–96% query coverage and E-values of 2.4 (e.g., on chromosomes 2, 5, 7, and 17), while most other alignments show 90–100% identity over 15–21 bases, with many shorter segments matching perfectly.

Overall, more than 50 significant hits were identified genome-wide, with multiple matching regions per chromosome (e.g., up to 6 on chromosome 5 or 8 on chromosome 8).

These findings indicate that the reverse primer sequence (when Y = T, V = A) is not unique to a single locus but corresponds to a common motif or highly similar repetitive element present in various regions throughout the human genome.

Y = T, V = C

When we substituted the CDC’s reverse primer Y ambiguity code for T and ambiguity code V for C, the results reveal significant alignments distributed across multiple human chromosomes, including chromosomes 1, 2, 4, 5, 7, 8, 10, 11, 12, 17, 20, 21, and X, as well as one alternate scaffold on chromosome 5.

The highest-scoring match achieves a score of 33.7 bits with 100% identity over 96% query coverage and an E-value of 0.69 on chromosome 2, while most other alignments show 90–100% identity over 15–20 bases, with many shorter segments matching perfectly or near-perfectly.

Overall, around 20–30 significant hits were identified genome-wide, with multiple matching regions per chromosome (e.g., up to 4 on chromosome 2).

These findings indicate that the reverse primer sequence (when Y = T, V = C) is not unique to a single locus but corresponds to a common motif or highly similar repetitive element present in various regions throughout the human genome.

Y = T, V = G

When we substituted the CDC’s reverse primer Y ambiguity code for T and ambiguity code V for G, the results reveal that the sequence produces numerous significant alignments distributed across most human chromosomes, including chromosomes 1 through 12, 14 through 18, 20 through 22, X, and Y, as well as several genomic patches and scaffolds.

The highest-scoring match achieves a score of 32.8 bits with 95% identity over 91% query coverage and an E-value of 2.4 on chromosome 20, while most other alignments show 94.74–100% identity over 16–21 bases, with many shorter segments matching perfectly.

Overall, more than 60 significant hits were identified genome-wide, with multiple matching regions per chromosome (e.g., up to 8 on chromosome 2 or 5 on chromosome 21).

These findings indicate that the reverse primer sequence (when Y = T, V = G) is not unique to a single locus but corresponds to a common motif or highly similar repetitive element present in various regions throughout the human genome.

Probe Results

When aligning the CDC PCR test probe sequence to the human genome, the results reveal that the sequence produces numerous significant alignments distributed across most human chromosomes, including chromosomes 1 through 5, 7 through 14, 16 through 21, and X, as well as several genomic patches and scaffolds.

The highest-scoring matches achieve scores of 31.9 bits with 90.91–100% identity over 92–100% query coverage and E-values of 2.4 (e.g., on chromosomes 10 and 18), while most other alignments show 88–100% identity over 15–23 bases, with many shorter segments matching perfectly or near-perfectly.

Overall, around 40–50 significant hits were identified genome-wide, with multiple matching regions per chromosome (e.g., up to 9 on chromosome 10).

These findings indicate that the probe sequence is not unique to a single locus but corresponds to a common motif or highly similar repetitive element present in various regions throughout the human genome.

Bottom Line

Every tested variant of the CDC’s influenza A forward primer (both Y=C and Y=T resolutions), the reverse primer (all six Y/V combinations), and the probe itself, each independently has dozens to over 100 significant partial alignments (often perfect over 15–18 bp core segments) scattered widely across the human genome on nearly every chromosome.

These are not rare or isolated hits—they are abundant, repetitive-like patterns for each sequence of the CDC’s influenza A PCR test.

The sheer number and distribution of these strong matches across all three components means that, in principle, there are many human genomic regions where one or more of the PCR primers and probe could bind with high affinity.

Whether those bindings ever align in the correct orientation, spacing, and combination to produce a detectable amplicon and fluorescent signal under the test’s specific conditions is an open empirical question that these BLAST data alone cannot fully resolve.

But the data does establish a non-trivial degree of sequence overlap between the entire influenza A PCR primer/probe set and widespread human genomic motifs.

That overlap is real, documented in our BLAST searches, and not insignificant in scale.

It warrants scrutiny regarding how specific the assay truly is to influenza A viral genetic material versus potential background from human DNA in respiratory samples, especially at high cycle thresholds or in so-called low-viral-load scenarios.

The evidence demonstrates a clear and repeated pattern of human genome homology across the full Influenza A detection system.

That pattern stands on its own as a finding worth serious consideration.

Especially because the incoming attempted bird flu pandemic will rely on PCR tests to justify case numbers.

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