In February 2023, The Wall Street Journal reported that the US Department of Energy had changed its assessment on how the Covid pandemic started – concluding with low confidence based on “new intelligence” that the pandemic most likely stemmed from a lab leak.

The scoop ricocheted across national media, with news outlets, including The New York Times and FOX News, quickly producing follow-up reports built around the same core narrative – that the DOE had shifted course.

But newly released internal records now suggest that the agency’s purported change might not have been an analytical pivot based on new information, but rather an effort to clarify its original conclusions that somehow got lost in translation.

The documents – obtained by US Right To Know through an ongoing Freedom of Information Act lawsuit against DOE – show that, in the months leading up to the agency’s reported change in thinking, Energy officials and national laboratory analysts grappled with how the department’s contribution to a 2021 report on spy agencies’ conclusions on the pandemic’s origin became misconstrued as it moved through the Intelligence Community, creating confusion for Congress, and later for the public.

The records indicate that, in August 2022, some Republican members of the US House Permanent Select Committee on Intelligence (HPSCI) had reviewed a National Intelligence Council (NIC) report and an accompanying Q&A document prepared by DOE that stirred confusion over what the agency had actually concluded.

In turn, the NIC and Office of the Director of National Intelligence (ODNI) went back to the agency for help drafting a letter to demystify that confusion, which, at least in part, had been created by internal disputes among DOE scientists over how the agency’s original assessment was conveyed in intelligence reports.

The distinction mattered because the Intelligence Community’s first public report on Covid’s origin assessments overwhelmingly favoured natural spillover, with DOE’s position described as “undecided.” The report’s outcome helped shape initial public perception that US spy agencies had largely dismissed the lab-leak hypothesis, even as internal views were more varied and more technically contested.

DOE did not respond to questions emailed last week about the newly released records that reveal the uncertainty over the agency’s original assessment. ODNI did not respond to specific questions either, but issued a brief statement saying that Director of National Intelligence Tulsi Gabbard “remains committed to declassifying COVID-19 information.”

An ODNI official added the agency “is investigating intelligence failures surrounding the Covid-19 pandemic, including investigating the potential suppression of the lab leak hypothesis inside the Intelligence Community.”

Most records remain hidden within the latest 186-page tranche released by the DOE, which has long run intelligence operations that leverage its unique scientific and technological expertise to protect national security. Only a relatively small number of pages, mostly of internal email discussions, contain substantive, readable material. The rest are heavily redacted, with the DOE claiming disclosure exemptions largely based on national security and protecting intelligence sources and methods. The redactions fully encompass the agency’s official assessment documents, captured in what analysts initially labelled a Technical Intelligence Note, or TIN.

But those records left visible reveal a sharp dispute within DOE among analysts based in three of its national laboratories that apparently contributed to later doubts over where the agency stood on the origin issue. That dispute centred on a genetic characteristic of SARS-COV-2, the virus that spawned the pandemic, and an unusually blunt warning from a DOE analyst that an internal memo comparing the feature to naturally occurring examples in other viruses was “either a large mistake or disingenuous.”

In August 2021, after President Biden ordered a 90-day review of intelligence on the pandemic’s roots, ODNI released a declassified summary report stating that most agencies leaned toward a natural origin with low confidence. One agency favoured a lab-associated incident with moderate confidence and two others – including the DOE – were described as “undecided.”

No agency assessment papers were released, no technical annexes were provided and no underlying intelligence was disclosed.

In June 2023, after Congress passed the Covid-19 Origin Act, ODNI issued an updated summary reflecting that both DOE and the FBI assessed, with low and moderate confidence respectively, that a lab-associated incident was most likely. Again, ODNI did not release any of the agencies’ own analyses or technical underpinnings.

Both summaries drew criticism from lawmakers and outside analysts who argued they were too general – describing confidence levels without providing the data or reasoning behind them, and offering the public little ability to evaluate the evidence or analytic disputes that drove each agency’s view.

The newly released DOE records suggest that this lack of detail also had a downstream consequence – confusion about what DOE had actually concluded in 2021, and whether the language used to describe it matched what DOE’s analysts had assessed.

According to the records, analysts at three of the DOE national laboratories – Los Alamos (LANL), Lawrence Livermore (LLNL) and Pacific Northwest (PNNL) – produced the agency’s assessment in 2021 for DOE’s Office of Intelligence and Counterintelligence. First referred to as a TIN, the report later was labelled a Biological Assessment Report (BAR), the records show.

That report also fed into the NIC’s classified assessment summary delivered to the president and other senior officials, and to the House intelligence committee. As part of its contribution, DOE also prepared a Q&A document explaining its reasoning and helping translate technical findings into language intended for policymakers and overseers.

The records reflect disagreement among the DOE labs that helped prepare the assessment about whether portions of the agency’s internal analyses were too technical and misleading, but don’t indicate whether or how those disputes were resolved.

A final report for the NIC was ultimately submitted by lab analysts to DOE headquarters in October 2021.

What remains unclear is whether DOE’s analytic leaning in 2021 was later conveyed clearly in the NIC’s memo to Congress and, eventually, to the public.

One of the few places where the readable records reveal specific scientific reasoning involves a feature of SARS-CoV-2 that has drawn scrutiny since early in the pandemic: the furin cleavage site.

That cleavage site is a spot on the virus’s spike protein where a scissors-like enzyme called furin is able to snip to help the virus enter human cells. Some viruses have cleavage sites to help them infect hosts more efficiently.

The furin cleavage site in SARS-CoV-2 became a focus for scientists because the virus appeared to spread efficiently in humans early on – and because genomic comparisons showed that none of its closest known SARS relatives possessed the same feature, raising suspicions that it had been engineered in a lab.

• A Tell Media report / By Lewis Kamb – an investigative reporter at US Right to Know