As I’m sure most of you are aware, there is an ongoing outbreak of a novel coronavirus causing something of a panic around the world. At the time of writing, it’s been eight weeks since Chinese health authorities first reported a cluster of pneumonia cases in Wuhan, the capital of Hubei province and major transport hub of central China. The earliest human infections are believed to have occurred by early December 2019, and a large meat market was linked to most – but not all – of the initial cases. The evidence from the initial outbreak suggested that the virus could not be easily spread between humans, but it soon became very clear that this was not the case. The virus then quickly spread from person to person and now has even found itself here in the UK. 2,468 deaths have so far been attributed to the virus, of which most were elderly patients, many of whom had pre-existing health conditions. At this moment in time there is no vaccine or specific antiviral treatment, with efforts typically aiming at managing symptoms and supportive therapy.
As I have previously said, no event of any significance in the world takes place without generating a flutter of conspiracy speculation, and this potential pandemic is no exception. Front and centre leading the troops is American radio show host and conspiracy theorist, Alex Jones, who believes the virus has been bioengineered using part of the HIV virus.
If you’ve spent any time online, you’ve probably stumbled upon one of Jones’s unhinged, nonsensical rants. Even after being banned from nearly all of the major content platforms, he still garners attention due to his outlandish claims and his perpetual outrage over the latest government conspiracy. In the past, I have criticised Alex for: perpetuating misinformation that Syngenta are “putting chemicals in the water that turn the freakin’ frogs gay!”; promoting Sandy Hook Elementary School shooting conspiracies; and giving a platform to Wolfgang Halbig, a notorious harasser of the parents of the children murdered, who has since been charged with unlawful possession of personal identification of another person. In this latest video, Alex tells his audience that HIV has been bioengineered into this pneumonia virus in the hope of reducing the world’s population, or as a “big drill for world government”…whatever that means.
When a new pathogen causes a global epidemic in humans, one key question is where does it come from. This is especially important for an infectious disease that spread from non-human animals to humans (zoonotic disease). Knowing the origin of such a pathogen can help to prevent further transmission and give us a clue about how transmission occurs. This however is a very time-consuming process which usually takes many years, as the cases for HIV-1, SARS, and MERS. Before the source of a new pathogen is clearly-defined, conspiracy theories regarding its origin are often rampant. Recently many have speculated online that the 2019-nCoV might be derived from genetic manipulation, or even for use as a bioweapon. This speculation has been further fanned by the publication of the report, ‘Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120 and Gag’, which some – like our friend Alex – believe is proof that the new novel coronavirus was bioengineered using HIV.
The report claimed to have shown that the 2019-nCoV spike glycoprotein gene (critical for the virus to enter its target cells when compared to other coronaviruses) had four similar, if not identical, insertions to HIV-1 in its genome. The paper went on to speculate that these insertions could provide an enhanced affinity towards host cell receptors, increase the range of host cells of the coronavirus, and that it acquired these abilities by gaining these gene fragments from HIV-1. What is important to note here is that the paper DOES NOT suggest that these insertions were deliberately placed into the virus in any way, shape or form, as Alex Jones reports.
The complete genome of this new coronavirus was quickly sequenced and made public on January 12th, only about two weeks after the disease was first reported. Phylogenetic analysis showed that it shares a high level of genetic similarity (96.3%) with a bat coronavirus (RaTG13), obtained from a bat in Yunnan in 2013. This suggests that RaTG13-like viruses are most likely the reservoir, but not the immediate sources of the current virus. Using this data, a group of scientists recently investigated the claims that 2019-nCoV might have gained advantage traits from HIV-1. They published their findings in the Emerging Microbes & Infections journal, in a paper entitled ‘HIV-1 did not contribute to the 2019-nCoV genome’, which – spoilers – found no evidence that the sequence of the four inserts in question were HIV-1 specific, or that the 2019-nCoV viruses obtained these insertions from HIV-1.
The report carefully examined the sequences of 2019-nCoV, other coronaviruses, and HIV-1.The results of their first BLAST (Basic Local Alignment Search Tool – a search algorithm which finds regions of similarity between biological sequences) showed that the top 100 identical or highly homologous hits were “all from host genes of mammalian, insects, bacterial and others”. Importantly, though, none of the top 100 were HIV-1 related. A BLAST against a viral sequence database also showed that these insertions exist in all kinds of viruses from bacteriophage and influenzas, to giant eukaryotic viruses. At this point the paper adds that these insertions are also found in the bat coronavirus RaTG13, stating that the similarity of the spike protein between RaTG13 and 2019-nCOv is 97.7%.
We still don’t know how the bat coronavirus RaTG13 obtained these four insertions, but what we do know is that for it to gain these gene fragments from HIV-1, a host cell would have to be infected with both HIV-1 and corona at the same time. As the host cells for bat coronavirus and HIV-1 are different, the chances of both exchanging genetic material is beyond negligible.
The paper ends by warning about the potential dangers of misinterpreting data and allowing your bias to seep in.
“The advances in bioinformatics analysis tools are widely used to easily and rapidly analyse newly obtained sequences. However, great care is required for comprehensive and thorough analysis to fully understand the real biological implications of the new genomic information. Biased, partial and incorrect analysis can dangerously lead to conclusions that fuel conspiracies and harm the process of true scientific discoveries and the effort to control the damage to public health.”
Although RaTG13 and 2019-nCoV are similar, they are not identical, and the genetic difference between them suggests that the bat coronavirus is not the immediate ancestor. More studies are required to identify the real source of the 2019-nCoV, which in all likelihood will take some time. But just because we don’t have all the answers right now (which I agree, is quite scary) doesn’t mean we should allow our imagination to run rampant and we shouldn’t entertain elaborate conspiracy theories about the coronavirus from the likes of Alex Jones.