Are retroviruses cytotoxic?

Are retroviruses cytotoxic?

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There are typically hundreds of retroviruses found in healthy human beings.

Are retroviruses then cytotoxic? (In other words, are they able to kill or damage other cells).

As you point out human beings (and other organisms) have hundreds of retroviruses and many can be seen in the human genome, some of which appear to be the remains of deactivated viruses, others which may be active. Most retroviruses are not pathogenic - they don't cause disease.

This is because many retroviruses replicate slowly, budding and secreting from the cell surface in small numbers without killing their host cell.

There are several disease-causing retroviruses. Human T-cell Leukemia Virus (HTLV) can cause T-cells to replicate in an uncontrolled fashion, resulting in leukemia. This is not a necessary result for HTLV to replicate, but it is a result of viral infection as viral replication tweaks the cell machinery to replicate.

While it's not clear exactly how, Human Immunodeficiency Virus (HIV) kills its hosts cells. Unfortunately HIV's hosts are CD4 immune cells. The fact that sporadic replication of HIV can cause all host immune cells to die entirely makes HIV a pathogen.

Disease is usually thought of as a lack of adaptation of a pathogen and host: viruses do better if they do not kill their host. Both these cases are possibly not the future for either virus: either could adapt to reproduce without causing a disease. Or they might have already , having spun off some strains into the pool of quiet retroviruses medical science does not concern itself with.

Adeno-associated virus

Adeno-associated viruses (AAV) are small viruses that infect humans and some other primate species. They belong to the genus Dependoparvovirus, which in turn belongs to the family Parvoviridae. They are small (20 nm) replication-defective, nonenveloped viruses and have linear single-stranded DNA (ssDNA) genome of approximately 4.8 kilobases (kb). [1] [2]

AAV are not currently known to cause disease. The viruses cause a very mild immune response. Several additional features make AAV an attractive candidate for creating viral vectors for gene therapy, and for the creation of isogenic human disease models. [3] Gene therapy vectors using AAV can infect both dividing and quiescent cells and persist in an extrachromosomal state without integrating into the genome of the host cell, although in the native virus integration of virally carried genes into the host genome does occur. [4] Integration can be important for certain applications, but can also have unwanted consequences. Recent human clinical trials using AAV for gene therapy in the retina have shown promise. [5]

Human endogenous retroviruses role in cancer cell stemness

Cancer incidence and mortality, metastasis, drug resistance and recurrence are still the critical issues of oncological diseases. In this scenario, increasing scientific evidences demonstrate that the activation of human endogenous retroviruses (HERVs) is involved in the aggressiveness of tumors such as melanoma, breast, germ cell, renal, ovarian, liver and haematological cancers. In their dynamic regulation, HERVs have also proved to be important determinants of pluripotency in human embryonic stem cells (ESC) and of the reprogramming process of induced pluripotent stem cells (iPSCs). In many types of tumors, essential characteristics of aggressiveness have been associated with the achievement of stemness features, often accompanied with the identification of defined subpopulations, termed cancer stem cells (CSCs), which possess stem cell-like properties and sustain tumorigenesis. Indeed, CSCs show high self-renewal capacity with a peculiar potential in tumor initiation, progression, metastasis, heterogeneity, recurrence, radiotherapy and drug resistance. However, HERVs role in CSCs biology is still not fully elucidated. In this regard, CD133 is a widely recognized marker of CSCs, and our group demonstrated, for the first time, the requirement of HERV-K activation to expand and maintain a CD133+ melanoma cell subpopulation with stemness features in response to microenvironmental modifications. The review will discuss HERVs expression as cancer hallmark, with particular focus on their role in the regulation of cancer stemness features and the potential involvement as targets for therapy.

Retroviruses can Promote A Perfect Storm of Illness

The retroviruses being discussed here do not directly cause diseases by themselves. A perfect storm of events need to come together to create acquired immune system deficiency (non-HIV AIDS). When conditions are right, the viruses create unrelenting inflammatory processes that disrupt the immune system.

The perfect storm occurs when human DNA is disturbed by retroviruses, when there are co-infections, when there is severe shock or trauma, when hormones are dysregulated, when there are genetically modified organisms and glyphosate in the diet, when there are pesticides and other toxic substances in food and the environment, and when there are genetic susceptibilities.

If some or all of these conditions occur together, then the immune system will be weakened to the point where the perfect storm occurs, and people become ill with some type of modern chronic disease.

Not everyone who has retroviruses in their bodies will develop one of these diseases, but for those who experience a perfect storm the possibility is much greater. The risks increase with age as the immune system naturally weakens.


Efficient sensing by the innate immune system is the first step towards an effective antiviral immune response. In an effort to determine which innate sensing pathways are critical for retrovirus infections in vivo, mice deficient in various innate sensors were infected with murine retroviruses such as MuLV. Previously, it was shown that TLR7 and MyD88 were required for a potent antiretroviral humoral immune response [11,12]. However, T cell responses were only partially affected by MyD88 signaling, and no data exists on sensors required for NK cell activity. Here, we demonstrate for the first time that TLR3 sensing is involved in cytotoxic T cell and NK cell responses during acute FV infection.

Interestingly, no differences in viral loads were observed between wild type and MyD88-deficient mice during acute infection (up to 1 week post infection) [11]. Our data showing that TLR7 does not impact acute FV infection (see Figure  1 C) is consistent with this finding, but contrasts recent data from the same group [30]. We hypothesize that the lack or inconsistent impact of TLR7/MyD88 on acute FV infection may reflect the fact that the neutralizing antibody responses do not play a significant role in inhibiting FV at the earliest infection time points [31]. Notably, at later time points (starting 2 weeks post infection) viral loads were increased in MyD88 −/− mice, consistent with a weakened humoral immune response. We recently provided evidence that NK cell responses could significantly inhibit acute FV replication in vivo [14]. Thus, our findings showing enhanced acute FV replication in TLR3 −/− mice are consistent with a strong impact of TLR3 on cytotoxic NK cell responses. TLR3 is strongly expressed by mDCs, whereas its expression is weak in murine B cell subsets [32]. In contrast, TLR7 is highly expressed by follicular B, marginal zone B, Peyer´s patch B and B-1B cells and the expression level in mDCs is rather low [32]. This may explain that TLR7 is required for efficient antibody responses [11,12] as it might directly influence B cell responses and not NK or T cell responses.

Other known innate sensors for retroviral infections are cGAS [2], DC-Sign [6], TLR9 [33] and zinc-finger antiviral protein [34]. They were all observed to be important for induction of type I IFN by retroviruses, but their influence on cellular or humoral immune responses has not been investigated so far. Antiviral immune responses can be affected by many sensors, which were described for other virus infections. This depends on the host cell type and on the time point of the infection. Especially TLRs are not ubiquitously expressed, but rather by specific immune cells like mDCs, pDCs, macrophages, B cells and others [35-37]. Other PRRs like MDA5 or Rig-I are found in the cytosol of almost every cell type making them efficient general sensors for viral infections. For influenza virus infection various PRRs were shown to be required for efficient induction of anti-viral immune responses. Influenza virus infection is sensed by many different PRRs (TLR3, TLR7 and Rig-I) (reviewed in [38]), and they all have distinct influences on the cellular and humoral immune responses against the virus. It was shown that TLR3, TLR7 and MyD88 signaling is not required for efficient T responses during influenza infection [39,40], but both TLR7 and MyD88 are critical for B cell responses during influenza infection [40]. Koyama and colleagues investigated that Rig-I is also not needed for a potent CD8 + T cell response, whereas B cells and CD4 + T cells require MyD88 and Rig-I [39]. West Nile virus (WNV) vaccination studies revealed that MyD88 and TLR3 are both required for efficient humoral immune responses [41], and during a WNV infection Rig-I and MDA5 [42-44], as well as TLR3 and TLR7 [45,46] are involved in immune recognition. Infection with Theiler`s murine encephalomyelitis virus requires sensing of both TLR3 and MDA5 [47,48]. Tabeta and colleagues reported that during mouse cytomegalovirus infection deficiency of TLR3 and TLR9 increases the infection due to reduced type I IFN secretion and NK cell activation [49]. This demonstrates that in many viral infections immune responses are initiated by various sensors and distinct PRRs have unique roles during viral defense.

Toll-like receptor 3 recognizes double-stranded RNA during viral infections [15]. Retroviruses consist of two single-stranded RNA strands which are entwined within the core. Together with the viral proteins they build a dimeric RNA complex [50]. These RNA strands form high order secondary structures like stem loops which might be targeted by TLR3 [17,18,51-53]. A recent study could show that TLR3 recognizes stem structures in single-stranded viral RNA [54] which indicates that TLR3 is a potential immune sensor of retroviruses.

In an earlier study we have used a synthetic ligand for TLR3 (polyinosinic:polycytidylic acid, poly I:C) to treat mice during acute FV infection [55]. Stimulation of TLR3 resulted in a significant reduction in viral loads and prevented virus-induced splenomegaly as well as the onset of lethal erythroleukemia. We showed that CD8 + T cell responses and especially their cytotoxicity (CD107a, GzmB expression) were improved by triggering TLR3 [55]. However, TLR3 stimulation alone can still not mediate complete viral clearance in retroviral infections leading to the development of chronic infections.

Others demonstrated that stimulation of macrophages with poly I:C reduces HIV-1 infection in vitro [56-59] which depends on the expression of microRNA-155 [60]. Lentiviral vectors [61] as well as in vitro transcribed HIV-1 gag mRNA [62] were shown to be sensed by TLR3. Another interesting observation reported that a common polymorphism in the human TLR3 mediates protection from HIV-1 by increased activation PBMCs and the production of the proinflammatory cytokines IL-6 and CCL-3 [63]. This indicates that targeting TLR3 during retroviral infections might improve host immune response and thus reduce viral loads which makes TLR3 as a potential target for antiretroviral immunotherapies.


In summary, we used TLR3 −/− mice to investigate the role of TLR3 in antiretroviral immunity utilizing the Friend retrovirus mouse model. Viral loads were significantly increased in these mice revealing that TLR3 participates in anti-FV immunity during acute infection. Specifically the cytotoxicity of NK cells and CD8 + T cells was significantly impaired in TLR3 −/− mice as compared to those of wild type controls. Triggering TLR3 activation might stimulate cytotoxic effector cells to eliminate virus-infected cells and thus be of interest to treat retroviral infections.

Why COVID-19 vaccines might affect fertility

Version en Español

Striking similarity between human syncytins and the sars-cov-2 spike protein: Why covid-19 vaccines might affect fertility

COVID-19 vaccines carry the spike protein (S or “Spike”) of the SARS-CoV-2 virus as an alleged antigen to trigger the immune response, which shares high genetic and protein similarity with two human proteins, Sincitin-1 and Sincitin-2.

Human syncytins are the product of the expression of the genes of the envelope (Env) of human endogenous retroviruses (HERV): they are proteins that mediate fusion between cells and have immunosuppressive properties.

Syncytins are physiologically expressed during pregnancy: they intervene in the development of the placenta, trophoblast differentiation, the implantation of the embryo in the mother’s uterus and the immunosuppression of the mother’s immune system to prevent allogeneic rejection of the embryo.

Because of the similarity between syncytins and the spike protein of SARS-CoV-2, COVID-19 vaccine-induced antibody responses could trigger a cross-reaction against syncytins, causing allergic, cytotoxic and/or autoimmune side effects affecting human health and reproduction.

mRNA vaccines have the potential to modify human DNA by the mechanism of gene silencing mediated by interference RNA. Syncytin gene could be silenced by using antisense oligonucleotide inhibitors. When the mRNA or the amount of syncytin protein decreases, severe defects in the placenta, poor differentiation of the human trophoblast and placental vascular dysfunction occur, leading to loss of gestation.

The companies developing COVID-19 vaccines are not acting ethically and responsibly, because they do not carry out the safety studies in the appropriate animal models, they are not respecting the times required to detect adverse effects in the medium and long term and, in addition, they are not providing the information about the true vaccine composition, which they consider “confidential”.

Volunteers are not being properly informed of all the risks involved in vaccination. By advancing and shortening the experimental phases, companies are shifting the risk from animals to humans, using people as models of animal challenge.

The consequences of inoculating foreign genes with COVID-19 vaccines may be catastrophic for the fate of mankind, considering the role of HERV envelope proteins (syncytins) in human physiology and their possible pathogenic effects on various types of cancers and autoimmune disorders.

The striking similarity between endogenous human retroviral proteins and the SARS-COV-2 spike protein.

Qualified scientific and medical researchers are warning the international community of the danger posed by vaccines against COVID-19 and are calling on the authorities to immediately halt Phase III clinical trials of vaccines containing the spike protein (S or “Spike”) mRNA of the SARS-CoV-2 virus 1, 2 .

One of the reasons for this urgent request is based on the fact that the S-protein, against which vaccine manufacturers are competing to develop a vaccine, shares a high degree of genetic and protein similarity (i.e. it is highly homologous in the sequence of nucleotides and amino acids) to two human proteins encoded by genes located on chromosomes 7 and 6, the so-called Sincitin-1 and Sincitin-2, respectively. (Figure 1)

Figure 1

Sincitin-1 is the protein of the endogenous human retrovirus W (HERV-W) envelope, whose function is necessary during pregnancy to allow the development of the placenta and the differentiation of trophoblast 3, due to it intervenes in the fusion of the placental cells and allows the implantation of the embryo in the maternal uterus 4 .

Sincitin-2 is the envelope protein of another member of the HERV family (HERV-FRD) and is also highly expressed in human placenta 5 . Although both syncytins 1 and 2 are proteins that mediate the cell-cell fusion of cytrotrophs to allow the formation of the multinucleated layer of the syncytiotrophoblast during placental development, Sincitin- 2 (but not Sincitin- 1) has additional properties, an immunosuppressive activity that makes the foetus invisible to the mother’s immune system, thus preventing allogeneic rejection, since the embryo is a unique and unrepeatable human being, genetically different from the mother.

The similarity between the structure of the syncytins and the SARS-Cov-2 S-protein is truly striking. The protein of mature syncytins (envelope protein, Env, of endogenous human retroviruses, HERV) consists of a tritium of heterodimers of two subunits, S1 and S2, linked by a labile disulfide bond between the two chains, which is cleaved by Furine after S1 binding at receptor 7, 8, 9 . (Figure 2)

Figure 2

The structure of the syncytins is the same as that described for the SARS-CoV-2 S protein. The S1 subunit of the spike binds to the receptor and then the separation between the two – the cut made by the enzyme Furine from the S1 and S2 subunits – allows the virus to enter the cells 10 .

Interestingly, the SARS-CoV-2 virus also has sequences identical to the syncytins that give it immunosuppressive activity 11, with which the virus manages to make itself “invisible” to the immune system of the infected person.

Why could COVID-19 vaccines affect human fertility?

Firstly, experimental vaccines against COVID-19 could affect human fertility due to the high similarity between syncytins and the spike protein of SARS-CoV-2 11 .

We do not yet know whether the antibodies generated by the action of the COVID-19 vaccination could cross react with the syncytins. If the antibodies against SARS-COV-2 recognise the human syncytins, these proteins would be blocked and neutralised by the antibodies, thus rendering them incapable of performing their function of fusing fetal cytotrophosphates, which play a key role in both the embryo implantation process and placental development. The result would be a miscarriage of the embryo in the vaccinated women, as the differentiation and nesting process in the mother’s womb is prevented by a direct inhibition of syncytins by antibodies induced by artificial immunisation with any of the experimental COVID-19 vaccines.

In fact, this statement is supported by the observation that the expression of recombinant syncytin in a wide variety of cell types induces the formation of giant syncites and the fusion of a human trophoblastic cell line expressing endogenous syncytin can be inhibited by an anti-synthetic antiserum. A rabbit polyclonal antibody produced against a mixture of Env-W peptics was able to inhibit in vitro cell fusion mediated by human syncytins 12 .

With the same logic, we could expect that antibodies directed against the spike could also cross recognise and neutralise Sincitin 2, and thus its immunosuppressive activity could be affected, leaving the embryo exposed to the recognition of the mother’s immune system, which could lead to maternal immune rejection of the foetus 13 .

It has been shown that the proteins of the HERV envelope (HERV-Env), on the one hand, trigger both innate and adaptive immunity, causing inflammatory, cytotoxic and apoptotic reactions. On the other hand, they have the capacity to prevent the activation of the immune response, presenting immunosuppressive properties and acting as immunoregulators 14 .

When there is such a high similarity to endogenous retroviral peptide motifs, the human immune system can detect it as a distinct antigen and can trigger an allergic response, such as those that occur when haptens (e.g. penicillin) bind to host proteins 11 .

With vaccination against COVID-19, IgE-type antibody responses and delayed-type hypersensitivity by T cells could also be induced, as was observed in mice, which after exposure to a SARS vaccine, caused them to have an allergic response 15, 16 .

Therefore, we already know that due to the similarity of the spike protein of the SARS-CoV-2 virus with the two human proteins, Sincitin 1 and Sincitin 2, it is unlikely that a safe COVID-19 vaccine will be obtained, without observing allergic, cytotoxic and/or autoimmune side effects and without these effects affecting sooner or later the delicate mechanism of human reproduction.

Secondly, experimental vaccines against COVID-19 could affect human fertility because the levels of expression of messenger ribonucleic acid (mRNA) from syncytins increase progressively from the beginning of conception, during the first trimester and until the end of the pregnancy 17 .

Both fusion and differentiation of trophoblast cells are associated with a concomitant increase in mRNA expression of the syncytin gene (HERV-W env) and the protein Sincitin. In simple terms, if the amount of protein or mRNA of the Syncytin gene decreases, defects in placental formation, poor trophoblast differentiation and vascular dysfunction in the placenta are observed.

Protein and transcription levels of the syncytin gene have been shown to be significantly decreased in placentas of women with pregnancy-induced hypertension, including patients with pre-eclampsia and gestational hypertension 18 .

Clinically, diminished expression and abnormal localisation of Sincitin-1 and Sincitin-2 was found in pre-eclampsia, a disorder of pregnancy characterised by defects in placental formation, poor trophoblast differentiation and vascular dysfunction in the placenta. This means that altered expression of the syncytin gene and altered cell location of its protein product may contribute to the aetiology of pre-eclampsia 19 . In other words, reduced placental expression of syncytin may contribute to altered cell fusion processes during placentagenesis and altered placental function in hypertensive disorders of pregnancy 20 .

On the other hand, determination of Syncytin-1 in human sperm and its receptor ASCT-2 in the human oocyte most likely suggests a role of Syncytin-1 in the fusion of sperm and oocyte during fertilization 21 . The receptor ASCT-2, but not Syncytin-1, is expressed in oocytes and the level of mRNA increases with increasing maturity of the oocytes. However, how gamete fusion is carried out by syncytins and their receptors is still unclear.

COVID-19 vaccines: A large-scale human transgenesis experiment

The mRNA vaccines against COVID-19 from the companies Moderna, Pfizer/BioNtech, and CureVac contain spike protein messenger RNA, which are administered coated with polyethylene glycol lipid nanoparticles in order to evade the body’s mechanisms and allow them to enter the cells.

This modified RNA therapy platform is totally new, it is an experimental form of inoculation of foreign genes into the human body that cannot be called “vaccination” since it does not involve administering attenuated or inactivated pathogens as simple antigens that stimulate immunity. It is the inoculation into the human body of injectable synthetic gene variants, so that they can penetrate into human cells and make them produce the spike (S) protein of the virus. This represents a true transgenesis experiment, never before performed in the history of mankind in order to confer immunity against human-transmitted infectious-contagious diseases.

Biotechnology companies are struggling to replicate the fact that mRNA vaccines do not have the ability to enter the nucleus to modify the DNA. They explain that the mRNA in the vaccine will only encode the spike glycoprotein (S) and merely transcribe it into the cell cytoplasm. It is noteworthy that experts and advisors from national and international health organisations are refraining from mentioning the epigenetic regulatory mechanism of mRNA. The ability to directly regulate gene expression is a mechanism widely recognised by molecular biology: gene silencing mediated by ribonucleic acids, the so-called inhibitory RNA (iRNA) 22 .

The Nobel Assembly of the Karolinska Institutet in Stockholm, Sweden, awarded the 2006 Nobel Prize in Physiology or Medicine jointly to researchers Andrew Fire (Stanford University School of Medicine, Stanford, California, USA) and Craig Mello (University of Massachusetts Medical School, Worchester, Massachusetts, USA) for their discovery of RNA interference. These scientists demonstrated gene silencing through the use of double-stranded iRNA 23 .

Through the mechanism of gene silencing mediated by iRNA, mRNA vaccines have the potential capacity to modify human DNA by inducing or silencing different genes in our genome. Interference RNA is a fundamental mechanism for controlling the flow of genetic information in cells.

In the specific case of syncytins, the use of RNA inhibitors (siRNA and shRNA), i.e. the use of antisense oligonucleotides specific to the syncytin gene, has already shown that the gene can be silenced and that inhibition of the expression of the Env-W protein leads to a reduction in fusion and differentiation of the human trophoblast 3 .

Through in vivo experiments on animals, tests were carried out on loss of function in the uterus of sheep by injection of antisense oligonucleotides on day 8 of pregnancy. The injections of these oligonucleotides blocked the production of protein from the ERV gene envelope in the sheep’s trophoectoderm.

Specific gene treatment to silence the expression of the ERV envelope gene in sheep inhibited the differentiation of giant binucleated trophoblast cells and led to the loss of gestation on day 20 in all sheep receiving antisense oligonucleotides 24 .

It should be noted that endogenous retroviruses (ERVs) are abundant in the genomes of vertebrates and play a fundamental role in mammalian reproduction, particularly in placental morphogenesis and implantation, which is why a similar result could be expected from specific gene inhibition of syncytins 1 and 2 in humans and primates 25 andpossibly of the two related env genes, syncytin A and syncytin B, in mice 26 .

Antisense oligonucleotides are designed to modulate the transfer of information from the gene to the protein, interfering with the function of the mRNA or pre-RNA. To achieve effective modulation of gene expression by antisense oligonucleotides, modifications of oligonucleotides that do not promote RNase-H degradation of the target RNA are used. For example, they are designed to specifically inhibit mRNA expression of the HERV envelope gene, so that they inhibit splicing and/or translation of mRNA by a steric blocking mechanism, which is independent of RNase-H. In addition to the effects of these inhibitory oligonucleotides in the short term, long-term gene regulation can be achieved by intracellularly expressed antisense RNA administered by viral vectors 27 .

Knowing the high homology that exists between syncytin and the spike protein of the SARS-CoV-2 virus, and knowing that the oligonucleotide sequences that silence the human syncytin gene have 100% homology with the sequences of the spike gene introduced in the vaccines, no one can guarantee that the mRNA injections contained in the vaccines will not end up affecting the expression of the endogenous human genes Syncytin-1 and Syncytin-2.

These safety aspects and adverse effects of the VID-19 vaccines on human fertility are not being assessed in the pre-clinical animal trials, nor in the phase I, II and III clinical trials already being carried out with volunteers who are not properly informed of all the risks involved in vaccination 28 .

It is important to note that there are authors who point out that syncytin genes are present in humans and Old World primates and differ from Env genes which are present in rodents 17, 25 . In this regard, pre-clinical trials of one of the mRNA candidate vaccines were conducted only in mice and hamsters and were published online at the end of October 2020 without peer review 29 after having started phase I and II clinical trials with volunteers.

Furthermore, the confidentiality clauses that have been granted by governments to the companies developing these vaccines will not allow us to know whether the constructs that make up the vectorised vaccines encode a SARS-CoV-2 spike gene and/or a single- or double-stranded iRNA with resistance to nucleases. Therefore, we also cannot know for sure if the vaccines that introduce modified RNAs have iRNA function and if they can target specific sites along the RNA transcription of a gene, in this case, the human syncytins, because of the high similarity they share in the sequence.

For all these reasons, the result of the inoculation of these experimental vaccines may end up leading to the production of antibodies “with 95% effectiveness” but it cannot be ruled out that, as a side effect, they may block the translation of a messenger RNA encoding a normal human protein. We know in advance that RNase H-resistant antisense oligonucleotides provide complete resistance to nucleases, exhibit good targeting ability, high efficiency in the cell and have sequence specificity 30 .

With the molecular biology tools available today, biotechnology companies can introduce destabilising modifications to mRNAs, can improve the effectiveness of inhibitory RNAs and can thus activate an alternative mechanism through which the sensed strand is removed, giving iRNA powerful silencing activity. If these modified RNAs are administered with the VID-19 vaccines, the world’s population will be subjected to a new and overlooked method of experimental gene therapy on a large scale, aimed at destabilising the expression of human genes by injecting foreign sequences, with possible resistance to nucleases and a proven ability to exert epigenic control.

The companies developing these vaccines are not acting ethically or responsibly, because they are not conducting safety studies in the appropriate animal models, nor are they respecting the timescales needed to observe severe adverse effects in the medium and long term, nor are they providing the necessary information that they consider “confidential”. By avoiding and improvising the pre-clinical testing phases and moving directly to the clinical testing phases I, II and III, companies are shifting the risk from animals to humans, using people as models of animal challenge.

In short, we are forced to denounce that if governments want to implement a massive and obligatory experimental vaccination of the population with vaccines that have not fulfilled the experimental phases and that are approved with “emergency” protocols, they are being complicit in possible crimes against humanity, because these ‘novel’ therapeutic platforms have the most widely accepted mechanisms of inhibitor RNA-induced gene silencing implicitly and invisibly in their designs, the effects of which are well known to the international scientific community and yet are being minimised by pharmaceutical companies, when they should be evaluated before these vaccines are commercially authorised.

The consequences of inoculating these foreign genes into the population with the VID-19 vaccines could be catastrophic for the fate of humanity, if we consider the role of HERV envelope proteins (syncytins) in human physiology and their possible pathogenic effects on several types of cancers and autoimmune disorders such as Multiple Sclerosis 31, 32, Amyotrophic Lateral Sclerosis 33, 34, 35 and Diabetes type 1 36 .

Immune Responses to Retroviruses

Retroviruses are genome invaders that have shared a long history of coevolution with vertebrates and their immune system. Found endogenously in genomes as traces of past invasions, retroviruses are also considerable threats to human health when they exist as exogenous viruses such as HIV. The immune response to retroviruses is engaged by germline-encoded sensors of innate immunity that recognize viral components and damage induced by the infection. This response develops with the induction of antiviral effectors and launching of the clonal adaptive immune response, which can contribute to protective immunity. However, retroviruses efficiently evade the immune response, owing to their rapid evolution. The failure of specialized immune cells to respond, a form of neglect, may also contribute to inadequate antiretroviral immune responses. Here, we discuss the mechanisms by which immune responses to retroviruses are mounted at the molecular, cellular, and organismal levels. We also discuss how intrinsic, innate, and adaptive immunity may cooperate or conflict during the generation of immune responses.


Herniou, E. et al. Retroviral diversity and distribution in vertebrates. J. Virol. 72, 5955–5966 (1998).

Aiewsakun, P. & Katzourakis, A. Endogenous viruses: connecting recent and ancient viral evolution. Virology 479–480, 26–37 (2015).

Xu, X., Zhao, H., Gong, Z. & Han, G.-Z. Endogenous retroviruses of non-avian/mammalian vertebrates illuminate diversity and deep history of retroviruses. PLOS Pathog. 14, e1007072 (2018).

Naville, M. & Volff, J.-N. Endogenous retroviruses in fish genomes: from relics of past infections to evolutionary innovations? Front. Microbiol. 7, 1197 (2016).

Gifford, R. & Tristem, M. The evolution, distribution and diversity of endogenous retroviruses. Virus Genes 26, 291–315 (2003).

Gifford, R. J. Viral evolution in deep time: lentiviruses and mammals. Trends Genet. 28, 89–100 (2012).

Lavialle, C. et al. Paleovirology of ‘syncytins’, retroviral env genes exapted for a role in placentation. Phil. Trans. R. Soc. B Biol. Sci. 368, 20120507 (2013).

Delviks-Frankenberry, K., Cingöz, O., Coffin, J. M. & Pathak, V. K. Recombinant origin, contamination, and de-discovery of XMRV. Curr. Opin. Virol. 2, 499–507 (2012).

Groom, H. C. T. & Bishop, K. N. The tale of xenotropic murine leukemia virus-related virus. J. Gen. Virol. 93, 915–924 (2012).

Suling, K., Quinn, G., Wood, J. & Patience, C. Packaging of human endogenous retrovirus sequences is undetectable in porcine endogenous retrovirus particles produced from human cells. Virology 312, 330–336 (2003).

Young, G. R., Stoye, J. P. & Kassiotis, G. Are human endogenous retroviruses pathogenic? An approach to testing the hypothesis. Bioessays 35, 794–803 (2013).

Babaian, A. & Mager, D. L. Endogenous retroviral promoter exaptation in human cancer. Mob. DNA 7, 24 (2016).

Mager, D. L. & Lorincz, M. C. Epigenetic modifier drugs trigger widespread transcription of endogenous retroviruses. Nat. Genet. 49, 974–975 (2017).

Young, G. R. et al. Resurrection of endogenous retroviruses in antibody-deficient mice. Nature 491, 774–778 (2012).

Stoye, J. P. & Coffin, J. M. The four classes of endogenous murine leukemia virus: structural relationships and potential for recombination. J. Virol. 61, 2659–2669 (1987).

Martinelli, S. C. & Goff, S. P. Rapid reversion of a deletion mutation in Moloney murine leukemia virus by recombination with a closely related endogenous provirus. Virology 174, 135–144 (1990).

Stoye, J. P., Moroni, C. & Coffin, J. M. Virological events leading to spontaneous AKR thymomas. J. Virol. 65, 1273–1285 (1991).

Benachenhou, F. et al. Evolutionary conservation of orthoretroviral long terminal repeats (LTRs) and ab initio detection of single LTRs in genomic data. PLOS ONE 4, e5179 (2009).

Benachenhou, F. et al. Conserved structure and inferred evolutionary history of long terminal repeats (LTRs). Mob. DNA 4, 5 (2013).

Copeland, N. G., Hutchison, K. W. & Jenkins, N. A. Excision of the DBA ecotropic provirus in dilute coat-color revertants of mice occurs by homologous recombination involving the viral LTRs. Cell 33, 379–387 (1983).

Weiss, R. A. The discovery of endogenous retroviruses. Retrovirology 3, 67 (2006).

Bannert, N. & Kurth, R. The evolutionary dynamics of human endogenous retroviral families. Annu. Rev. Genomics Hum. Genet. 7, 149–173 (2006).

Gifford, R., Kabat, P., Martin, J., Lynch, C. & Tristem, M. Evolution and distribution of class II-related endogenous retroviruses. J. Virol. 79, 6478–6486 (2005).

Belshaw, R., Katzourakis, A., Pac˘es, J., Burt, A. & Tristem, M. High copy number in human endogenous retrovirus families is associated with copying mechanisms in addition to reinfection. Mol. Biol. Evol. 22, 814–817 (2005).

Magiorkinis, G., Gifford, R. J., Katzourakis, A., De Ranter, J. & Belshaw, R. Env-less endogenous retroviruses are genomic superspreaders. Proc. Natl Acad. Sci. USA 109, 7385–7390 (2012).

Jern, P., Sperber, G. O. & Blomberg, J. Use of endogenous retroviral sequences (ERVs) and structural markers for retroviral phylogenetic inference and taxonomy. Retrovirology 2, 50 (2005).

Hayward, A., Cornwallis, C. K. & Jern, P. Pan-vertebrate comparative genomics unmasks retrovirus macroevolution. Proc. Natl Acad. Sci. USA 112, 464–469 (2015).

Bénit, L., Dessen, P. & Heidmann, T. Identification, phylogeny, and evolution of retroviral elements based on their envelope genes. J. Virol. 75, 11709–11719 (2001).

King, A. M. Q., Adams, M. J., Carstens, E. B. & Lefkowitz, E. J. (eds) Virus Taxonomy: Classification and Nomenclature of Viruses: The Ninth Report of the International Committee on Taxonomy of Viruses (Elsevier, 2011).

Gifford, R. J. et al. Nomenclature for endogenous retrovirus (ERV) loci. Retrovirology 15, 59 (2018).

Martin, J., Herniou, E., Cook, J., O’Neill, R. W. & Tristem, M. Interclass transmission and phyletic host tracking in murine leukemia virus-related retroviruses. J. Virol. 73, 2442–2449 (1999).

Hayward, A., Grabherr, M. & Jern, P. Broad-scale phylogenomics provides insights into retrovirus-host evolution. Proc. Natl Acad. Sci. USA 110, 20146–20151 (2013).

Henzy, J. E. & Johnson, W. E. Pushing the endogenous envelope. Phil. Trans. R. Soc. B Biol. Sci. 368, 20120506 (2013).

Farkašová, H. et al. Discovery of an endogenous deltaretrovirus in the genome of long-fingered bats (Chiroptera: Miniopteridae). Proc. Natl Acad. Sci. USA 114, 3145–3150 (2017). This paper is the first to identify an ERV related to modern deltaretroviruses, the genus that includes human T-lymphotropic viruses and the bovine leukaemia virus.

Hron, T. et al. Remnants of an ancient deltaretrovirus in the genomes of horseshoe bats (Rhinolophidae). Viruses 10, 185 (2018).

Katzourakis, A., Tristem, M., Pybus, O. G. & Gifford, R. J. Discovery and analysis of the first endogenous lentivirus. Proc. Natl Acad. Sci. USA 104, 6261–6265 (2007).

Gifford, R. J. et al. A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proc. Natl Acad. Sci. USA 105, 20362–20367 (2008).

Gilbert, C., Maxfield, D. G., Goodman, S. M. & Feschotte, C. Parallel germline infiltration of a lentivirus in two Malagasy lemurs. PLOS Genet. 5, e1000425 (2009).

Cui, J. & Holmes, E. C. Endogenous lentiviruses in the ferret genome. J. Virol. 86, 3383–3385 (2012).

Han, G.-Z. & Worobey, M. A primitive endogenous lentivirus in a colugo: insights into the early evolution of lentiviruses. Mol. Biol. Evol. 32, 211–215 (2015).

Hron, T., Fábryová, H., Pačes, J. & Elleder, D. Endogenous lentivirus in Malayan colugo (Galeopterus variegatus), a close relative of primates. Retrovirology 11, 84 (2014).

Hron, T., Farkašová, H., Padhi, A., Pačes, J. & Elleder, D. Life history of the oldest lentivirus: characterization of ELVgv integrations in the dermopteran genome. Mol. Biol. Evol. 33, 2659–2669 (2016).

Marchi, E., Kanapin, A., Byott, M., Magiorkinis, G. & Belshaw, R. Neanderthal and Denisovan retroviruses in modern humans. Curr. Biol. 23, R994–R995 (2013).

Lee, A. et al. Novel Denisovan and Neanderthal retroviruses. J. Virol. 88, 12907–12909 (2014).

Lenz, J. HERV-K HML-2 diversity among humans. Proc. Natl Acad. Sci. USA 113, 4240–4242 (2016).

Holloway, J. R., Williams, Z. H., Freeman, M. M., Bulow, U. & Coffin, J. M. Gorillas have been infected with the HERV-K (HML-2) endogenous retrovirus much more recently than humans and chimpanzees. Proc. Natl Acad. Sci. USA 116, 1337–1346 (2019). This study uncovers multiple young ERVs in gorilla genomes related to human HERV-K(HML2), indicating recent activity in the gorilla lineage and raising the possibility that modern gorillas host an active HML-2 virus.

Goldstone, D. C. et al. Structural and functional analysis of prehistoric lentiviruses uncovers an ancient molecular interface. Cell Host Microbe 8, 248–259 (2010). This paper describes X-ray crystallography of the capsid proteins of two ancient lentiviruses in complex with host factor cyclophilin A. It also uses structures to infer phylogenetic relationships between extinct and extant lentiviruses.

Aiewsakun, P. & Katzourakis, A. Marine origin of retroviruses in the early Palaeozoic Era. Nat. Commun. 8, 13954 (2017). This paper describes the discovery and analysis of foamy-virus-like ERVs in marine vertebrates and suggests retroviruses may have originated early during vertebrate evolution.

Diehl, W. E., Patel, N., Halm, K. & Johnson, W. E. Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals. eLife 5, e12704 (2016). This paper describes the use of ERV loci to retrace the origins and global spread of an ancient gammaretrovirus among mammals between 15 million and 33 million years ago, spanning the late Oligocene and early Miocene epochs.

Katzourakis, A. et al. Discovery of prosimian and afrotherian foamy viruses and potential cross species transmissions amidst stable and ancient mammalian co-evolution. Retrovirology 11, 61 (2014).

Escalera-Zamudio, M. et al. A novel endogenous betaretrovirus in the common vampire bat (Desmodus rotundus) suggests multiple independent infection and cross-species transmission events. J. Virol. 89, 5180–5184 (2015).

Zhuo, X. & Feschotte, C. Cross-species transmission and differential fate of an endogenous retrovirus in three mammal lineages. PLOS Pathog. 11, e1005279 (2015).

Holmes, E. C. The evolution of endogenous viral elements. Cell Host Microbe 10, 368–377 (2011).

Kamath, P. L. et al. The population history of endogenous retroviruses in mule deer (Odocoileus hemionus). J. Hered. 105, 173–187 (2014).

Greenwood, A. D., Ishida, Y., O’Brien, S. P., Roca, A. L. & Eiden, M. V. Transmission, evolution, and endogenization: lessons learned from recent retroviral invasions. Microbiol. Mol. Biol. Rev. 82, e00044–17 (2018).

Lee, A., Nolan, A., Watson, J. & Tristem, M. Identification of an ancient endogenous retrovirus, predating the divergence of the placental mammals. Phil. Trans. R. Soc. B Biol. Sci. 368, 20120503 (2013).

Blanco-Melo, D., Gifford, R. J. & Bieniasz, P. D. Co-option of an endogenous retrovirus envelope for host defense in hominid ancestors. eLife 6, 11 (2017). This study uses ancestral node reconstruction to establish that an intact env gene in the human genome can mediate superinfection interference and may have functioned to restrict entry of an ancient exogenous virus.

Blanco-Melo, D., Gifford, R. J. & Bieniasz, P. D. Reconstruction of a replication-competent ancestral murine endogenous retrovirus-L. Retrovirology 15, 34 (2018). This paper reports on the resurrection and experimental investigation of an ancient, extinct retrovirus using ancestral node reconstruction. This retrovirus is the oldest ERV (ERV-L) successfully reconstructed so far.

Johnson, W. E. & Coffin, J. M. Constructing primate phylogenies from ancient retrovirus sequences. Proc. Natl Acad. Sci. USA 96, 10254–10260 (1999).

Martins, H. & Villesen, P. Improved integration time estimation of endogenous retroviruses with phylogenetic data. PLOS ONE 6, e14745 (2011).

Dangel, A. W., Baker, B. J., Mendoza, A. R. & Yu, C. Y. Complement component C4 gene intron 9 as a phylogenetic marker for primates: long terminal repeats of the endogenous retrovirus ERV-K(C4) are a molecular clock of evolution. Immunogenetics 42, 41–52 (1995).

Magiorkinis, G., Blanco-Melo, D. & Belshaw, R. The decline of human endogenous retroviruses: extinction and survival. Retrovirology 12, 8 (2015).

Wildschutte, J. H. et al. Discovery of unfixed endogenous retrovirus insertions in diverse human populations. Proc. Natl Acad. Sci. USA 113, E2326–E2334 (2016). This study capitalizes on human genomic variation captured in databases, such as the 1000 Genomes Project, to detect and describe rare, unfixed HERV-K(HML-2) loci in the human population.

Subramanian, R. P., Wildschutte, J. H., Russo, C. & Coffin, J. M. Identification, characterization, and comparative genomic distribution of the HERV-K (HML-2) group of human endogenous retroviruses. Retrovirology 8, 90 (2011).

Bhardwaj, N., Montesion, M., Roy, F. & Coffin, J. M. Differential expression of HERV-K (HML-2) proviruses in cells and virions of the teratocarcinoma cell line Tera-1. Viruses 7, 939–968 (2015).

Domansky, A. N. et al. Solitary HERV-K LTRs possess bi-directional promoter activity and contain a negative regulatory element in the U5 region. FEBS Lett. 472, 191–195 (2000).

Boeke, J. D., Garfinkel, D. J., Styles, C. A. & Fink, G. R. Ty elements transpose through an RNA intermediate. Cell 40, 491–500 (1985).

Heidmann, T., Heidmann, O. & Nicolas, J. F. An indicator gene to demonstrate intracellular transposition of defective retroviruses. Proc. Natl Acad. Sci. USA 85, 2219–2223 (1988).

Esnault, C. et al. APOBEC3G cytidine deaminase inhibits retrotransposition of endogenous retroviruses. Nature 433, 430–433 (2005).

Heslin, D. J. et al. A single amino acid substitution in a segment of the CA protein within Gag that has similarity to human immunodeficiency virus type 1 blocks infectivity of a human endogenous retrovirus K provirus in the human genome. J. Virol. 83, 1105–1114 (2009).

Chudak, C. et al. Identification of late assembly domains of the human endogenous retrovirus-K(HML-2). Retrovirology 10, 140 (2013).

Hanke, K. et al. Reconstitution of the ancestral glycoprotein of human endogenous retrovirus k and modulation of its functional activity by truncation of the cytoplasmic domain. J. Virol. 83, 12790–12800 (2009).

Robinson, L. R. & Whelan, S. P. J. Infectious entry pathway mediated by the human endogenous retrovirus K envelope protein. J. Virol. 90, 3640–3649 (2016).

Robinson-McCarthy, L. R. et al. Reconstruction of the cell entry pathway of an extinct virus. PLOS Pathog. 14, e1007123 (2018). This paper and that of Robinson and Whelan (2016) use an infectious rhabdovirus vesicular stomatitis virus (VSV) engineered to express an ancient Env protein in place of the VSVG protein to dissect the entry pathway of an ancient human endogenous retrovirus.

Soll, S. J., Neil, S. J. D. & Bieniasz, P. D. Identification of a receptor for an extinct virus. Proc. Natl Acad. Sci. USA 107, 19496–19501 (2010).

Kaiser, S. M., Malik, H. S. & Emerman, M. Restriction of an extinct retrovirus by the human TRIM5alpha antiviral protein. Science 316, 1756–1758 (2007).

Dewannieux, M. et al. Identification of an infectious progenitor for the multiple-copy HERV-K human endogenous retroelements. Genome Res. 16, 1548–1556 (2006).

Lee, Y. N. & Bieniasz, P. D. Reconstitution of an infectious human endogenous retrovirus. PLOS Pathog. 3, e10 (2007). This paper and that of Dewannieux et al. (2006) describe the first successful reconstructions of functional infectious human endogenous retrovirus particles, in both cases on the basis of the HERV-K(HML2) family of ERV loci.

Lee, Y. N., Malim, M. H. & Bieniasz, P. D. Hypermutation of an ancient human retrovirus by APOBEC3G. J. Virol. 82, 8762–8770 (2008).

Brady, T. et al. Integration target site selection by a resurrected human endogenous retrovirus. Genes Dev. 23, 633–642 (2009). This study describes the first global analysis of integration site preferences for an ancient, reconstituted endogenous retrovirus (HERV–Kcon), enabling direct comparison of integration site preferences to the locations of fixed HERV-K(HML2) loci in the human genome.

Gould, S. J. & Vrba, E. S. Exaptation—a missing term in the science of form. Paleobiology 8, 4–15 (2016).

McClintock, B. Controlling elements and the gene. Cold Spring Harb. Symp. Quant. Biol. 21, 197–216 (1956).

Britten, R. J. & Davidson, E. H. Gene regulation for higher cells: a theory. Science 165, 349–357 (1969).

Nethe, M., Berkhout, B. & van der Kuyl, A. C. Retroviral superinfection resistance. Retrovirology 2, 52 (2005).

Sommerfelt, M. A. & Weiss, R. A. Receptor interference groups of 20 retroviruses plating on human cells. Virology 176, 58–69 (1990).

Malfavon-Borja, R. & Feschotte, C. Fighting fire with fire: endogenous retrovirus envelopes as restriction factors. J. Virol. 89, 4047–4050 (2015).

Bolze, P.-A., Mommert, M. & Mallet, F. Contribution of syncytins and other endogenous retroviral envelopes to human placenta pathologies. Prog. Mol. Biol. Transl Sci. 145, 111–162 (2017).

Dupressoir, A., Lavialle, C. & Heidmann, T. From ancestral infectious retroviruses to bona fide cellular genes: role of the captured syncytins in placentation. Placenta 33, 663–671 (2012).

Cornelis, G. et al. Retroviral envelope gene captures and syncytin exaptation for placentation in marsupials. Proc. Natl Acad. Sci. USA 112, E487–E496 (2015).

Cornelis, G. et al. An endogenous retroviral envelope syncytin and its cognate receptor identified in the viviparous placental Mabuya lizard. Proc. Natl Acad. Sci. USA 114, E10991–E11000 (2017). This paper gives the first description of a syncytin in a nonmammalian species.

Dupressoir, A. et al. A pair of co-opted retroviral envelope syncytin genes is required for formation of the two-layered murine placental syncytiotrophoblast. Proc. Natl Acad. Sci. USA 108, E1164–E1173 (2011).

Johnson, W. E. Rapid adversarial co-evolution of viruses and cellular restriction factors. Curr. Top. Microbiol. Immunol. 371, 123–151 (2013).

Meyerson, N. R. & Sawyer, S. L. Two-stepping through time: mammals and viruses. Trends Microbiol. 19, 286–294 (2011).

Robinson, H. L., Astrin, S. M., Senior, A. M. & Salazar, F. H. Host susceptibility to endogenous viruses: defective, glycoprotein-expressing proviruses interfere with infections. J. Virol. 40, 745–751 (1981).

Ikeda, H. & Odaka, T. A cell membrane ‘gp70’ associated with Fv-4 gene: immunological characterization, and tissue and strain distribution. Virology 133, 65–76 (1984).

Gardner, M. B., Kozak, C. A. & O’Brien, S. J. The Lake Casitas wild mouse: evolving genetic resistance to retroviral disease. Trends Genet. 7, 22–27 (1991).

Kozak, C. A., Gromet, N. J., Ikeda, H. & Buckler, C. E. A unique sequence related to the ecotropic murine leukemia virus is associated with the Fv-4 resistance gene. Proc. Natl Acad. Sci. USA 81, 834–837 (1984).

Inaguma, Y., Yoshida, T. & Ikeda, H. Scheme for the generation of a truncated endogenous murine leukaemia virus, the Fv-4 resistance gene. J. Gen. Virol. 73, 1925–1930 (1992).

Jung, Y. T., Lyu, M. S., Buckler-White, A. & Kozak, C. A. Characterization of a polytropic murine leukemia virus proviral sequence associated with the virus resistance gene Rmcf of DBA/2 mice. J. Virol. 76, 8218–8224 (2002).

Wu, T., Yan, Y. & Kozak, C. A. Rmcf2, a xenotropic provirus in the Asian mouse species Mus castaneus, blocks infection by polytropic mouse gammaretroviruses. J. Virol. 79, 9677–9684 (2005).

Ito, J. et al. Refrex-1, a soluble restriction factor against feline endogenous and exogenous retroviruses. J. Virol. 87, 12029–12040 (2013).

Sugimoto, J., Sugimoto, M., Bernstein, H., Jinno, Y. & Schust, D. A novel human endogenous retroviral protein inhibits cell-cell fusion. Sci. Rep. 3, 1462 (2013).

Villesen, P., Aagaard, L., Wiuf, C. & Pedersen, F. S. Identification of endogenous retroviral reading frames in the human genome. Retrovirology 1, 32 (2004).

de Parseval, N., Lazar, V., Casella, J.-F., Bénit, L. & Heidmann, T. Survey of human genes of retroviral origin: identification and transcriptome of the genes with coding capacity for complete envelope proteins. J. Virol. 77, 10414–10422 (2003).

Young, G. R. et al. HIV-1 infection of primary CD4 + T cells regulates the expression of specific human endogenous retrovirus HERV-K (HML-2) elements. J. Virol. 92, e01507–17 (2018).

Terry, S. N. et al. Expression of HERV-K108 envelope interferes with HIV-1 production. Virology 509, 52–59 (2017).

Henzy, J. E., Gifford, R. J., Kenaley, C. P. & Johnson, W. E. An intact retroviral gene conserved in Spiny-rayed fishes for over 100 My. Mol. Biol. Evol. 34, 634–639 (2017). This paper describes what may be the oldest reported intact retroviral env gene, which inserted between 109 million and 140 million years ago and is shared by thousands of species of modern fish.

Heidmann, O. et al. HEMO, an ancestral endogenous retroviral envelope protein shed in the blood of pregnant women and expressed in pluripotent stem cells and tumors. Proc. Natl Acad. Sci. USA 114, E6642–E6651 (2017). This paper describes the discovery and functional characterization of an unusual ERV-encoded Env expressed as a secreted protein in placental tissues and in the blood of pregnant women.

Barnett, A. L., Davey, R. A. & Cunningham, J. M. Modular organization of the Friend murine leukemia virus envelope protein underlies the mechanism of infection. Proc. Natl Acad. Sci. USA 98, 4113–4118 (2001).

Brody, B. A., Rhee, S. S. & Hunter, E. Postassembly cleavage of a retroviral glycoprotein cytoplasmic domain removes a necessary incorporation signal and activates fusion activity. J. Virol. 68, 4620–4627 (1994).

Rein, A., Mirro, J., Haynes, J. G., Ernst, S. M. & Nagashima, K. Function of the cytoplasmic domain of a retroviral transmembrane protein: p15E-p2E cleavage activates the membrane fusion capability of the murine leukemia virus Env protein. J. Virol. 68, 1773–1781 (1994).

Taylor, G. M., Gao, Y. & Sanders, D. A. Fv-4: identification of the defect in Env and the mechanism of resistance to ecotropic murine leukemia virus. J. Virol. 75, 11244–11248 (2001).

Ito, J., Baba, T., Kawasaki, J. & Nishigaki, K. Ancestral mutations acquired in refrex-1, a restriction factor against feline retroviruses, during its cooption and domestication. J. Virol. 90, 1470–1485 (2015).

Bénit, L., Calteau, A. & Heidmann, T. Characterization of the low-copy HERV-Fc family: evidence for recent integrations in primates of elements with coding envelope genes. Virology 312, 159–168 (2003).

Bonnaud, B. et al. Evidence of selection on the domesticated ERVWE1 env retroviral element involved in placentation. Mol. Biol. Evol. 21, 1895–1901 (2004).

Nakaya, Y. & Miyazawa, T. The roles of syncytin-like proteins in ruminant placentation. Viruses 7, 2928–2942 (2015).

Goff, S. P. in Fields Virology (eds Knipe, D. M. & Howley, P. M.) 6th edn 1424–1473 (Lippincott Williams and Wilkins, 2013).

Marco, A. & Marín, I. CGIN1: a retroviral contribution to mammalian genomes. Mol. Biol. Evol. 26, 2167–2170 (2009).

Best, S., Le Tissier, P., Towers, G. & Stoye, J. P. Positional cloning of the mouse retrovirus restriction gene Fv1. Nature 382, 826–829 (1996).

Pincus, T., Hartley, J. W. & Rowe, W. P. A major genetic locus affecting resistance to infection with murine leukemia viruses. I. Tissue culture studies of naturally occurring viruses. J. Exp. Med. 133, 1219–1233 (1971).

Bénit, L. et al. Cloning of a new murine endogenous retrovirus, MuERV-L, with strong similarity to the human HERV-L element and with a gag coding sequence closely related to the Fv1 restriction gene. J. Virol. 71, 5652–5657 (1997).

Boso, G., Buckler-White, A. & Kozak, C. A. Ancient evolutionary origin and positive selection of the retroviral restriction factor Fv1 in muroid rodents. J. Virol. (2018).

Young, G. R., Yap, M. W., Michaux, J. R., Steppan, S. J. & Stoye, J. P. Evolutionary journey of the retroviral restriction gene Fv1. Proc. Natl Acad. Sci. USA 115, 10130–10135 (2018).

Yap, M. W., Colbeck, E., Ellis, S. A. & Stoye, J. P. Evolution of the retroviral restriction gene Fv1: inhibition of non-MLV retroviruses. PLOS Pathog. 10, e1003968 (2014).

Mortuza, G. B. et al. High-resolution structure of a retroviral capsid hexameric amino-terminal domain. Nature 431, 481–485 (2004).

Mura, M. et al. Late viral interference induced by transdominant Gag of an endogenous retrovirus. Proc. Natl Acad. Sci. USA 101, 11117–11122 (2004).

Arnaud, F., Murcia, P. R. & Palmarini, M. Mechanisms of late restriction induced by an endogenous retrovirus. J. Virol. 81, 11441–11451 (2007).

Monde, K., Contreras-Galindo, R., Kaplan, M. H., Markovitz, D. M. & Ono, A. Human endogenous retrovirus K Gag coassembles with HIV-1 Gag and reduces the release efficiency and infectivity of HIV-1. J. Virol. 86, 11194–11208 (2012).

Campillos, M., Doerks, T., Shah, P. K. & Bork, P. Computational characterization of multiple Gag-like human proteins. Trends Genet. 22, 585–589 (2006).

Pastuzyn, E. D. et al. The neuronal gene Arc encodes a repurposed retrotransposon Gag protein that mediates intercellular RNA transfer. Cell 172, 275–288 (2018).

Ashley, J. et al. Retrovirus-like Gag protein Arc1 binds RNA and traffics across synaptic boutons. Cell 172, 262–274 (2018). This paper and that of Pastuzyn et al. (2018) describe neuronal proteins that are related to retroviral Gag proteins and that form capsid-like structures that package RNA and are released extracellularly.

Bernard, D. et al. Identification and characterization of a novel retroviral-like aspartic protease specifically expressed in human epidermis. J. Invest. Dermatol. 125, 278–287 (2005).

Katzourakis, A., Gifford, R. J., Tristem, M., Gilbert, M. T. P. & Pybus, O. G. Macroevolution of complex retroviruses. Science 325, 1512–1512 (2009).

Frankel, W. N., Rudy, C., Coffin, J. M. & Huber, B. T. Linkage of Mls genes to endogenous mammary tumour viruses of inbred mice. Nature 349, 526–528 (1991).

Ross, S. R. Mouse mammary tumor virus molecular biology and oncogenesis. Viruses 2, 2000–2012 (2010).

Golovkina, T. V., Chervonsky, A., Dudley, J. P. & Ross, S. R. Transgenic mouse mammary tumor virus superantigen expression prevents viral infection. Cell 69, 637–645 (1992).

Mertz, J. A., Simper, M. S., Lozano, M. M., Payne, S. M. & Dudley, J. P. Mouse mammary tumor virus encodes a self-regulatory RNA export protein and is a complex retrovirus. J. Virol. 79, 14737–14747 (2005).

Hofacre, A. & Fan, H. Jaagsiekte sheep retrovirus biology and oncogenesis. Viruses 2, 2618–2648 (2010).

Grow, E. J. et al. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature 522, 221–225 (2015).

Magin, C., Löwer, R. & Löwer, J. cORF and RcRE, the Rev/Rex and RRE/RxRE homologues of the human endogenous retrovirus family HTDV/HERV-K. J. Virol. 73, 9496–9507 (1999).

Yang, J. et al. An ancient family of human endogenous retroviruses encodes a functional homolog of the HIV-1 Rev protein. Proc. Natl Acad. Sci. USA 96, 13404–13408 (1999).

Yang, Z. & Bielawski, J. Statistical methods for detecting molecular adaptation. Trends Ecol. Evol. (Amst.) 15, 496–503 (2000).

Katzourakis, A. & Gifford, R. J. Endogenous viral elements in animal genomes. PLOS Genet. 6, e1001191 (2010).

Aswad, A. & Katzourakis, A. Paleovirology and virally derived immunity. Trends Ecol. Evol. (Amst.) 27, 627–636 (2012).

Kozak, C. A. Origins of the endogenous and infectious laboratory mouse gammaretroviruses. Viruses 7, 1–26 (2014).

Anai, Y. et al. Infectious endogenous retroviruses in cats and emergence of recombinant viruses. J. Virol. 86, 8634–8644 (2012).

Jern, P. & Coffin, J. M. Effects of retroviruses on host genome function. Annu. Rev. Genet. 42, 709–732 (2008).

Cohen, C. J., Lock, W. M. & Mager, D. L. Endogenous retroviral LTRs as promoters for human genes: a critical assessment. Gene 448, 105–114 (2009).

Thompson, P. J., Macfarlan, T. S. & Lorincz, M. C. Long terminal repeats: from parasitic elements to building blocks of the transcriptional regulatory repertoire. Mol. Cell 62, 766–776 (2016).

Fuentes, D. R., Swigut, T. & Wysocka, J. Systematic perturbation of retroviral LTRs reveals widespread long-range effects on human gene regulation. eLife 7, e35989 (2018). This study uses a modified CRISPR system to induce or silence multiple HERV-K(HML2) LTRs in parallel, revealing long-range effects on expression of hundreds of genes.

Santoni, F. A., Guerra, J. & Luban, J. HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. Retrovirology 9, 111 (2012).

Kapusta, A. et al. Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLOS Genet. 9, e1003470 (2013).

Fort, A. et al. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat. Genet. 46, 558–566 (2014).

Chuong, E. B., Elde, N. C. & Feschotte, C. Regulatory activities of transposable elements: from conflicts to benefits. Nat. Rev. Genet. 18, 71–86 (2017).

Lynch, V. J. A copy-and-paste gene regulatory network. Science 351, 1029–1030 (2016).

Khodosevich, K., Lebedev, Y. & Sverdlov, E. Endogenous retroviruses and human evolution. Comp. Funct. Genomics 3, 494–498 (2002).

Chuong, E. B., Elde, N. C. & Feschotte, C. Regulatory evolution of innate immunity through co-option of endogenous retroviruses. Science 351, 1083–1087 (2016).

Wang, T. et al. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc. Natl Acad. Sci. USA 104, 18613–18618 (2007). This paper and that of Chuong et al. (2016) reveal that co-option of ERV LTRs contributed to concerted evolution of interferon-regulated gene networks and many p53 regulated genes, respectively.

Ito, J. et al. Systematic identification and characterization of regulatory elements derived from human endogenous retroviruses. PLOS Genet. 13, e1006883 (2017).

Simonti, C. N., Pavlicev, M. & Capra, J. A. Transposable element exaptation into regulatory regions is rare, influenced by evolutionary age, and subject to pleiotropic constraints. Mol. Biol. Evol. 34, 2856–2869 (2017).

Carroll, S. B. Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell 134, 25–36 (2008).

Monteiro, A. & Podlaha, O. Wings, horns, and butterfly eyespots: how do complex traits evolve? PLOS Biol. 7, e37 (2009).

Lesbats, P., Engelman, A. N. & Cherepanov, P. Retroviral DNA integration. Chem. Rev. 116, 12730–12757 (2016).

Hughes, J. F. & Coffin, J. M. Human endogenous retroviral elements as indicators of ectopic recombination events in the primate genome. Genetics 171, 1183–1194 (2005).

Kijima, T. E. & Innan, H. On the estimation of the insertion time of LTR retrotransposable elements. Mol. Biol. Evol. 27, 896–904 (2010).

Trombetta, B., Fantini, G., D’Atanasio, E., Sellitto, D. & Cruciani, F. Evidence of extensive non-allelic gene conversion among LTR elements in the human genome. Sci. Rep. 6, 28710 (2016).

Schlesinger, S. & Goff, S. P. Retroviral transcriptional regulation and embryonic stem cells: war and peace. Mol. Cell. Biol. 35, 770–777 (2015).

Cullen, B. R., Lomedico, P. T. & Ju, G. Transcriptional interference in avian retroviruses — implications for the promoter insertion model of leukaemogenesis. Nature 307, 241–245 (1984).

Hughes, J. F. & Coffin, J. M. Human endogenous retrovirus K solo-LTR formation and insertional polymorphisms: implications for human and viral evolution. Proc. Natl Acad. Sci. USA 101, 1668–1672 (2004).

Belshaw, R. et al. Rate of recombinational deletion among human endogenous retroviruses. J. Virol. 81, 9437–9442 (2007).

Martin, J., Kabat, P., Herniou, E. & Tristem, M. Characterization and complete nucleotide sequence of an unusual reptilian retrovirus recovered from the order Crocodylia. J. Virol. 76, 4651–4654 (2002).

Henzy, J. E., Gifford, R. J., Johnson, W. E. & Coffin, J. M. A novel recombinant retrovirus in the genomes of modern birds combines features of avian and mammalian retroviruses. J. Virol. 88, 2398–2405 (2014).

de Souza, F. S. J., Franchini, L. F. & Rubinstein, M. Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong? Mol. Biol. Evol. 30, 1239–1251 (2013).

Hobbs, M. et al. Long-read genome sequence assembly provides insight into ongoing retroviral invasion of the koala germline. Sci. Rep. 7, 15838 (2017).

Montesion, M., Bhardwaj, N., Williams, Z. H., Kuperwasser, C. & Coffin, J. M. Mechanisms of HERV-K (HML-2) transcription during human mammary epithelial cell transformation. J. Virol. 92, e01258–17 (2018).

Niu, D. et al. Inactivation of porcine endogenous retrovirus in pigs using CRISPR-Cas9. Science 357, 1303–1307 (2017). This paper describes the parallel inactivation of two dozen related porcine ERV (PERV) loci in a single fetal fibroblast cell using a customized CRISPR–Cas9 protocol followed by nuclear transfer to create a line of pigs free of functional PERV loci.

Ellermann, V. & Bang, O. Experimentelle leukämie bei hühnern [German]. Zentralbl. Bakteriol. Parasitenkd. Infectionskr. Hyg. Abt. Orig. 46, 595–609 (1908).

Rous, P. A sarcoma of the fowl transmissible by an agent separable from the tumor cells. J. Exp. Med. 13, 397–411 (1911).

Dietrich, M. R. in Evolutionary Genetics: Concepts and Case Studies (eds Wolf, J. B. & Fox, C. W.) (Oxford Univ. Press, 2006).

Krupovic, M. et al. Ortervirales: new virus order unifying five families of reverse-transcribing viruses. J. Virol. 92, e00515–18 (2018).


We present here a comparative analysis of HIV-1 and PTLV evolutionary rates and selective constraints. Although both pathogens have many retroviral features in common, their evolutionary dynamics show remarkable differences. Using a scanning approach we have provided systematic evolutionary rates across the HIV-1 and PTLV genome. The range of the evolutionary rate estimates and the variability across the genome are quantitatively similar to previous studies based on single or multiple genes ( Korber et al. 1997 Salemi et al. 2001). It should be noted that the extent of rate variability in sliding window analysis depends on the window size. For example, smaller window sizes might reveal subtler differences in evolutionary rate, but this might also result in a loss of the temporal distinction between the sequences. HIV, with a nucleotide substitution rate ranging from 4.27 × 10 −4 to 2.71 × 10 −3 substitutions/site/year, has one of the fastest evolving genomes ( Wain-Hobson 1993). This lentivirus owes its evolutionary potential to a combination of a high mutation rate ( Mansky and Temin 1995 Gao et al. 2004), a short generation time ( Ho et al. 1995 Wei et al. 1995), and a large number of infected cells ( Buckley et al. 2001). With a range of 2.64 × 10 −7 to 6.64 × 10 −7 substitutions/site/year, PTLV evolutionary rates are several orders of magnitude lower than HIV-1. PTLV is also subjected to stronger purifying selection than HIV. About 10% of the sites in the HIV genome appear to be positively selected, in agreement with the findings of widespread adaptive evolution in the HIV-1 genome ( Yang, Bielawski, and Yang 2003). No class of positively selected sites was inferred for the complete PTLV genome.

The relationship between dN/dS and evolutionary rate we demonstrated is an expected one. However, it forms the basis for further comparative analyses between HIV-1 and PTLV. Extrapolating on this relationship, HIV-1 and PTLV evolutionary rates are about 3 logs different, independent of the dN/dS ratio ( fig. 4). A similar conclusion was obtained by comparing the rates of synonymous substitution. Therefore, different selective constraints do not provide an adequate explanation for the observed differences in evolutionary rate. Instead, the reason should most probably be sought in the underlying process by which genetic variation is generated. Differences in mutation rate between HIV (3.5 × 10 −5 per base per cycle) and HTLV (7 × 10 −6 per base per cycle) are also insufficient to explain the enormous substitution rate difference ( Mansky and Temin 1995 Mansky 2000). It has been argued that the number of successive replication cycles is probably more important than mutation rate in establishing viral genetic variation ( Coffin 1990). However, HTLV maintains high proviral loads while remaining genetically stable ( Wattel et al. 1992 Albrecht et al. 1998 Gabet et al. 2000). This discrepancy has been resolved by the finding of clonal expansion of the infected cells ( Wattel et al. 1995). Cell-associated provirus replication makes use of a DNA polymerase with proofreading capacity and generates only limited genetic variation. It has been suggested through a squirrel monkey model that HTLV-1 infection is characterized by a transient phase of reverse transcription followed by the persistent multiplication of infected cells ( Mortreux et al. 2001). However, the exact contribution of replication through reverse transcription has yet to be elucidated. Recent findings suggest an important role for persistent virion replication in maintaining high proviral loads, and other factors are limiting genetic diversity for HTLV ( Taylor et al. 1999 Wodarz and Bangham 2000 Overbaugh and Bangham 2001). For example, cells that start to express the transactivator protein T ax after infection are likely to be killed by a T ax-specific cytotoxic T lymphocyte (CTL) response before completing the viral replication cycle ( Bangham 2000 Hanon et al. 2000). Such mechanisms are not selective constraints in an evolutionary sense because they act irrespective of the phenotype of newly generated variants (except if this would be specific CTL escape mutant in tax). Therefore, our analysis using dN/dS ratios is not able to distinguish between such constraints and predominant clonal expansion. The difference in natural selection between HIV-1 and PTLV most probably results from a different impact of the host immune system. It is well known that HIV successfully fixes mutations to evade immune responses (generated by neutralizing antibodies, T-helper cells, and CTL). HTLV is able to transform cells and spreads through cell-to-cell contact, suggesting a limited exposure to selection pressure exerted by antibodies ( Bangham 2003). However, HTLV is persistently transcribed, and there is a strong CTL response to HTLV-1 with tax as the dominant target antigen ( Kannagi et al. 1991). Niewiesk et al. (1995) showed that CTL selection favored the emergence of variant T ax sequences. The latter, however, appeared defective in their transactivating activity ( Niewiesk et al. 1995). This suggests that functional constraints, and thus purifying selection, might not allow for significant immune escape. However, immune escape for HTLV infection needs to be further investigated.

We are aware that this analysis compares viral populations with a distinct epidemiological and demographic history. HIV-1 group M originated through a relatively recent cross-species transmission of simian immunodeficiency virus from chimpanzees to humans ( Gao et al. 1999 Korber et al. 2000 Salemi et al. 2001), resulting in an explosive spread in the human population. PTLV viruses have frequently crossed the species barrier between humans and simians ( Vandamme, Salemi, and Desmyter 1998), and the contemporary strains are the result of evolution during a considerably longer time span ( Salemi, Desmyter, and Vandamme 2000 Van Dooren, Salemi, and Vandamme 2001). Due to the genetic stability of HTLV, we have chosen to analyze a comprehensive data set including HTLV-1, HTLV-2, and interspersed simian T-cell lymphotropic virus (STLV) sequences. A calibration date for a node in the phylogeny was provided by anthropological information ( Yanagihara et al. 1995 Salemi, Desmyter, and Vandamme 2000). HIV sequences sampled at different time points usually have a statistical significant accumulation of genetic differences over time, which allows estimating the rate of molecular evolution ( Drummond et al. 2003). The PTLV and HIV-1 date sets inevitably represent very different scales of evolution. While the time to the most recent common ancestor (TMRCA) is around 70 years for HIV-1 group M ( Korber et al. 2000), the TMRCA for the PTLV phylogeny is about 4 orders of magnitude larger (Salemi 2000). Therefore, we also attempted to analyze an HTLV-1 subset excluding all simian strains. However, molecular clock estimates were not powerful enough to correlate with dN/dS estimates (data not shown). Crossing the species barrier might also have had its influence on the evolutionary parameters we have inferred for PTLV. However, in the light of recent findings it seems plausible that effect of different hosts on the evolution of the virus is subtler than the differences we observe between PTLV and HIV-1. Gabet, Gessain, and Wattel (2003) have shown that, as for HTLV-1, STLV-1 combines extremely high proviral loads with inter- and intra-animal genetic stability. Moreover, the same paradoxical combination for this simian oncovirus could also be explained by the demonstration of clonal expansion in vivo ( Gabet, Gessain, and Wattel 2003).

The sliding window approach estimated evolutionary parameters under a single-tree topology. However, frequent recombination might result in different phylogenies along the HIV-1 genome. Moreover, due to overlapping data in the sliding window analyses, the windows cannot be considered as completely independent and we might be too confident in the relation between evolutionary rate and dN/dS. To address this, we also estimated evolutionary rates using a Bayesian coalescent method that allows comparing linked or unlinked evolutionary histories among nonoverlapping partitions of the HIV-1 genome. Although the discrete model of unlinked evolutionary histories will not fully accommodate for recombination, our comparison is at least expected to indicate a possible bias of assuming a single evolutionary history. As in the sliding window analysis, these rates were also significantly correlated with the dN/dS values. Thus for HIV-1, this relationship appears to be robust to some of our statistical model assumptions. Interestingly, the date for the MRCA of HIV-1 group M (1929, CI: 1920–1938) is in perfect agreement with previous estimates ( Korber et al. 2000 Salemi et al. 2001), and, considering the CIs, this estimate is only marginally earlier than the MRCAs for the single loci ( table 2). Previous simulations studies have suggested that assuming a single evolutionary history will result in an overestimation of the time to the MRCA when recombination has significantly shaped the sequence data ( Schierup and Forsberg 2001 Worobey 2001). Our findings, suggest that this effect of recombination can be noticeable when estimating rates and dates for HIV sequences, but it might be less severe than expected. A full discussion of estimates under the unlinked model compared to simulation results is available elsewhere ( Lemey et al. 2004). In conclusion, our scanning approach can reveal the relationship between selective pressure and evolutionary rate, which provides useful information on the evolutionary dynamics of viral populations.

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