COVID-19: Does SARS-CoV-2 Modulate Acanthamoeba Epigenetics to Enhance Survival and Transmission in the Environment?

Abstract

For the first time, we propose the role of epigenetic mechanisms in severe acute respiratory syndrome coronavirus-2 survival inside Acanthamoeba and possible transmission via airborne cysts.

A rapid and persistent transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is puzzling given the global efforts in the application of a plethora of disinfection strategies. These findings suggest that viruses may take refuge inside disinfectant-resistant hosts for their survival and wider transmission. In addition to respiratory droplets, we proposed the role of Acanthamoeba in the transmission of SARS-CoV-2. In particular, amoebae cysts are hardy against physiological, biochemical, and radiological conditions and they can also be airborne. The fact that SARS-CoV-2 has been found in hospitals and cruise ship air-conditioning ducts,¹ a habitat that is more common to free-living amoebae, suggest amoebae interactions with the virus. Furthermore, Acanthamoeba is one of the most ubiquitous protists on this planet and well-known to be a Trojan horse of the microbial world, hosting viruses, bacteria, protozoa, and yeast. How pathogens such as SARS-CoV-2 modulate intracellular pathways to evade killing by host amoebae is not known. Here, for the first time, we discuss possible epigenetic changes employed by SARS-CoV-2 to escape amoebae phagocytic degradation.

Previous studies showed that coronaviruses such as MERS-CoV and SARS-CoV-1 mediate epigenetic alterations by antagonizing host antigen presentation or activating interferon-response genes.² Recently, we reported 19 novel genes that SARS-CoV-2 might be epigenetically modulating in the host cell, including ULBP2, FOXJ1, LRRC56, MME, CBR3, CECR7, DERL3, DSC3, HS3ST2, HSPA1L, KLRG2, NIPAL1, NR4A1, PRADC1, SLC19A2, SYT2, ULBP3, USP53, and VMAC. In particular, the HSPAIL (Hsp70 protein) promoter methylation level was significantly lower, and gene expression was higher in severe COVID-19 patients compared to healthy controls.³ As the HSPA1L expression was found to be highly upregulated in COVID-19 lung autopsies (Figure 1A), the expression of other HSPA family genes was explored. The results revealed that among the HSPA family of genes, HSPA1L was significantly upregulated in COVID-19 lungs, and the log2FC value was far greater than those of all the other heat shock protein (HSP) genes (Figure 1B). The role of Hsp70 is well-documented, and it is known to be essential for viral replication and pre- and postentry events. Hsp70 proteins produced by the host cell in response to stressful conditions can function as intracellular chaperones. Most viruses need these cellular chaperones during infection. Hsp70 has also been reported to play an important role in rabies virus and Zika virus infection processes affecting viral entry, replication, and exit from the host, suggesting the potential use of Hsp70 inhibitors to control viral replication and protein synthesis.^4,5 Taken together, these findings suggest that SARS-CoV-2 infected cells epigenetically upregulate HSPA1L, leading to the overproduction of Hsp70 proteins to facilitate SARS-CoV-2 replication in host cells.

Figure 1.

Mean and relative mRNA expression of HSPA family of genes in COVID-19 patients’ lung autopsies compared to healthy individuals. (A) RNaseq data set GSE150316 obtained from the National Center for Biotechnology Information Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/) was analyzed. This data set contained transcriptomic expression profiles from autopsy samples (Formalin-fixed paraffin-embedded lung tissues) from 5 healthy lungs and 16 lung tissue samples from 5 COVID-19 patients. (B) Mean mRNA expression was calculated and presented as Log2 fold change (Log2FC).

Interestingly, Acanthamoeba exhibits the presence of several heat shock proteins, including Hsp70.⁶ Notably, Hsp70 in human and Acanthamoeba castellanii exhibited high amino acid sequence homology (55.99%) as well as structural similarity (Figure 2). Based on the 3D structural comparison, this value indicates significant similarity between the HSP proteins but does not necessarily reflect an evolutionary relationship. Homologous sequences have similar structures and likely exhibit similar functions. These findings suggest that SARS-CoV-2 may employ demethylation strategies to upregulate Hsp70 in Acanthamoeba to replicate and survive, as in human cells. Most of the available antiviral therapies are targeting viral proteins that are prone to mutations, whereas host targets, such as Hsp70 protein, have a broad spectrum of action and they are refractory to drug-resistant treatment. Hence, knowing that this virus depends on the host epigenetic machinery, the use of preknown epigenetic drugs could be exploited for antiviral therapy and transmission control. Taken together, we postulate that free-living amoebae such as Acanthamoeba can provide an ideal environmental host for the SARS-CoV-2. The airborne transmission of hardy amoebae cysts together with the ability of amoebae to act as a genetic mixer can contribute to viral persistence. Hence, the use of combination disinfection strategies that target both the host as well as the virus would prove effective. Although research is needed to determine the value of combinatorial approaches, we believe that disinfection strategies should not only focus on the terror cell but the host that harbors the terror cells for effective eradication of the SARS-CoV-2.

Figure 2.

Heat shock protein amino acid sequence alignment and sequence identity of human Hsp70 and Acanthamoeba castellanii high molecular weight HSP. (A) Amino acid sequence alignment, (B) 3D structures, and (C) comparison of the amino acid sequences of human HSP70 (Template) and A. castellanii HSP (Target); structural identity is shown in green. (The following databases were utilized to obtain these results: https://www.uniprot.org/; https://amoebadb.org/amoeba/app/; https://swissmodel.expasy.org/).

Author Contributions

R.S. and N.A.K. envisioned the concept amid critical discussions with J.S.M. J.S.M. reviewed the literature and prepared the first draft of the article and the figures under the supervision of N.A.K. All authors contributed to the manuscript and will act as guarantors.

The authors declare no competing financial interest.