Modifiable contributing factors to COVID-19: A comprehensive review

The devastating complications of coronavirus disease 2019 (COVID-19) result from an individual's dysfunctional immune response following the initial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Multiple toxic stressors and behaviors contribute to underlying immune system dysfunction. SARS-CoV-2 exploits the dysfunctional immune system to trigger a chain of events ultimately leading to COVID-19. The current study identifies eighty immune system dysfunction-enabling toxic stressors and behaviors (hereafter called modifiable contributing factors (CFs)) that also link directly to COVID-19. Each CF is assigned to one of the five categories in the CF taxonomy shown in Section 3.3.: Lifestyle (e.g., diet, substance abuse); Iatrogenic (e.g., drugs, surgery); Biotoxins (e.g., micro-organisms, mycotoxins); Occupational/Environmental (e.g., heavy metals, pesticides); Psychosocial/Socioeconomic (e.g., chronic stress, lower education). The current study shows how each modifiable factor contributes to decreased immune system capability, increased inflammation and coagulation, and increased neural damage and neurodegeneration. It is unclear how real progress can be made in combatting COVID-19 and other similar diseases caused by viral variants without addressing and eliminating these modifiable CFs.

Contributing factors common to COVID‑19 and gastrointestinal cancer

The devastating complications of coronavirus disease 2019 (COVID-19) result from the dysfunctional immune response of an individual following the initial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Multiple toxic stressors and behaviors contribute to underlying immune system dysfunction. SARS-CoV-2 exploits the dysfunctional immune system to trigger a chain of events, ultimately leading to COVID-19. The authors have previously identified a number of contributing factors (CFs) common to myriad chronic diseases. Based on these observations, it was hypothesized that there may be a significant overlap between CFs associated with COVID-19 and gastrointestinal cancer (GIC). Thus, in the present study, a streamlined dot-product approach was used initially to identify potential CFs that affect COVID-19 and GIC directly (i.e., the simultaneous occurrence of CFs and disease in the same article). The nascent character of the COVID-19 core literature (~1-year-old) did not allow sufficient time for the direct effects of numerous CFs on COVID-19 to emerge from laboratory experiments and epidemiological studies. Therefore, a literature-related discovery approach was used to augment the COVID-19 core literature-based ‘direct impact’ CFs with discovery-based ‘indirect impact’ CFs [CFs were identified in the non-COVID-19 biomedical literature that had the same biomarker impact pattern (e.g., hyperinflammation, hypercoagulation, hypoxia, etc.) as was shown in the COVID-19 literature]. Approximately 2,250 candidate direct impact CFs in common between GIC and COVID-19 were identified, albeit some being variants of the same concept. As commonality proof of concept, 75 potential CFs that appeared promising were selected, and 63 overlapping COVID-19/GIC potential/candidate CFs were validated with biological plausibility. In total, 42 of the 63 were overlapping direct impact COVID-19/GIC CFs, and the remaining 21 were candidate GIC CFs that overlapped with indirect impact COVID-19 CFs. On the whole, the present study demonstrates that COVID-19 and GIC share a number of common risk/CFs, including behaviors and toxic exposures, that impair immune function. A key component of immune system health is the removal of those factors that contribute to immune system dysfunction in the first place. This requires a paradigm shift from traditional Western medicine, which often focuses on treatment, rather than prevention.

Common contributing factors to COVID-19 and inflammatory bowel disease

The devastating complications of coronavirus disease 2019 (COVID-19) result from an individual's dysfunctional immune response following the initial severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Multiple toxic stressors and behaviors contribute to underlying immune system dysfunction. SARS-CoV-2 exploits the dysfunctional immune system to trigger a chain of events ultimately leading to COVID-19. We have previously identified many contributing factors (CFs) (representing toxic exposure, lifestyle factors and psychosocial stressors) common to myriad chronic diseases. We hypothesized significant overlap between CFs associated with COVID-19 and inflammatory bowel disease (IBD), because of the strong role immune dysfunction plays in each disease. A streamlined dot-product approach was used to identify potential CFs to COVID-19 and IBD. Of the fifty CFs to COVID-19 that were validated for demonstration purposes, approximately half had direct impact on COVID-19 (the CF and COVID-19 were mentioned in the same record; i.e., CF---→COVID-19), and the other half had indirect impact. The nascent character of the COVID-19 core literature (∼ one year old) did not allow sufficient time for the direct impacts of many CFs on COVID-19 to be identified. Therefore, an immune system dysfunction (ID) literature directly related to the COVID-19 core literature was used to augment the COVID-19 core literature and provide the remaining CFs that impacted COVID-19 indirectly (i.e., CF---→immune system dysfunction---→COVID-19). Approximately 13000 potential CFs for myriad diseases (obtained from government and university toxic substance lists) served as the starting point for the dot-product identification process. These phrases were intersected (dot-product) with phrases extracted from a PubMed-derived IBD core literature, a nascent COVID-19 core literature, and the COVID-19-related immune system dysfunction (ID) core literature to identify common ID/COVID-19 and IBD CFs. Approximately 3000 potential CFs common to both ID and IBD, almost 2300 potential CFs common to ID and COVID-19, and over 1900 potential CFs common to IBD and COVID-19 were identified. As proof of concept, we validated fifty of these ∼3000 overlapping ID/IBD candidate CFs with biologic plausibility. We further validated 24 of the fifty as common CFs in the IBD and nascent COVID-19 core literatures. This significant finding demonstrated that the CFs indirectly related to COVID-19 -- identified with use of the immune system dysfunction literature -- are strong candidates to emerge eventually as CFs directly related to COVID-19. As discussed in the main text, many more CFs common to all these core literatures could be identified and validated. ID and IBD share many common risk/contributing factors, including behaviors and toxic exposures that impair immune function. A key component to immune system health is removal of those factors that contribute to immune system dysfunction in the first place. This requires a paradigm shift from traditional Western medicine, which often focuses on treatment, rather than prevention.

Treatment repurposing for inflammatory bowel disease using literature-related discovery and innovation

Inflammatory bowel disease (IBD) incidence has been increasing steadily, most dramatically in the Western developed countries. Treatment often includes lifelong immunosuppressive therapy and surgery. There is a critical need to reduce the burden of IBD and to discover medical therapies with better efficacy and fewer potential side-effects. Repurposing of treatments originally studied in other diseases with similar pathogenesis is less costly and time intensive than de novo drug discovery. This study used a treatment repurposing methodology, the literature-related discovery and innovation (LRDI) text mining system, to identify potential treatments (developed for non-IBD diseases) with sufficient promise for extrapolation to treatment of IBD. By searching for desirable patterns of twenty key biomarkers relevant to IBD (e.g., inflammation, reactive oxygen species, autophagy, barrier function), the LRDI-based query retrieved approximately 9500 records from Medline. The most recent 350 records were further analyzed for proof-of-concept. Approximately 18% (64/350) met the criteria for discovery (not previously studied in IBD human or animal models) and relevance for application to IBD treatment. Many of the treatments were compounds derived from herbal remedies, and the majority of treatments were being studied in cancer, diabetes, and central nervous system disease, such as depression and dementia. As further validation of the search strategy, the query identified ten treatments that have just recently begun testing in IBD models in the last three years. Literature-related discovery and innovation text mining contains a unique search strategy with tremendous potential to identify treatments for repurposing. A more comprehensive query with additional key biomarkers would have retrieved many thousands more records, further increasing the yield of IBD treatment repurposing discovery.

Occlusive fungal tracheitis in 4 captive bottlenose dolphins (Tursiops truncatus)

Respiratory disease is common in dolphins, primarily affecting pulmonary parenchyma and sparing large airways. Over a 10-year period, 4 captive adult bottlenose dolphins succumbed to chronic, progressive respiratory disease with atypical recurrent upper respiratory signs. All dolphins had severe, segmental to circumferential fibrosing tracheitis that decreased luminal diameter. Histologically, tracheal cartilage, submucosa, and mucosa were distorted and replaced by extensive fibrosis and pyogranulomatous inflammation centered on fungal hyphae. In 3 of 4 cases, hyphae were morphologically compatible with Aspergillus spp and confirmed by culture in 2 cases. Amplification of fungal DNA from tracheal tissue was successful in one case, and sequences had approximately 98% homology to Aspergillus fumigatus. The remaining case had fungi compatible with zygomycetes; however, culture and polymerase chain reaction were unsuccessful. Lesions were evaluated immunohistochemically using antibodies specific to Aspergillus spp. Aspergillus-like hyphae labeled positively, while presumed zygomycetes did not. These cases represent a novel manifestation of respiratory mycoses in bottlenose dolphins.

Multi-host pathogens and carnivore management in southern Africa

A retrospective serosurvey of multi-host feline and canine viruses among carnivore species in southern Africa (n = 1018) identified widespread pathogen exposure even in remote protected areas. In contrast to mortality experienced in East African predators, canine distemper virus (CDV) infection among African wild dogs (Lycaon pictus) in Botswana was not associated with identifiable change in pup survivorship or disease related mortality of adults. A disease outbreak of unknown aetiology occurred in the same population over 4 weeks in 1996. Outbreak boundaries coincided with ecotones, not the spatial distribution of contiguous packs, highlighting the potential importance of landscape heterogeneities in these processes. Direct management of pathogens in domestic animal reservoirs is complicated by the apparent complexity of pathogen maintenance and transmission in these large systems. Conservation effort should be focused at securing large metapopulations able to compensate for expected episodic generalist pathogen invasion and attention directed to addressing underlying causes of population depression such as habitat loss and wildlife conflict.

Disseminated blastomycosis in two California sea lions (Zalophus californianus)

Two captive California sea lions (Zalophus californianus) from different facilities were diagnosed with disseminated blastomycosis. The first, a 12-yr-old male, died after a 3-wk history of progressive anorexia and lethargy. Gross examination revealed acute jejunitis with focal perforation and associated peritonitis, along with severe purulent bronchopneumonia. The second, a 15-yr-old female, was euthanized after a 2-wk history of severe cutaneous ulceration and declining clinical condition. Gross examination revealed severe pyogranulomatous bronchopneumonia and ulcerative dermatitis. Histopathologic examination in both individuals revealed severe multifocal subacute to chronic pyogranulomatous pneumonia associated with massive numbers of fungal organisms morphologically compatible with Blastomyces sp. Fungal organisms were 8-20-microm-diameter broad-based budding yeasts with thick, refractile, double-contoured walls. The male sea lion had multifocal transmural Blastomyces-induced enteritis with subsequent rupture and peritonitis. The organism was also present in the liver, with minimal associated inflammation. The female had severe multifocal pyogranulomatous ulcerative dermatitis associated with large numbers of intralesional fungal organisms. Dissemination to the spleen had occurred in both animals. A serologic immunodiffusion test for Blastomyces dermatitidis was positive in the male. The presumptive primary pathogen in both cases was Blastomyces dermatitidis.

Gastric spiral bacteria and intramuscular sarcocysts in African lions from Namibia

Six juvenile male, one adult male, and three adult, female African lions (Panthera leo) from Etosha National Park, Republic of Namibia were presented for necropsy. Two of four adults and one of six juveniles had moderate numbers of gastric spiral bacteria. Additionally, four of four adults had sarcocysts. All juveniles had enteric Sarcocystis sp. oocysts, but no sarcocysts. The gastric spiral bacteria were located extracellularly in fundic and pyloric glands, and also apparently intracellularly within parietal cells in the fundic region. The organisms were 4 to 8 microns long, 0.63 micron wide, with a periodicity of 0.60 micron. The bacteria had blunted ends with multiple flagella. No periplasmic fibrils were observed. The histologic and ultrastructural characteristics of the bacteria were considered most consistent with species in the genus Helicobacter or incompletely identified Helicobacter-like organisms. Gastric inflammation did not differ significantly between infected and uninfected individuals. The bacteria may be commensals, or an opportunistic pathogen. The sarcocysts were observed in hindlimb skeletal muscle of four individuals, with one individual also containing a single sarcocyst within glossal musculature. All observed cysts were mature, and were contained within individual myocytes. The cyst wall consisted of a 44 to 66 nm, granular, electron dense parasitophorous membrane with subjacent, 0.8 to 1.3 microns thick, granular and fibrillar ground substance which also extended into the cyst interior as thin septa. The membrane was folded and lined irregularly spaced, 0.8 to 1.3 microns tall villi centrally containing ground substance. The membrane was continuous in the villar projections, but divided into discrete aggregations of the electron dense material between the villi. Bradyzoites within the interior of the cyst were 3 by 12 microns. The sarcocysts were determined to be Sarcocystis felis based on the characteristic ultrastructural appearance of the cyst wall.