On The Origin Of The Home Of COVID-19 - 16

"V" for Prophages

I. Retro

I have pointed out in previous posts of this series, in various ways, that meat, eggs, and offal transport microbes and viruses (On The Origin Of The Home Of COVID-19, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15).

It has been known in the realms of microbiology and virology for some time that hundreds of species of bacteria inhabit the stomach (rumen) of animals that become food on our tables at meal time, or in Big Macs and Whoppers.

Not to mention the food on our plates at restaurants.

This has caused serious concern to some international entities:

[in the rumen]"Bacteria... (> 200 species) ..." (p. 11)
...
"Both human health and disease are often linked to ruminant animals: health through the nutritive value of meat and dairy products, and disease predominantly through the direct spread of zoonotic organisms or the contamination of food and the environment with manure. Worldwide the meat industry has found itself in the midst of controversy over a number of large-scale food-borne contamination incidents. These include bovine spongiform encephalopathy (BSE), E. coli O157:H7 infection, Salmonella typhimurium DT 104 with multiple antibiotic resistance, and chemical residues, which have led to the perception that meat, is not always a 'safe' product."
...
"The animal industry not only produces meat but is also the source of manure and waste effluent which are used as fertiliser. Manure and effluent are potential sources of contamination by enteric pathogens to crops (both for animal and human consumption) and waterways (Wallace, 1999; McQuigge et al., 2000). The upsurge in organic farming with increased use of manure could be a source of increased contamination if manure is not properly stored or composted (Himathongkham et al., 1999; Guan and Holley, 2003; Duffy, 2003). It is paradoxical that incidences of food-borne disease are increasing in industrialised countries. The factors involved in this increasing incidence are complex: production and distribution systems for food have changed as well as eating and cooking habits, and there is increased movement of people globally (Altekruse and Swerdlow, 1996; Lederberg, 1997)."
...
"Current intensive animal husbandry practises promote pathogens in the animal populations through contaminated feed (often by rodents or birds), and environmental (soil and water) contamination (Johnston, 1990; McEwan and Fedorka-Cray, 2002). Potential pathways for the spread of these organisms from animals to humans are shown in Figure 2. There is also concern that intensive animal production systems may be contributing to the evolution of antibiotic resistance in human infections through the transmission of resistant gut bacteria and associated genetic elements from animals to humans (Khachatourians, 1998; McEwan and Fedorka-Cray, 2002)." (p. 20)
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"Rumen Bacteriophage diversity: Bacteriophages are abundant (10⁷ – 10⁹ particles per ml) in the rumen ecosystem but the diversity of these viruses is poorly understood as well as their interactions with the other microorganisms in this ecosystem. They appear to influence other microbial population structure and density through bacterial lysis in the rumen as well as being intimately involved in the exchange of genetic information with other microbial populations (Klieve et al., 1991; Klieve and Swain, 1993; Swain et al., 1996; Klieve and Hegarty, 1999). The first comprehensive metagenomic analysis of the bovine rumen virome was reported recently in which 28,000 different viral genotypes were identified (Berg Miller et al., 2012)."
...
"The genotypes belonged to the following Families in descending order of prevalence; Siphoviridae, Myoviridae, Podoviridae, Unclassified, Herpesviridae, Phycodnaviridae, Mimiviridae, Poxviridae, Baculoviridae, Iridoviridae, Polydnaviridae, Adenoviridae, Bicaudaviridae. Prophages dominated lytic phages by 2:1." [Bacteria and archaea serve as natural hosts to these families - in other words bacteria are he natural homes of viruses]
...
"The sequence analysis indicated that the phages [viruses] were associated with the main bacterial phyla including Firmicutes, Proteobacteria and Bacteroidetes thus suggesting a role in shaping these bacterial communities. Rumen phage also influence the efficiency of digestion in the rumen through the spontaneous lysis of bacterial populations by lytic phage which will also influence protein supply to the animal from microbial protein synthesized in the rumen (Swain et al., 1996)." (pp. 27-28)

(COMMISSION ON GENETIC RESOURCES FOR FOOD AND AGRICULTURE MICRO-ORGANISMS AND RUMINANT DIGESTION: STATE OF KNOWLEDGE, TRENDS AND FUTURE PROSPECTS, emphasis added). It is disconcerting that "Unclassified" is the forth most prevalent inhabitant of the rumen of animals that become food in countries around the world.

II. Coronavirus In Food Animals

It has also been know for some time that the coronavirus is rampant in food animals:

"Bovine respiratory disease (BRD) has a major impact on the cattle industry, with economic losses occurring due to morbidity, mortality, treatment and prevention costs, loss of production, and reduced carcass value (1). Infectious agents associated with BRD include viruses [bovine herpesvirus-1 (BHV-1), bovine parainfluenza-3 (PI-3V), bovine viral diarrhea virus (BVDV) 1 and 2, bovine respiratory syncytial virus (BRSV), bovine adenoviruses (BAdV), bovine coronavirus (BCV)], and bacteria (Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma spp.) (1,2). From the virus standpoint, BCV has received recent attention as BRD continues to be a problem in the industry, despite the presence and widespread use of modified live virus (MLV) and killed BHV-1, BVDV, PI-3V, and BRSV products.
...
"Clinicians and diagnosticians are often called upon to examine for agents other than the 4 viruses listed, bacteria, and Mycoplasma spp. Bovine coronavirus (BCV) has been identified in cattle pulled and treated for BRD and/or in healthy cattle in numerous studies in the United States and Canada and in European countries using viral isolations from nasal swabs and serology-detecting seroconversions indicating active infections (3,4,5−12). These cited studies have focused on virus isolations from the nasal cavity for the materials for virus isolation. Bovine coronavirus has also been identified in pneumonic lungs, often in combination with other viruses, bacteria, and/or Mycoplasma spp. (2,13,14). Experimental studies have identified BCV-infected cattle with epithelial lesions in the turbinates, trachea, and lungs as well as with interstitial pneumonia (15)."
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"Previous studies have demonstrated that the presence or absence of various levels of BCV antibodies can be used to predict whether a calf would be treated in the feedlot (9,10). Several studies have indicated that cattle may be shedding BCV in the nasal secretions on arrival at the feedlot (d 0) or perhaps before delivery to the feedlot (6,12). It is therefore important to examine practices in the beef-breeding herd and the immune status of the calves for BCV before their entry into the auction-market system where they might be exposed to cattle that are shedding BCV. The objectives of the present study were to: 1) compare BCV antibody levels in beef calves from different herds in samples collected post-weaning and before commingling with other herds; 2) correlate serum BCV antibodies in fresh calves (ranch-reared, non-commingled) collected before delivery to commercial feedlot with treatment for BRD after arrival at the feedlot; and 3) use virus isolation from nasal swabs and from lungs and serology to determine the dynamics of BCV infection in commingled, mixed-source calves transported to a research feedlot." (The Canadian Journal of Veterinary Research, p. 191)
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"Of the 22 calves used as sentinel calves in OSU-1, 9 out of 22 (40.9%) were BCV virus positive in both the nasal swabs and the BAL samples on the day of processing, day 0 (Table I). Calves shedding the virus on day 0 cleared the virus by day 8 as nasal swab and BAL samples were all negative at collection day 8. Convalescent serum was not collected from 2 of the calves as 1 calf died with BRD (#562) and another calf (#544) was removed from the study due to lameness. Fifteen of the remaining 20 sentinel calves (75%) seroconverted. Calves that were shedding BCV at day 0 had BCV antibody levels of 8, 4, or , 4 on day 0, whereas calves with BCV antibody titers of 32 or higher at d 0 did not shed virus during the study, although they often seroconverted. Six sentinel animals remained healthy and seroconverted to BCV."
...
"The current study also identified and confirmed that calves com- mingled from mixed sources, from auction-market sources, and from wide geographic regions across the midwestern and south-central US states probably have BCV-active infections upon delivery to the feedlot and are shedding the virus. Similar to those in other studies, the calves in this study cleared the infections by day 8 after arrival. Also similar to other studies, the virus was found in the nasal swabs. In this study, BCV was also recovered in lung samples [bronchoalveolar lavage (BAL)], which were collected along with the nasal swabs. While BCV is not unlike other viruses that are shed in the nasal swabs during active infections, the finding of the BCV in the lung-derived samples suggests that BVC probably plays a role in lung lesions such as pneumonias."
...
"Bovine coronavirus (BCV) appears to be an early type of infection among the commingled calves. Calves in 2 different groups in this study identified BCV infections (nasal swab and BAL virus isolations) from sick calves in the first 4 d after arrival, but not from calves from 5 to 14 d after arrival. Another aspect of this study was that BCV was recovered from some healthy calves as well. In addition, active infections for BCV appear quite common as noted by the large number of seroconversions in both sick and healthy animals. It is common to find seroconversions to several bovine viruses among cattle under feedlot conditions as noted for BVDV, PI-3V, and BRSV (20,21)." (p. 197)

(Bovine coronavirus (BCV) infections in transported commingledbeef cattle and sole-source ranch calves, The Canadian Journal of Veterinary Research, 2011; 75:191–199, emphasis added).

III. All In The Family

The coronavirus "family" is noted in the genomic data of SARS-CoV-2 (SARS coronavirus 2) as has been shown in previous posts in this series.

In other words, the genetic data indicates that the SARS-CoV-2 coronavirus can be found in humans, poulty, swine, and cattle.

It is not at all unusual to find a caronavirus in humans, poulty, swine, and cattle:

"Coronaviruses (CoVs) cause respiratory and gastrointestinal disease in humans, poultry, swine, and cattle."

(Emerging Infectious Diseases • www.cdc.gov/eid • Vol. 26, No. 2, February 2020, p. 255). That is keeping it in the family:

"Coronavirus is the common name for Coronaviridae and Orthocoronavirinae, also called Coronavirinae. Coronaviruses cause diseases in mammals and birds. In humans, the viruses cause respiratory infections, including the common cold, which are typically mild, though rarer forms such as SARS (including the one causing COVID-19) and MERS can be lethal. Symptoms vary in other species: in chickens, they cause an upper respiratory disease, while in cows and pigs coronaviruses cause diarrhea. There are no vaccines or antiviral drugs to prevent or treat human coronavirus infections. They are enveloped viruses with a positive-sense single-stranded RNA genome and a nucleocapsid of helical symmetry. The genome size of coronaviruses ranges from approximately 26 to 32 kilobases, among the largest for an RNA virus (second only to a 41-kb nidovirus recently discovered in planaria)."

(Wikipedia, emphasis added). The coronavirus lineage evinces  a lot of changes because of the way they are "made" (the destruction of their natural place inside bacteria when antibiotics and other toxins destroy their "home").

IV. Closing Comments

Look through the following appendices (to previous posts in this series) and you will see lists of the lineage of SARS-CoV-2 in animals and humans going back to Coronaviridae (Appendix MT276327 A, Appendix MN997409 C, Appendix AN-1-99).

Remember to be careful when a friend or colleague tells you, as you are driving down a road after a hurricane, "that sign we just passed that said 'bridge out ahead' is not proof that the bridge ahead is really out".

There are different kinds of proof (I like to tell some of my lawyer friends that "proof" is something the jury provides ... all we can provide is "evidence").

The next post in this series is here, the previous post in this series is here.