28 July 2021 Episode 157 Origin evolution and reservoirs

Ep 157-1: Based on a method, developed in conservation or extinction science, the estimate of the first SARS-CoV-2 case in China is between early October and mid November 2019.  It had spread globally already in January 2019.

But where did it come from?

Ep 157-2: Machado points to the well-known bat CoV RatG13 (full length sequence similarity with SARS-CoV-2 is 96.2 %), which was found in Pu’er (Yunnan province of China) in 2013.  This is in the border area with Vietnam, Laos, Cambodia and Myanmar, 2000 km south-west of Wuhan.  There is serological evidence of SARS-like viruses having infected rural human populations in 2015 in Jinning County, Yunnan province.  The (unproven) suggestion is that people from this area then brought the virus to Wuhan.

These authors apply extensive phylogeny on > 2000 OrthoCoV and conclude:

• Alpha HuCoV-NL-63 originates directly from bats; while HuCoV 229E came also from bats (Chiroptera), but most likely then via camels to humans.
• Beta HuCoV-HKU1 came from rodents and HuCoV-OC43 from bovids.
• Beta HuCoV-MERS came from bats and was transmitted to both dromedary and humans, with frequent interspecies transmission, but also further inter-human transmission (e.g. outbreak in Korea, where no dromedaries were involved).  Unlike SARS (which has disappeared), MERS is still circulating in humans and may persist in camels and related animals.
• Beta HuCoV SARS and SARS-CoV-2 both derive from bats.  There have been suggestions of an intermediate host: civets for SARS, pangolins and other animals (minks, marmots, snakes, squirrels…) for SARS-CoV-2, but these authors  refute all these hypotheses, based on lower sequence similarity and the unlikely contact with humans (pangolins are close to extinction in China).
• The laboratory-based manipulation is also refuted, because SARS-CoV-2 Wuhan-Hu-1 RBD is suboptimal for receptor binding and it could have been improved with minimal modifications if it had been purposefully manipulated.  The alpha to delta variants that have arisen in the meantime have shown that RBD optimization is relatively easy.

Ep 157-3: Jelinek proposes some hypotheses on how SARS-CoV-2 could have been transmitted from bats to human:

• Human activity leading to disturbance of the bat habitat, with detrimental effect on the health of these animal (more susceptibility to viral pathogens and increased viral shedding).
• People eating bats or preparing medicinal products from bat feces

Ep 157-4: a thorough phylogenetic analysis in Nat Microbiol. indicates that:

• SARS-CoV-2 itself is not a recombinant of any sarbecoviruses detected to date, and its receptor-binding motif (RBD, important for  binding to ACE2, appears to be an ancestral trait shared with bat viruses and not one acquired recently via recombination.
• Viruses closely related to SARS-CoV-2 have been circulating in horseshoe bats for many decades.
• The unsampled (hence not characterized) diversity descended from the SARS-CoV-2/RaTG13 common ancestor forms a clade of bat sarbecoviruses with generalist properties—with respect to their ability to infect a range of mammalian cells—that facilitated its jump to humans and may do so again.
• Although the human ACE2-compatible RBD was very likely to have been present in a bat sarbecovirus lineage that ultimately led to SARS-CoV-2, this RBD sequence has hitherto been found in only a few pangolin viruses. (but the authors do not favor the hypothesis that pangolins are an intermediary host)
• Furthermore, the other key feature thought to be instrumental in the ability of SARS-CoV-2 to infect humans—a polybasic cleavage site insertion in the S protein— has not yet been seen in another close bat relative of the SARS-CoV-2 virus.

So, clearly, these authors feel that most probably SARS-CoV-2 derives directly from the bat reservoir and that such a phenomenon may occur again.

Note: the term SARBECOVIRUS is lineage B of the beta-CoV and includes the human, SARS-Cov; SARS-CoV-2 and the 2 related bat viruses (WIV-1 and RaTG13).  See https://en.wikipedia.org/wiki/Betacoronavirus#Sarbecovirus_(lineage_B)  

Ep 157-5: An intriguing paper in Cell suggests that one particular mutation in Spike: replacing threonine (in the bat virus) to alanine (in SARS-CoV-2) at position T372A (in the receptor binding domain) may have increased the affinity to human ACE-2 sufficiently to cross the species barrier. 

What about animal reservoirs?

Clearly, we are discussing here secondary reservoirs: animal species that are infected by humans (= reverse zoonosis), where the SARS-CoV-2 may evolve and be transmitted back to humans (= zoonosis), which could lead to new epidemics, with the potential danger that those variants are less susceptible to infection- or vaccine-induced immunity.

Ep 157-6: Review on susceptibility and transmission capacity of domestic animals.

• Cats, ferrets, minks and hamsters are highly susceptible to SARS-CoV-2; dogs are less susceptible.   Infections in almost 500 mink farms worldwide, of which 290 in Denmark and 69 in the Netherlands.
• Of these hamsters are most suited as experimental models, because they are replicating many aspects of human disease, including very easy airborne transmission.  Ferrets and cats are also possible models.
• Transmission from minks to humans has clearly been demonstrated, but not from cats or dogs.

Ep 157-7: Other susceptible domestic or zoo animal species: non-human primates, rabbits, lions, tigers.  Evidence of human-to-animal (cats-dogs, lions, tigers) or experimental (rabbits, NHP) transmission, but, except for minks, no evidence of animal-to-human transmission.

Ep 157-8:  In depth analysis of 16 mink farms in neighboring villages in the southern Netherlands with evidence of :

• Viral evolution within the minks, who became ill and died
• Back-transmission of mink virus to humans.
• Spread from farm to farm.

Ep 157-9:  Experimental evidence that some peri-domestical animals are susceptible and others not:

• Deer mice, bushy-tailed woodrats, and striped skunks, are susceptible to SARS-CoV-2 and can shed the virus in respiratory secretions.
• Cottontail rabbits, fox squirrels, Wyoming ground squirrels, black-tailed prairie dogs, house mice, and racoons are not susceptible to SARS-CoV-2 infection.

Ep 157-10: Epidemiological evidence?   Capture of small mammals around mink farms with SARS-CoV-2 outbreaks in Utah: all 11 escaped minks were seropositive, 3 of those also-RT-PCR positive.  Apparently no transmission to  wild minks, not to raccoons, skunks, deer mice, squirrels.  Of the house mice, 1 was RT-PCR positive in rectal swab but antibody negative, presumably by ingestion of contaminated material (?)

Experimental studies of rodents suggest that Old World rodents (e.g., Mus) are resistant to SARS-CoV-2 infection and New World species (e.g., Peromyscus) are susceptible (!)

Ep 157-11: Epidemiological evidence? Urban Norvegian rats from the Antwerp sewage system were also negative for antibodies and virus.

Clearly, although some species are experimentally susceptible, no epidemiological evidence, but rather small-scale studies

Perspectives

Ep 157-12:  Amalio Telenti et al provide some important elements:

• SARS-CoV-2 has lower mutation rate than Flu, but accumulates mutations more rapidly.
• Recombination between two different variants or two different coronaviruses in one human host is possible
• Immunosuppressed people, who harbor chronic infections, may favor viral evolution (emergence of new variants).
• Human-animal interface may also generate new important mutations:
  • Y453F mutation occurred during transmission from human to mink and has a higher fitness in humans
  • N501Y mutation in human alpha, beta and gamma VOC makes the virus infectious in old world mice: possible expansion of host range?
• Role of mutations outside spike has received little attention.
• Respiratory infections are difficult to control with vaccines, especially when the reproductive number is high (e.g. measles) or many cases are non-symptomatic (e.g. rubella) → repeated childhood vaccination with high coverage needed
• Correlates of protection is more than neutralizing antibodies alone (e.g. CD4 and CD8 T cells also against non-S proteins) still not really known →  extensive monitoring will be needed.

Research Questions

Epidemiology

• What are the effects of geographic and socioeconomic variations in vaccine coverage and disease on the ability to convert the pandemic to an endemic/epidemic disease?

• What is the contribution of immunosuppressed populations to the rapid evolution of SARS-CoV-2?

Virology

• What are the mechanisms by which viruses adapt to different hosts thereby crossing species barriers?

• Is viral sequence evolution effectively reduced by vaccination?

Immunology

• What are the correlates of protection for vaccines and natural immunity? -

• What is the impact of antigenic drift?

• What are the criteria for renewal or boosting of vaccines?

• What is the role of mucosal immunity in limiting viral shedding and preventing severe disease?

Tools and Technologies needed

Vaccines

• Pansarbecovirus vaccines and monoclonal antibodies that will address both SARS-CoV-2 variants and the future introduction of pandemic coronaviruses into the human population.

Therapeutics

• Next generation therapeutics in the form of cheap oral antiviral agents.

• Long-acting monoclonal antibody prophylaxis for persons not likely to achieve effective vaccination.

• Addressing significant inequalities in pandemic health care and access worldwide to the most effective vaccine and therapeutics.

Sone general conclusions:

• Most evidence points to a direct bat origin of SARS-CoV-2, potentially in the Yunnan province. Pangolin and lab hypotheses not likely.
• Some key characteristics are important: T372A in S; polybasic cleavage site.  Contribution of areas outside S understudied.
• The potential of new bat viruses to infect humans is very real.

• Various domestic and peri-domestic animals are susceptible to SARS-CoV-2,
  • Reverse zoonosis to domestic cat, tigers, lions), dogs and minks shown.
  • Back-zoonosis until now only observed from minks
  • Until now no evidence of a peri-domestic reservoir (but limited studies done)
  • Viral evolution could result in additional susceptibility (e.g. N501Y and mice)
  • Most suitable animal models: Syrian hamsters, non-human primates and human ACE-2 transgenic mice.

Hope you enjoyed….

Best wishes,

Guido