LEGEND
SARS-CoV-2 =
COVID-19 outbreak
In view of following revelations:-
Most NYC Covid-19 Cases Came From Europe, Genome Researchers Say
Read more:
https://www.bloomberg.com/news/arti...cases-came-from-europe-genome-researchers-say
The hunt for patient zero: Where did the coronavirus outbreak start?
Read more:
https://www.newscientist.com/articl...the-coronavirus-outbreak-start/#ixzz6J7vZ8Df9
- I decided to review ongoing scientific work, and I have some observations to share.
Scientific research have narrowed down to
horseshoe bats as being chief carriers and transmitters of coronaviruses worldwide, and coronaviruses have
recombinogenic properties which are not apparent in other types of viruses:
Evolutionary origins of the SARS‐CoV‐2 sarbecovirus lineage responsible for the COVID-19 pandemic
Abstract
There are outstanding evolutionary questions on the recent emergence of coronavirus SARS-CoV-2/hCoV-19 in Hubei province that caused the COVID-19 pandemic, including (1) the relationship of the new virus to the SARS-related coronaviruses, (2) the role of bats as a reservoir species, (3) the potential role of other mammals in the emergence event, and (4) the role of recombination in viral emergence. Here, we address these questions and find that the sarbecoviruses – the viral subgenus responsible for the emergence of SARS-CoV and SARS-CoV-2 – exhibit frequent recombination, but the SARS-CoV-2 lineage itself is not a recombinant of any viruses detected to date. In order to employ phylogenetic methods to date the divergence events between SARS-CoV-2 and the bat sarbecovirus reservoir, recombinant regions of a 68-genome sarbecovirus alignment were removed with three independent methods. Bayesian evolutionary rate and divergence date estimates were consistent for all three recombination-free alignments and robust to two different prior specifications based on HCoV-OC43 and MERS-CoV evolutionary rates. Divergence dates between SARS-CoV-2 and the bat sarbecovirus reservoir were estimated as 1948 (95% HPD: 1879-1999), 1969 (95% HPD: 1930-2000), and 1982 (95% HPD: 1948-2009). Despite intensified characterization of sarbecoviruses since SARS, the lineage giving rise to SARS-CoV-2 has been circulating unnoticed for decades in bats and been transmitted to other hosts such as pangolins.
The occurrence of a third significant coronavirus emergence in 17 years together with the high prevalence and virus diversity in bats implies that these viruses are likely to cross species boundaries again.
In Brief
The Betacoronavirus SARS-CoV-2 is a member of the sarbecovirus subgenus which shows frequent recombination in its evolutionary history. We characterize the extent of this genetic exchange and identify non-recombining regions of the sarbecovirus genome using three independent methods to remove the effects of recombination. Using these non-recombining genome regions and prior information on coronavirus evolutionary rates, we obtain estimates from three approaches that the most likely divergence date of SARS-CoV-2 from its most closely related available bat sequences ranges from 1948 to 1982.
Key Points
- RaTG13 is the closest available bat virus to SARS-CoV-2; a sub-lineage of these bat viruses is able to infect humans. Two sister lineages of the RaTG13/SARS-CoV-2 lineage infect Malayan pangolins.
- The sarbecoviruses show a pattern of deep recombination events, indicating that there are high levels of co-infection in horseshoe bats and that the viral pool can generate novel allele combinations and substantial genetic diversity; the sarbecoviruses are efficient ‘explorers’ of phenotype space.
- The SARS-CoV-2 lineage is not a recent recombinant, at least not involving any of the bat or pangolin viruses sampled to date.
- Non-recombinant regions of the sarbecoviruses can be identified, allowing for phylogenetic inference and dating to be performed. We constructed three such regions using different methods.
- We estimate that RaTG13 and SARS-CoV-2 diverged 40 to 70 years ago. There is a diverse unsampled reservoir of generalist viruses established in horseshoe bats.
- While an intermediate host responsible for the zoonotic event cannot be ruled out, the relevant evolution for spillover to humans very likely occurred in horseshoe bats.
Full read in the following link:
https://www.biorxiv.org/content/biorxiv/early/2020/03/31/2020.03.30.015008.full.pdf (PDF format)
The aforementioned findings motivate a look at the global distribution of
horseshoe bats and
genome sequences:
(1)
Figure 1. Maximum-likelihood phylogeny based on the complete genome sequences of 17 bat CoV species released by ICTV in 2018. A general time-reversible model of nucleotide substitution with estimated base frequencies, the proportion of invariant sites, and the γ distribution of rates across sites were used in the maximum-likelihood analysis. Bootstrap values are shown next to the branches. The scale bar indicates the number of nucleotide substitutions per site. Different colors represent different genera. Red, Alphacoronavirus; blue, Betacoronavirus. Updated subgenera clusters are labelled Setracovirus, Myotacovirus, Rhinacovirus, Colacovirus, Pedacovirus, Decacovirus, Minunacovirus, Nyctacovirus for the Alphacoronavirus and Nobecovirus, Hibecovirus, Sarbecovirus, Merbecovirus for the Betacoronavirus.
(2)
Figure 2. Geographical distribution of bat CoVs from the genera Alphacoronavirus and Betacoronavirus. Each colored region represents the country which reported the discovery of bat CoV. Red regions represent the countries which discovered bat Alphacoornavirus. Green regions represent the countries which discovered bat Betacoronavirus. Red-green striped regions represent the countries which discovered both bat Alphacoronavirus and Betacoronavirus.
(3)
Figure 3. Pie chart showing the relative detection rate of different bat CoVs from different subgenera of Alphacoronavirus and Betacoronavirus in Hong Kong from 2008 to 2017. The potential zoonotic transmission routes of each sub-genus of bat CoV detected are shown. Unclassified Alphacoronavirus represents those without complete genome sequences or genome characterization. Red color represents the sub-genera from Alphacoronavirus; Blue color represents the sub-genera from Betacoronavirus.
(4)
Figure 4. Geographical distribution of different horseshoe bats which were discovered to carry SARS-like BatCoV [
114,
115,
116,
117,
118,
119,
120,
121,
122,
123,
124,
125]. Each colored rectangular box represents the geographical distribution of a specific horseshoe bat species respectively: red box, Rhinolophus affinis; orange box, Rhinolophus blasii; yellow box, Rhinolophus euryale; green box, Rhinolophus ferrumequinum; turquoise box, Rhinolophus hildebrantii; indigo box, Rhinolophus hipposideros; purple box, Rhinolophus macrotis; brown box, Rhinolophus mehelyi; pink box, Rhinolophus pearsonii; gold box, Rhinolophus pusillus; blue-gray box, Rhinolophus rex; black box, Rhinolophus sinicus; lime box, Rhinolophus thomasi. Orange circle represents Yunnan Province; Red circle represents the origin of SARS & SADS outbreaks.
(5)
Figure 5. Geographical distribution of bat CoVs from the genus Betacoronavirus. Each colored region represents the country which reported the discovery of bat CoV from different sub-genera. Navy-blue regions represent the countries which discovered bat CoVs from Sarbecovirus. Yellow regions represent the countries which discovered bat CoVs from Merbecovirus. Purple regions represent the countries which discovered bat CoVs from Nobecovirus.
Aforementioned images
(1)(2)(3)(4)(5) taken from the following study:
Global Epidemiology of Bat Coronaviruses
Abstract
Bats are a unique group of mammals of the order Chiroptera. They are highly diversified and are the group of mammals with the second largest number of species. Such highly diversified cell types and receptors facilitate them to be potential hosts of a large variety of viruses. Bats are the only group of mammals capable of sustained flight, which enables them to disseminate the viruses they harbor and enhance the chance of interspecies transmission. This article aims at reviewing the various aspects of the global epidemiology of bat coronaviruses (CoVs). Before the SARS epidemic, bats were not known to be hosts for CoVs. In the last 15 years, bats have been found to be hosts of >30 CoVs with complete genomes sequenced, and many more if those without genome sequences are included. Among the four CoV genera, only alphaCoVs and betaCoVs have been found in bats. As a whole, both alphaCoVs and betaCoVs have been detected from bats in Asia, Europe, Africa, North and South America and Australasia; but alphaCoVs seem to be more widespread than betaCoVs, and their detection rate is also higher. For betaCoVs, only those from subgenera Sarbecovirus, Merbecovirus, Nobecovirus and Hibecovirus have been detected in bats. Most notably, horseshoe bats are the reservoir of SARS-CoV, and several betaCoVs from subgenus Merbecovirus are closely related to MERS-CoV. In addition to the interactions among various bat species themselves, bat–animal and bat–human interactions, such as the presence of live bats in wildlife wet markets and restaurants in Southern China, are important for interspecies transmission of CoVs and may lead to devastating global outbreaks.
Full read in the following link:
https://www.mdpi.com/1999-4915/11/2/174
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In light of the above, it make sense to
retrace PATIENT ZERO in every country:
https://www.weforum.org/agenda/2020/03/coronavirus-covid-19-patient-zero/
This information is useful to those who are looking forward to help combating COVID-19 outbreak and/or already involved in any capacity, and will also help quell affiliated conspiracy theories floating around in this forum and elsewhere. At minimum, this information will contribute to knowledge of people.
Regards and take care.
