A Study of the Evolution of HBV Virus By Sequencing Samples Up To 4000 Years Old.

[NNadir]

The paper I will discuss in this post is this one: Ancient hepatitis B viruses from the Bronze Age to the Medieval period. (Eske Willerslev et al.Nature Volume 557, pages 418–423 (2018))

Recently I've become interested in the biophysical chemistry of nucleic acids, developing a somewhat amateurish understanding of the topic that despite being primitive is nonetheless awe inspiring. The development of modern sequencing techniques, stimulated by a Government investment - the human genome project set in motion by the Clinton administration - that ultimately stimulating great success in the private sector, has resulted in incredible scientific advances in this age of rising popular ignorance. It's probably as stimulating for biology, biochemistry, and medicine as the Government investment in the more popularly dramatic landings on the moon -set in motion by the Kennedy administration in response to developments in the Truman/Eisenhower era - were to the computer industry.

A terrifying aside:

The days of great government stimulated science are ending since primitive troglodytes - the result of a highly effective Russian attack on the United States applauded by people who nonetheless obscenely wrap themselves in American flags, claim moral superiority while kidnapping children and glorifying rape: George Orwell's "doublespeak" brought depressingly to life - have ended up controlling the government. Future generations will justifiably curse us for allowing this to pass.

They uniformly hate everything that's beautiful, a hatred of science being only one aspect.

Anyway. Enough. There still is beauty to be seen, and perhaps it will rise again. Anyway.

This interest in nucleic acids drew my attention to the paper cited at the outset of this post. It appears that scientists have sequenced the viral genome from samples thousands of years old.

From the introductory text:

HBV is transmitted perinatally or horizontally via blood or genital fluids3. The estimated global prevalence is 3.6%, ranging from 0.01% (UK) to 22.38% (South Sudan)4. In high endemicity areas, in which prevalence is over 8%, 70–90% of the adult population show evidence of past or present infection...

...Approximately 257 million people are chronically infected and around 887,000 people died in 2015 owing to associated complications...

...Despite the prevalence and public health impact of HBV, its origin and evolution remain unclear6,7. Inference of HBV nucleotide substitution rates is complicated by the fact that the virus genome consists of four overlapping open reading frames8, and that mutation rates differ between phases of chronic infection9. Studies based on heterochronous sequences, sampled over a relatively short time period, find higher substitution rates, whereas rates estimated using external calibrations tend to be lower, leading to a wide range of estimated HBV substitution rates (7.72?×?10^?4–3.7?×?10^?6 substitutions per site per year)10,11,12...

The authors report that the virus exhibits 9 subtypes, and that efforts to attribute the distribution of these subtypes by tracing, for example, human migration give ambiguous results, as does the study of the viral sequences that infect other species affected by HBV, including other primates and animals like squirrels and bats.

Here's a figure from the text showing the distribution of some HPV subtypes:



The caption:

a, Distribution of modern human HBV genotypes7. Genotypes relevant to this Letter are shown in colour. Coloured shapes indicate the locations of the HBV-positive samples included for further analysis. b, Locations of analysed Bronze Age samples1 are shown as circles and Iron Age and later samples2 are shown as triangles. Coloured markers indicate HBV-positive samples. Ancient genotype A samples are found in regions in which genotype D predominates today, and HBV-DA27 is of sub-genotype D5 which today is found almost exclusively in India.

To get a better understanding of the history of this virus and the disease it causes, they do a remarkable thing as implied by the comment "b" in the caption: They examine viruses obtained from tissue samples that are hundreds and even thousands of years old.

A remark from the text:

For an initial phylogenetic grouping, we estimated a maximum likelihood tree using the ancient HBV genomes together with modern human, non-human primate, rodent and bat HBV genomes (dataset 1, see Methods). All ancient viruses fell within the diversity of Old World primate HBV genotypes, which includes all human and other great ape genotypes with the exception of human genotypes F and H.

Recombination is known to occur in HBV24. We found strong evidence that an ancient sequence (HBV-DA51) and an unknown parent recombined to form the ancient genotype A sequences. Although this cannot literally be the case owing to sample ages, the logical interpretation is that an ancestor of HBV-DA51 was involved in the recombination. The same recombination is also suggested for the two modern genotype A sequences that were included in the analysis. The ancient genotype B (HBV-DA45), a modern genotype B and two modern genotype C sequences were not similarly flagged, which suggests that the possible recombination occurred after genotypes A, B and C had diverged.

Recombination is a type of genetic modification which is known to take place naturally in a wide range of living things; however when this process is the result of human engineering, it generates a huge amount of protest from people like those benighted people who join organizations like Greenpeace; while it may be true that all Republican members of the House, Senate, and the current administration are anti-science troglodytes, it is not true that all anti-science troglodytes are Republican government office holders and their supporters.

The authors construct a putative evolutionary tree from there study of ancient DNA.

Here's a figure from the text:



The caption:

A log-normal relaxed clock and coalescent exponential population prior were used. Grey horizontal bars indicate the 95% HPD interval of the age of the node. Larger numbers on the nodes indicate the median age and 95% HPD interval of the age (in parentheses) under a strict clock and Bayesian skyline tree prior. Clades of genotypes C (except clade C4), E, F, G and H are collapsed and shown as dots. The figure includes a possible tenth genotype, J, based on a single human isolate. Taxon names for ancient samples indicate era (BA, Bronze Age; IA, Iron Age or later), sample name, sample age in years, ISO 3166 three-letter abbreviation of country of sequence origin, and region of sequence origin. Taxon names for modern samples indicate human genotype or subgenotype or host species if non-human, GenBank accession number, sample age in years, ISO 3166 three-letter abbreviation of country of sequence origin, and region of sequence origin.

The authors discuss their data thus:

The ancient HBV genome data enable us to formally evaluate hypotheses concerning HBV origins using path sampling of calibrated phylogenies based on appropriate external divergence date assumptions. We tested several calibration points that would be implied by a co-expansion of HBV with humans after leaving Africa for support of congruence between migrations and geographical locations of HBV clades11. We find weak evidence for the split of the F and H clade occurring between 13.4 and 25.0 ka under a strict, but not a relaxed, clock model. We do not find support for the divergence of subgenotype C3 strains between 5.1 and 12.0 ka (hypothesized to have led to its distribution in different regions of Polynesia11) or for divergence of Haitian A3 strains from other genotype A strains between 0.2 and 0.5 ka...

...Sequences HBV-DA27, HBV-DA29, HBV-DA51 and HBV-DA222 phylogenetically group with the modern genotype D. They have high sequence identity (96.99–98.74%) with modern genotype D sequences (Extended Data Table 4a), and have the typical 33-nucleotide deletion in the preS1 region of the S gene, encoding the three HBV surface proteins8 (Table 2).

Sequences HBV-RISE154, HBV-RISE254 and HBV-RISE563 are in a sister relationship with the chimpanzee–gorilla HBV clade (Fig. 2). HBV-RISE254 and HBV-RISE563 have the same 33-nucleotide deletion in the preS1 sequence that is shared with non-human primate HBVs and human genotype D (Table 2). HBV-RISE563 does not encode a functional pre-core peptide (Table 2). On the basis of sequence similarity across the whole genome, HBV-RISE563 and HBV-RISE254 together might be classified as a new human HBV genotype that is extinct today, and HBV-RISE154 might possibly be classified as another

The authors have a very interesting discussion of the geography of their samples and the sequences found and identified in those regions, Central Asia, Hungary, Kazakhstan, India...etc etc.

The beauty of science is that unlike the increasingly common assertions of orthodoxy and dogma - no one should be so smug as to assume immunity - science can and does question itself; science is a process of questioning what one knows or thinks one knows.

Some closing text along these lines:

They show the existence of ancient HBV genotypes in locations incongruent with their present-day distribution, contradicting previously suggested geographical or temporal origins of genotypes or sub-genotypes; evidence for the creation of genotype A via recombination and the emergence of the genotype outside Africa; at least one now-extinct human genotype; ancient genotype-level localized diversity; and demonstrate that the viral substitution rate obtained from modern heterochronously sampled sequences is probably misleading. Together, these findings suggest that the difficulty in formulating a coherent theory for the origin and spread of HBV may be due to genetic evidence of an earlier evolutionary scenario being overwritten by relatively recent alterations, as has previously been suggested in the context of recombination24. The lack of ancient sequences limits our understanding of the evolution of HBV and very probably of other viruses. Discovery of additional ancient viral sequences may provide a clearer picture of the true origin and early diversification of HBV, enable us to address questions of palaeo-epidemiology, and broaden our understanding of the contributions of natural and cultural changes (including migrations and medical practices) to human disease burden and mortality.

Scientists can use the words "probably misleading," whereas our political figures define what is deliberately misleading and now more obviously outright lies, as "truth," truth being in their case, again, in the Orwellian sense.

It's an interesting article, quite awe inspiring, and yet depressing in the sense that we face great risks if we do not stop these awful people occupying our government.

I despite these threats to our way of life and to our hope for progress, you are having a wonderful week.