Where and when did a virus lineage travel?
The scientific problem
The collapse of Indigenous populations after the European colonisation of the Americas is attributed in part to introduced pathogens, but the identity of the agents involved has rested on historical accounts, on bioarchaeology and on phylogenetic inference from present day viral strains rather than on material from the period. The deadliest outbreaks recorded in New Spain, referred to as Cocoliztli, have no established cause. Guzmán-Solís 2021 identifies the gap as the absence of direct molecular evidence for which viruses were circulating, and asks whether viral genomes can be recovered from human remains buried in Colonial epidemic contexts in Mexico City and read alongside the ancestry and geographic origin of the individuals who carried them.
This is a question about where a lineage has been, not about how a virus behaves in a cell. The methods are those of ancient DNA, paleovirology, bioarchaeology and virus phylogenetics.
What this laboratory contributed
This theme rests on a single publication, and that publication was led elsewhere. The work was carried out by the Ávila Arcos group at the Universidad Nacional Autónoma de México, with Daniel Blanco-Melo, formerly of the tenOever laboratory and at the time affiliated with Mount Sinai and the Fred Hutchinson Cancer Research Center, as co-corresponding author and a principal conceptual contributor. Benjamin tenOever is eleventh of thirteen authors, is neither a corresponding nor a senior author, and his stated contribution is resources and manuscript review. The record classifies the paper as collaborative rather than lab-led on that basis.
The connection to the rest of this corpus runs through an alumnus rather than through a scientific lineage. The record for this publication states that nothing in its reference list or content links it to the tenOever laboratory's own published research, and its related publications list is deliberately empty of corpus links. No methodological or conceptual continuity with the barcoded library work or with the engineering line should be inferred, and asserting one would not be supported by this paper.
How the work evolved
The paper stands alone in the corpus. It has no predecessor here and no successor here, and the area document for viral populations, evolution and transmission treats it as a genuinely discontinuous thread rather than as a stage in a program.
What the study established is worth recording on its own terms. Dental remains from 26 individuals were sampled at two Colonial sites in Mexico City, a hospital whose mass burials indicate urgent simultaneous disposal of bodies and a chapel ten kilometres away. Shotgun sequencing with metagenomic classification identified seventeen samples with at least one normalised viral hit, twelve were carried into a targeted capture using biotinylated RNA probes against clinically important human viruses, and a virus negative library was carried through capture as the specificity control. Enrichment yielded three human parvovirus B19 genomes at 92 to 99 percent coverage of the coding region and one hepatitis B virus genome at 90 percent coverage, all authenticated by best hit filtering against the full nucleotide database and by the terminal deamination damage characteristic of ancient DNA.
Geography came from the genotypes. The hepatitis B virus genome carries the genotype A core gene insertion and clusters with sub-genotype A4, previously recovered only from African individuals in Belgium and never in the Americas. All three parvovirus B19 genomes fall in genotype 3, which predominates in West Africa, whereas only genotype 1 had been described molecularly in Mexico. Three hosts fall within African genetic variation by principal component analysis and carry L mitochondrial haplogroups, enamel strontium ratios in two of them resemble West African values against bone values matching the Trans Mexican Volcanic Belt, and radiocarbon dates of 1442 to 1608 and 1472 to 1625 CE fall in the early Colonial period when arrivals of enslaved people were highest. The authors read that convergence as direct molecular evidence of introduction during the transatlantic slave trade. A fourth individual, from the chapel site and of Indigenous ancestry, also carried genotype 3, which the authors describe as the first genotype 3 genome obtained from a non-African individual and read as onward transmission across populations.
The limits are stated plainly in the paper and should travel with the result. Four viral genomes from four of 26 sampled individuals is a thin basis for statements about what circulated in Colonial Mexico City. The capture panel covered only DNA viruses and RNA viruses with a DNA intermediate, so the leading candidate agents of the Colonial epidemics, which are RNA viruses, could not be sought at all. Hospital individuals were selected on morphological and dental indicators previously interpreted as African ancestry, which shapes which ancestry and lineage combinations could be found. Genotype geography is inferred from modern sampling that is itself uneven, and sub-genotype A4 in particular rests on a contested set of sequences. No causal link to any epidemic, to Cocoliztli or to the individuals' deaths is established, and the authors say so repeatedly. The suggestion that some sixteenth century cases recorded as measles might have been parvovirus B19 is offered as a hypothesis, alongside an explicit statement that the study does not reject a role for measles.
Supporting publications
Guzmán-Solís 2021 is the only publication in this theme, and it is a collaborative study led by another group.
Connections
There is no methodological or conceptual connection between this theme and the other three themes of the area. The link to the corpus is personnel, through Daniel Blanco-Melo, who was a co-author on tenOever laboratory work including Aguado 2018 and Blanco-Melo 2020 before this study. That is a fact about careers rather than about science, and it is the only connection the record supports.
Publications referenced
Publications in this theme
2021 · eLife · collaborative
Targeted ancient DNA capture applied to skeletal remains from a Colonial hospital and chapel in Mexico City recovers three human parvovirus B19 genomes and one hepatitis B virus genome whose closest relatives are African strains, in hosts whose genetic ancestry and strontium isotope signatures point to African birth, giving direct molecular evidence that these viruses reached New Spain during the transatlantic slave trade.