An APOBEC3 molecular clock to estimate the date of emergence of hMPXV

A further update to these posts:
Initial observations about putative APOBEC3 deaminase editing driving short-term evolution of MPXV since 2017
Update to observations about putative APOBEC3 deaminase editing in the light of new genomes from USA

Áine O’Toole & Andrew Rambaut
Institute of Ecology and Evolution
University of Edinburgh
2022-06-05

We gratefully acknowledge the groups that have been publicly sharing MPXV genome sequence data which makes analyses such as this possible. These data are listed and cited in Table 1.

In a previous post we hypothesised that the current monkeypox virus (MPXV) epidemic had arisen from a non-human animal to human jump prior to 2017. This was based on the observation of a preponderance of a specific mode of mutation that is characteristic of cytosine deamination by molecules in the APOBEC3 family.

Here we show a linear accumulation of these mutation with time of collection of genome sequences, estimate the rate of accumulation and extrapolate back to estimate the time that these mutation started to accumulate. If we assume that APOBEC3-type mutations are indicative of replication within human cells and that all such mutations reconstructed in the phylogenetic tree of hMPXV1 genomes are the result of APOBEC3, then a simple extrapolation provides an estimate for the date of jump into the human population (Figure 1).

We estimate that APOBEC3-type mutations accumulate during human to human transmission at the rate of about 9 per year (8.74 with a 95% interval 7.34 – 10.15) which corresponds to an evolutionary rate of 4.43 × 10-5 substitutions per site per year (3.72 – 5.15 × 10-5) for a genome length of 197,210 nucleotides. This rate is approximately 20-fold greater than the long term evolutionary rate estimated for MPXV in the non-human animal reservoir of 1.93 × 10-6 (95% highest posterior density interval 1.21–2.66 × 10-6) (Patrono et al. 2020).

The estimate for the date of emergence of hMPXV1 in the human population is 5-Apr-2016 (95% highest posterior density intervals of 14-Jul-2015 – 18-Dec-2016).


Figure 1 | Root to tip linear regression of APOBEC3-type mutations against time of collection. Slope is an estimate of the rate in substitutions per year (mean 8.74, 95% interval 7.34 – 10.15). Red density is an estimate of the time at y=0 (mean 2016.26, 95% highest posterior density interval 2015.54 – 2016.97).

Methods

The genomes used in this study are listed in Table 1. We arbitrarily selected 7 genomes from the B.1 lineage to span the time range for this lineage. The genome sequences were aligned to the Clade 3 reference genome (accession NC_063383) using minimap2 (Li 2018) and Squirrel. A maximum likelihood phylogenetic tree was constructed using IQTree2 (Minh et al. 2020) using KJ642617 (Nigeria, 1971) and KJ642615 (Nigeria, 1978) as outgroups (Figure 2). The putative ancestral genomes we reconstructed at each node using IQTree2 and then cumulative numbers of APOBEC3-type mutations (GA->AA or TC->TT dinucleotide transitions) were counted for each tip in the tree.

A linear model of APOBEC3-type mutations against date of collection was fitted using the quadratic approximation (quap function in the Rethinking package in R).


Figure 2 | The phylogenetic tree of the genomes listed here with APOBEC3-type and other mutations reconstructed. The red arrow represents the putative point at which the virus emerged into the human population if all APOBEC3-type mutations accrued in humans.

Caveats

The tips of the tree are not independent data because they share evolutionary history through common ancestry. Where genomes had known epidemiological linkage, only one representative was included. This effect can be seen in Figure 1 where the data points for particular lineages cluster together (e.g., A.1). This will tend to result in an underestimate of the uncertainty of the parameters.

C->T and G->A mutations are the most common so we would expect some APOBEC3-like mutations to occur by chance due to polymerase error alone (in a presumed non-human animal host). Thus the date of emergence should be considered an upper bound assuming all such mutations occurred after the jump to humans.

Table 1 | MPXV genome sequences used in this study.

Accession Name Country Year Clade/Lineage Reference
KJ642617 Nigeria-SE-1971 Clade 3 Nigeria 1971 Nakazawa et al. 2015
KJ642615 W-Nigeria Clade 3 Nigeria 1978 Nakazawa et al. 2015
MK783027 3018 hMPXV1 A Nigeria 2017-11-09 Yinka-Ogunleye et al. 2019
MK783028 3019 hMPXV1 A Nigeria 2017-11-09 Yinka-Ogunleye et al. 2019
MK783029 3029 hMPXV1 A Nigeria 2017-12-06 Yinka-Ogunleye et al. 2019
MK783030 3025 hMPXV1 A Nigeria 2017-11-30 Yinka-Ogunleye et al. 2019
MK783031 3020 hMPXV1 A Nigeria 2017-11-09 Yinka-Ogunleye et al. 2019
MK783032 3030 hMPXV1 A Nigeria 2017-11-01 Yinka-Ogunleye et al. 2019
MK783033 2920 hMPXV1 A Nigeria 2017-10-09 Yinka-Ogunleye et al. 2019
NC_063383 M5312_HM12 hMPXV1 A Nigeria 2018-08-15 Mauldin et al., 2022
MT903341 M5320_M15 hMPXV1 A.1 Nigeria 2018-08-14 Mauldin et al., 2022
MT903342 Singapore hMPXV1 A.1 Singapore 2019-04-30 Mauldin et al., 2022
MT903343 UK_P1 hMPXV1 A.1 UK 2018-09-07 Mauldin et al., 2022
MT903344 UK_P2 hMPXV1 A.1 UK 2018-09-11 Mauldin et al., 2022
MT903345 UK_P3 hMPXV1 A.1 UK 2018-09-22 Mauldin et al., 2022
MN648051 Israel hMPXV1 A.1 Israel 2018-10-04 Cohen-Gihon et al. 2020
MT250197 Singapore_2019 hMPXV1 A.1 Singapore 2019-05-08 Yong et al. 2020
ON676708 MD001 hMPXV1 A.1.1 USA 2021-11-16 Gigante et al. 2022
ON674051 FL001 hMPXV1 A.2.1 USA 2022-05-22 Gigante et al. 2022
ON676707 TX001 hMPXV1 A.2 USA 2021-07-15 Gigante et al. 2022
ON675438 VA001 hMPXV1 A.2 USA 2022-05-27 Gigante et al. 2022
ON563414 MA001 hMPXV1 B.1 USA 2022-05-19 Gigante et al. 2022
ON803417 UN-NML-2836 hMPXV1 B.1 Canada 2022-05-17 Knox et al. 2022
ON880542 UN-NML-3348 hMPXV1 B.1 Canada 2022-05-31 Duggan et al. 2022
ON959143 MPX-96 hMPXV1 B.1 Finland 2022-06-16 Kant et al. 2022
OP062230 UN-NML-3864 hMPXV1 B.1 Canada 2022-06-22 Duggan et al. 2022
OP062235 UN-NML-3934 hMPXV1 B.1 Canada 2022-06-30 Duggan et al. 2022
OX248696 RNA hMPXV1 B.1 Slovakia 2022-07-04 Comenius University of Bratislava, Ilkovicova 8, 841 04 Bratislava, Slovakia

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