Yuri Deigin

To gain insight into how researchers of aging perceive the process they study, we conducted a survey among experts in the field. While highlighting some common features of aging, the survey exposed broad disagreement on the foundational issues. What is aging? What causes it? When does it begin? What constitutes rejuvenation? Not only was there no consensus on these and other core questions, but none of the questions received a majority opinion—even regarding the need for consensus itself. Despite many researchers believing they understand aging, their understanding diverges considerably. Importantly, as different processes are labeled as “aging” by researchers, different experimental approaches are prioritized. The survey shed light on the need to better define which aging processes this field should target and what its goals are. It also allowed us to categorize contemporary views on aging and rejuvenation, revealing critical, yet largely unanswered, questions that appear disconnected from the current research focus. Finally, we discuss ways to address the disagreement, which we hope will ultimately aid progress in the field.

HKU4-related coronaviruses (CoVs) are merbecoviruses related to Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV). In 2022 and 2023, two HKU4-related CoV strains were discovered in Manis javanica (Malayan pangolin) metagenomic datasets derived from organ samples: HKU4-P251T and MjHKU4r-CoV-1. Together with the Tylonycteris robustula bat CoV 162275, which was discovered in 2022, pangolin CoVs HKU4-P251T and MjHKU4r-CoV-1 form a novel phylogenetic clade distinct from all previously documented HKU4-related CoVs. In this study, we identified a novel HKU4-related CoV in a pangolin single-cell sequencing dataset generated by BGI-Shenzhen in Shenzhen, Guangdong, China in 2020. The CoV phylogenetically belongs to the same newly identified clade. The single cell datasets were reported as generated from organ samples of a single pangolin that died of natural causes. 98% of the HKU4-related CoV reads were found in only one of the seven single cell datasets — a large intestine cell dataset, cells of which exhibit low expression of DPP4. Bacterial contamination was found to be moderately correlated with HKU4-related CoV presence. We further identified with high confidence that the RNA-Seq dataset supporting one of four near identical variants of MjHKU4r-CoV-1 is a Sus scrofa (wild pig) metagenomic dataset, with only a trace level of Manis javanica genomic content. The presence of HKU4-related CoV reads in the dataset are almost certainly laboratory research-related and not from a premortal pangolin or pig infection. Our findings raise concerns about the provenance of the novel HKU4-related CoV we identify here, MjHKU4r-CoV-1 and its four near-identical variants.

Pekar et al. (2022) propose that SARS-CoV-2 was a zoonotic spillover that first infected humans in the Huanan Seafood Market in Wuhan, China. They propose that there were two separate spillovers of the closely related lineages A and lineage B in a short period of time. The two lineages are differentiated by two SNVs; hence, a single-SNV A-B intermediate must have occurred in an unsampled animal host if the two-spillover hypothesis is correct. Consequently, confirmation of the existence of an intermediate A-B genome from humans would falsify their hypothesis of two spillovers. Pekar et al. identified and excluded 20 A-B intermediate genomes from their analysis. A variety of exclusion criteria were applied, including low read depth and the assertion of repeated erroneous base calls at lineage-defining positions 8782 and 28144. However, data from GISAID show that most of the genomes were sequenced to high average sequencing depth, appearing inconsistent with these criteria. The decision to exclude the majority of genomes was based on personal communications, with raw data unavailable for inspection. Multiple errors, biases, and inconsistencies were observed in the exclusion process. For example, 12 intermediate genomes from one study were excluded; however, 54 other genomes from the same study were included, indicating selection bias. Puzzlingly, two intermediate genomes from Beijing were discarded despite an average sequencing depth of 2175X; however, four genomes from the same sequencing study were included in the analysis. Lastly, we discuss 14 additional possible intermediate genomes not discussed by Pekar et al. and note that genome sequence filtration is inappropriate when considering the presence or absence of a specific SNV pair in an outbreak. Consequently, we find that the exclusion of many of the intermediate genomes is unfounded, leaving the conclusion of two natural zoonoses unsupported.

HKU4-related coronaviruses are a group of betacoronaviruses belonging to the same merbecovirus subgenus as Middle Eastern Respiratory Syndrome coronavirus (MERS-CoV), which causes severe respiratory illness in humans with a mortality rate of over 30%. The high genetic similarity between HKU4-related coronaviruses and MERS-CoV makes them an attractive subject of research for modeling potential zoonotic spillover scenarios. In this study, we identify a novel coronavirus contaminating agricultural rice RNA sequencing datasets from Wuhan, China. The datasets were generated by the Huazhong Agricultural University in early 2020. We were able to assemble the complete viral genome sequence, which revealed that it is a novel HKU4-related merbecovirus. The assembled genome is 98.38% identical to the closest known full genome sequence, Tylonycteris pachypus bat isolate BtTp-GX2012. Using in silico modeling, we identified that the novel HKU4-related coronavirus spike protein likely binds to human dipeptidyl peptidase 4 (DPP4), the receptor used by MERS-CoV. We further identified that the novel HKU4-related coronavirus genome has been inserted into a bacterial artificial chromosome in a format consistent with previously published coronavirus infectious clones. Additionally, we have found a near complete read coverage of the spike gene of the MERS-CoV reference strain HCoV-EMC/2012, and identify the likely presence of a HKU4-related-MERS chimera in the datasets. Our findings contribute to the knowledge of HKU4-related coronaviruses and document the use of a previously unpublished HKU4 reverse genetics system in apparent MERS-CoV related gain-of-function research. Our study also emphasizes the importance of improved biosafety protocols in sequencing centers and coronavirus research facilities.

Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2 related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here, we examine the novel SARS2r-CoV we previously identified in game animal metatranscriptomic datasets sequenced by the Nanjing Agricultural University in 2022, and find that sections of the partial genome phylogenetically group with Guangxi pangolin CoVs (GX PCoVs), while the full RdRp sequence groups with bat-SL-CoVZC45. While the novel SARS2r-CoV is found in 6 pangolin datasets, it is also found in 10 additional NGS datasets from 5 separate mammalian species and is likely related to contamination by a laboratory researched virus. Absence of bat mitochondrial sequences from the datasets, the fragmentary nature of the virus sequence and the presence of a partial sequence of a cloning vector attached to a SARS2r-CoV read suggests that it has been cloned. We find that NGS datasets containing the novel SARS2r-CoV are contaminated with significant Homo sapiens genetic material, and numerous viruses not associated with the host animals sampled. We further identify the dominant human haplogroup of the contaminating H. sapiens genetic material to be F1c1a1, which is of East Asian provenance. The association of this novel SARS2r-CoV with both bat CoV and the GX PCoV clades is an important step towards identifying the origin of the GX PCoVs.

Understanding how SARS-CoV-2 entered the human population, thereby causing the COVID-19 pandemic, is one of the most urgent questions in science today. Two hypotheses are widely acknowledged as being most likely to explain the pandemic’s origin in late 2019: (i) the “natural origin” hypothesis that one or more cross-species transmissions from animals into humans occurred, most likely at the Huanan Seafood Market in Wuhan, China; (ii) the “laboratory origin” hypothesis, that scientific research activities led to the unintentional leak of SARS-CoV-2 from a laboratory into the general population. A recent analysis of SARS-CoV-2 genomes by Pekar et al. [ Science 377 :960-966 (2022)] claims to establish at least two separate spillover events from animals into humans, thus claiming to provide strong evidence for the natural origin hypothesis. However, here we use outbreak simulations to show that the findings of Pekar et al. are heavily impacted by two methodological artifacts: the dubious exclusion of informative SARS-CoV-2 genomes, and their reliance on unrealistic phylodynamic models of SARS-CoV-2. Absent models that incorporate these effects, one cannot conclude multiple SARS-CoV-2 spillovers into humans. Our results cast doubt on a primary point of evidence in favor of the natural origin hypothesis. Lay Summary: It is not known if SARS-CoV-2 spilled over from animals into humans at the Huanan Seafood Market, or arose as a result of research activities studying bat coronaviruses. Two recent papers had claimed to answer this question, but here we show those papers are both inconclusive as they fail to account for biases in how medical managers became alerted to SARS-CoV-2 and how public health authorities sampled early cases. Additionally, key data points conflicting with the authors’ conclusions were improperly excluded from the analysis. The papers’ methods do not justify their conclusions, and the origin of SARS-CoV-2 remains an urgent, open question for science.

Pangolins are the only animals other than bats proposed to have been infected with SARS-CoV-2related coronaviruses (SARS2r-CoVs) prior to the COVID-19 pandemic. Here we examine thenovel SARS2r-CoV we previously identified in game animal metatranscriptomic datasetssequenced by He et al. (2022) and find that sections of the partial genome phylogenetically groupwith Guangxi (GX) pangolin CoVs (GX PCoVs), while the full RdRp sequence groups with bat-SL-CoVZC45. While the novel SARS2r-CoV is found in 6 pangolin datasets, the same CoV isalso found in 10 additional NGS datasets from 5 separate mammalian species and is likelyrelated to contamination by a laboratory researched virus. Absence of bat mitochondrialsequences from the datasets, the fragmentary nature of the virus sequence and the presence of apartial sequence of a cloning vector attached to a SARS2r-CoV read suggests that it has beencloned. We find that NGS datasets containing the novel SARS2r-CoV are contaminated withsignificant Homo sapiens genetic material, and numerous viruses not associated with the hostanimals sampled. We further identify the dominant human haplogroup of the contaminatingH.sapiens genetic material to be F1c1a1, which is of East Asian provenance. The association ofthis novel CoV with both bat CoV and the Guangxi pangolin CoV (GX PCoV) clades is animportant step towards identifying the origin of the GX PCoVs.

Metagenomic datasets from pangolin tissue specimens have previously yielded SARS-related coronaviruses which show high homology in their receptor binding domain to SARS-CoV-2, suggesting a potential zoonotic source for this feature of the human virus, possibly via recombination (Liu et al. 2019, Lam et al. 2020, Xiao et al. 2020, Liu et al. 2020). Here we re-examine these published datasets. We report that only a few pangolin samples were found to contain coronavirus reads, and even then in low abundance, while other non-pangolin hosted viruses were present in higher abundance. We also discovered extensive contamination with human, rodent, and other mammalian gene sequences, which was a surprising finding. Furthermore, we uncovered a number of pangolin CoV sequences embedded in standard laboratory cloning vectors, which suggests the pangolin specimens could have been contaminated with sequences derived from synthetic biology experiments. Finally, we discover a third pangolin dataset (He et al. 2022) with low levels of SARSr-CoV sequences and unambiguous extensive contamination of several pangolin samples. For these reasons, we find it unlikely that the pangolins in question had a coronavirus infection while alive, and all current versions of the cited papers claiming a zoonotic infection of pangolins with a SARS-r CoV require substantial corrections and should be retracted until such corrections are made.

Pour le moment, la meilleure explication aux origines du COVID-19 semble être que le virus s’est échappé de l’Institut de Virologie de Wuhan, où des scientifiques étaient engagés à créer de nouvelles chimères de type SARS et à surcharger potentiellement leur transmissibilité et leur pathogénicité.

Questions about the origins of COVID-19 are of more than academic interest. For the moment, the best explanation for the origins of COVID-19 seems to be that the virus escaped from the Wuhan Institute of Virology, where scientists were engaged in creating novel SARS-like chimeras and potentially supercharging their transmissibility and pathogenicity.