Phylogenetic and Ancestral Sequence Reconstruction of SARS-CoV-2 Reveals Latent Capacity to Bind Human ACE2 Receptor

Binding affinity between coronavirus spike protein and human ACE2 receptor

Coronaviruses (CoVs) pose a major risk to global public health due to their ability to infect diverse animal species and potential for emergence in humans. The CoV spike protein mediates viral entry into the cell and plays a crucial role in determining the binding affinity to host cell receptors. With particular emphasis on α- and β-coronaviruses that infect humans and domestic animals, current research on CoV receptor use suggests that the exploitation of the angiotensin-converting enzyme 2 (ACE2) receptor poses a significant threat for viral emergence with pandemic potential. This review summarizes the approaches used to study binding interactions between CoV spike proteins and the human ACE2 (hACE2) receptor. Solid-phase enzyme immunoassays and cell binding assays allow qualitative assessment of binding but lack quantitative evaluation of affinity. Surface plasmon resonance, Bio-layer interferometry, and Microscale Thermophoresis on the other hand, provide accurate affinity measurement through equilibrium dissociation constants (KD). In silico modeling predicts affinity through binding structure modeling, protein-protein docking simulations, and binding energy calculations but reveals inconsistent results due to the lack of a standardized approach. Machine learning and deep learning models utilize simulated and experimental protein-protein interaction data to elucidate the critical residues associated with CoV binding affinity to hACE2. Further optimization and standardization of existing approaches for studying binding affinity could aid pandemic preparedness. Specifically, prioritizing surveillance of CoVs that can bind to human receptors stands to mitigate the risk of zoonotic spillover.

Preeclampsia and severe acute respiratory syndrome coronavirus 2 infection: a systematic review

OBJECTIVE

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the cause of the coronavirus disease 2019 (COVID-19) disease that has rapidly spread worldwide, causing hundreds of thousand deaths. Normal placentation is characterized by many processes strictly regulated during pregnancy. If placentation is impaired, it can lead to gestational disorders, such as preeclampsia that is a multisystem disorder that occurs in 2-8% of pregnancies worldwide.

METHODS

We performed a systematic search to understand the potential involvement of SARS-CoV-2 in preeclampsia onset using the databases, PubMed and Web of Science until 31 January 2022.

RESULTS

SARS-CoV-2 infection not only causes damage to the respiratory system but also can infect human placenta cells impairing pivotal processes necessary for normal placenta development. The inflammatory response trigged by COVID-19 disease is very similar to that one found in preeclampsia pregnancies suggesting a possible link between SARS-CoV-2 infection and preeclampsia onset during pregnancy.

CONCLUSION

Some studies showed that pregnancies affected by COVID-19 had higher incidence of preeclampsia compared with SARS-CoV-2-negative ones. However, increased blood pressure found in COVID-19 pregnancies does not allow to associate COVID-19 to preeclampsia as hypertension is a common factor to both conditions. At present, no diagnostic tools are available to discriminate real preeclampsia from preeclampsia-like syndrome in patients with SARS-CoV-2 infection. Thus, new specific diagnostic tools are necessary to assure an appropriate diagnosis of preeclampsia in these patients, especially in case of severe COVID-19 disease.

ARPIP: Ancestral sequence Reconstruction with insertions and deletions under the Poisson Indel Process

Modern phylogenetic methods allow inference of ancestral molecular sequences given an alignment and phylogeny relating present day sequences. This provides insight into the evolutionary history of molecules, helping to understand gene function and to study biological processes such as adaptation and convergent evolution across a variety of applications. Here we propose a dynamic programming algorithm for fast joint likelihood-based reconstruction of ancestral sequences under the Poisson Indel Process (PIP). Unlike previous approaches, our method, named ARPIP, enables the reconstruction with insertions and deletions based on an explicit indel model. Consequently, inferred indel events have an explicit biological interpretation. Likelihood computation is achieved in linear time with respect to the number of sequences. Our method consists of two steps, namely finding the most probable indel points and reconstructing ancestral sequences. First, we find the most likely indel points and prune the phylogeny to reflect the insertion and deletion events per site. Second, we infer the ancestral states on the pruned subtree in a manner similar to FastML. We applied ARPIP on simulated datasets and on real data from the Betacoronavirus genus. ARPIP reconstructs both the indel events and substitutions with a high degree of accuracy. Our method fares well when compared to established state-of-the-art methods such as FastML and PAML. Moreover, the method can be extended to explore both optimal and suboptimal reconstructions, include rate heterogeneity through time and more. We believe it will expand the range of novel applications of ancestral sequence reconstruction.

SARS-CoV-2: tracing the origin, tracking the evolution

The origin of SARS-CoV-2 is uncertain. Findings support a "bat origin" but results are not highly convincing. Studies found evidence that SARS-CoV-2 was around for many years before the pandemic outbreak. Evidence has been published that the progenitor of SARS-CoV-2 already had the capability to bind strongly to the human ACE2 receptor. This may be an indication that many other animal viruses are capable to jump to humans, having already affinity for a human receptor. This is quite worrying since current ecosystems' collapse brings people to high proximity with animals, increasing probabilities for random viral transitions. On the other hand, future adaptation of SARS-CoV-2 is of great concern. Virus-host interactions are complicated and unfortunately, we still do not have accurate tools for predicting viruses' future evolution. Viral adaptation is a multifactorial process and probably SARS-CoV-2 will not become soon, as we wish, a harmless infection. However, humanity is currently under the largest vaccination program and it's of great interest to see if vaccinations will change the evolutionary game against the virus.