key: cord-0755139-ixhaq0az
authors: Nath, Himadri; Mallick, Abinash; Roy, Subrata; Sukla, Soumi; Biswas, Subhajit
title: Computational modelling supports that Dengue virus envelope antibodies can bind to SARS-CoV-2 receptor binding sites: Is pre-exposure to dengue virus protective against COVID-19 severity?
date: 2020-12-29
journal: Comput Struct Biotechnol J
DOI: 10.1016/j.csbj.2020.12.037
sha: 9de5af775fc3f18e10c8c2215206ce5a3d76d66b
doc_id: 755139
cord_uid: ixhaq0az

The world is going through the scourge of the COVID-19 pandemic since January 2020. However, the pandemic appears to be less severe in highly dengue endemic countries. In this connection, several studies reported that sero-diagnostic tests for DV yielded considerable false-positive results for SARS-CoV-2 and vice versa in dengue endemic regions, thereby indicating towards potential cross-reactivity between these two viruses. We anticipated that SARS-CoV-2 and DV might share antigenic similarity and performed computational docking studies to test this hypothesis. Our results predicted with high confidence that human DV antibodies can indeed, bind to RBD of SARS-CoV-2 Spike protein. Some of these interactions can also potentially intercept human ACE2 receptor binding to RBM. Dengue serum samples predating the COVID-19, had been found to cross-react with SARS-CoV-2 Spike and this provides direct experimental validation of our predictions. Our analysis also showed that m396 and 80R antibodies (against SARS-CoV-1) did not dock with RBM of SARS-CoV-2, a fact already proven experimentally. This confirmed reliability and robustness of our approach. So, it is highly probable that immunological memory/antibodies to DV in endemic countries may reduce the severity and spread of COVID-19. It is not known whether SARS-CoV-2 antibodies will hinder DV infections by binding to DV particles and reduce dengue incidences in the future or, augment DV infection and severity by deploying antibody-dependent enhancement.

Since the beginning of 2020, people around the world are confronting the COVID-19 42 pandemic, caused by SARS-CoV-2, a beta coronavirus. As of 26 th August, 2020, 23,697,273 43 confirmed cases with 814,438 deaths have been reported worldwide [1] . This infection is 44 believed to originate from Wuhan city, Hubei province, China in December, 2019. The virus 45 is highly contagious and easily transmissible from human to human. The virus caused 46 numerous outbreaks across the globe and WHO declared a public health emergency of 47 international concern (PHEIC) on January 30, 2020.

Initially studying the global map of the COVID-19 pandemic, it occurred to us that SARS- the same period cumulative deaths per million population in South-East Asia was only 12 [4] .

As an exception to our proposition, Brazil, a DV-endemic country recorded 3,622,861 64 infections and 115,309 deaths as on 26 th August, 2020 [1] . It is universally accepted and 65 recommended that preventive measures are crucial to contain the spread of COVID-19 like 66 social distancing, quarantine and lockdown in the early phases of the pandemic. In support of 67 our hypothesis, a recent study from Brazil revealed that states reporting higher incidences of 68 dengue during 2019-20 recorded lower COVID-19 cases and deaths. The exponential 69 community transmission was also delayed due to slower SARS-CoV-2 growth rates [5]. The 70 same study also described four major factors that contributed to the COVID-19 epidemic in 71 Brazil including "super-spreader" events [5] .

Even in the face of COVID-19 pandemic, dengue remains the most important arboviral 73 disease of global concern. In last few years incidence of dengue cases has increased rapidly 74 although a vast majority of the cases (~80%) are mild, asymptomatic and self-limiting. . From the above observations, it appeared that pre-exposure to DV may render partial protection against COVID-19 as may be the case in highly dengue endemic 89 regions of the world. This epidemiological observation has now been supported by biological 90 evidences. One report from Singapore stated that an elderly man and a woman were actually 91 SARS-CoV-2 positive but mis-diagnosed for dengue due to similarities in disease were only considered, as the immunogenic epitopes of the virus fall in this region [19] . (B) Amino acids marked red are crucial for interactions between RBD and ACE2 receptor.

Among these receptor binding residues of SARS-CoV-2 Spike, the green highlighted positions denote the residues of the RBD that were predicted to interact also with DV antibodies.

143 crucial for interaction with ACE2 receptor 144 It is notable that DV antibodies were also found to bind to RBD amino acid residues that are 145 crucial for interaction with the human ACE2 receptors, important for SARS-CoV-2 entry into 146 the cells. SARS-CoV-2 Spike RBD interaction with ACE2 receptor has already been 147 elucidated through crystal structure analysis with resolution of 2.45Å [20] . A total of 17 148 residues (with a distance cut-off of 4Å) of SARS-CoV-2 RBD interact with 20 residues of 149 ACE2 receptor [20] . In our docking study, we discovered that DV-EDE antibodies bind with 150 several of the above-mentioned S protein residues with a distance cut-off of 3.5Å. EDE1 C10

Ab contacts with four amino acid residues with a total frequency of 13 among 20 predictions.

Similarly, EDE1 C8 Ab interacts with four amino acid residues in RBM (with a total 153 frequency of 9) that have been predicted to interact with ACE2 receptors. Likewise, EDE2 154 B7 Ab and EDE2 A11 Ab bind with different receptor-engaging amino acid residues in RBD 155 on 14 and 5 occasions respectively (Table 1) . Overall, the DV Abs used in this study, docked 156 with eight S protein amino acids that are crucial for binding to ACE2 receptor. These eight 157 amino acid residues appeared on 41 occasions with repetitions in total 80 predictions (Table   158 1).

2 ---Total frequency 9 13 14 5 Total interaction events in 80 predictions: 41 Table 1 . Amino acid residues of SARS-CoV-2 RBD that interact with ACE2 receptor including the ones that were predicted to interact also with DV antibodies. Columns to the right show frequencies of interactions of DV Abs with some of the ACE2-engaging amino acid residues (bold, left column). These frequencies were obtained from the ZDOCK and ClusPro predictions. 160 Several neutralizing Abs against SARS-CoV-1 (like m396, 80R) are known to interact with 161 RBD of Spike protein and compete with ACE2 receptor for binding [21] . But these 162 antibodies do not bind with SARS-CoV-2 RBD as determined experimentally [13] . We 163 "docked" m396 crystal structure (PDB ID: 2G75) with SARS-CoV-2 Spike in the same 164 procedure as done before (Fig. 1F) . Analysis of 10 ZDOCK and 10 ClusPro predictions 

Our computational modelling studies predicted, with high confidence, that DV Abs can 185 interact with SARS-CoV-2 RBD (Fig. 1, Fig. 3A ) and are also capable of intercepting eight 186 key RBD interactions that are crucial for binding to ACE2 receptors (Fig. 3B, Table 1 ). From 187 these findings we propose that DV Abs have the potential to compete with ACE2 receptors 188 for access to RBD of SARS-CoV-2. So, theoretically, they can "mask" SARS-CoV-2 RBD 189 and block its interaction with host cell receptors and thereby prevent virus entry. Our CoV-2, a fact already confirmed experimentally by others [13] and that WNV NS1 antibody 204 also did not bind satisfactorily with SARS-CoV-2 Spike protein RBD with no interaction in similarities proposed in the other study [10] .

The four DV Abs used in this study, are known to neutralize DV and were identified from 219 serum of dengue fever convalescent patients [11] . This ensures that both asymptomatic and 220 symptomatic patients recovering from DV infection will possess immunological memory to 221 these Abs. In highly Dengue endemic countries, where infections occur regularly, majority of 222 the population has pre-exposure to DV and has turned DV sero-positive. In our present study 223 only four Abs have been considered but immunological response against any pathogen 224 comprises of a repertoire of Abs; so, it is likely there will a larger repertoire of DV antibodies 225 which can bind to and block RBD in humans (Fig. 4) . One limitation of our study is that we 226 used only four DV antibodies to test binding to Spike protein, although there can be much 227 higher number of antigen-antibody interactions in reality. Here, we were limited by available 228 crystal structures for DV envelope antibodies. Nevertheless, we still believe these four 229 antibodies were relevant and closer to real life scenario as they were originally isolated from Interestingly, some studies predicted pre-exposure of humans to animal coronaviruses from 234 syananthropic animals such as bovines and dogs and it was speculated that antibodies elicited 235 against animal coronaviruses could confer partial protection against SARS-CoV-2 [26-28].

In this One-Health approach, epitope mapping by homology modeling revealed high degree 237 of similarity in nucleocapsid and envelope proteins between SARS-CoV-2 and taxonomically 238 related coronaviruses [27, 28] . In this context, it is noteworthy that human to animal 239 transmission has been reported to be more common but the reverse is rare so far [29] . This 319 We used the PyMOL Molecular Graphics System, Version 2.3.3, Schrödinger, LLC for 320 analyzing the predicted PDB structures obtained from both the servers. For each predicted 321 docked complex, the interaction surface between antigen and antibody was determined 322 through the "find any interaction within 3.5Å cut-off" plugin. Amino acid residues of the 323 Spike antigen within RBD region that were involved in an interaction with the target antibody, were identified and marked. All pictures were also refined and modified using the 

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