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Abstract and Figures

We are currently witnessing a major epidemic caused by the 2019 novel coronavirus (2019- nCoV). The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses. Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV-1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute the receptor binding site. The finding of 4 unique inserts in the 2019-nCoV, all of which have identity /similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be fortuitous in nature. This work provides yet unknown insights on 2019-nCoV and sheds light on the evolution and pathogenicity of this virus with important implications for diagnosis of this virus.
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Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp120
and Gag
Prashant Pradhan$1,2, Ashutosh Kumar Pandey$1, Akhilesh Mishra$1, Parul Gupta1, Praveen
Kumar Tripathi1, Manoj Balakrishnan Menon1, James Gomes1, Perumal Vivekanandan*1and
Bishwajit Kundu*1
1Kusuma School of biological sciences, Indian institute of technology, New Delhi-110016, India.
2Acharya Narendra Dev College, University of Delhi, New Delhi-110019, India
$Equal contribution
* Corresponding authors- email: bkundu@bioschool.iitd.ac.in
vperumal@bioschool.iitd.ac.in
Abstract:
We are currently witnessing a major epidemic caused by the 2019 novel coronavirus (2019-
nCoV). The evolution of 2019-nCoV remains elusive. We found 4 insertions in the spike
glycoprotein (S) which are unique to the 2019-nCoV and are not present in other coronaviruses.
Importantly, amino acid residues in all the 4 inserts have identity or similarity to those in the HIV-
1 gp120 or HIV-1 Gag. Interestingly, despite the inserts being discontinuous on the primary
amino acid sequence, 3D-modelling of the 2019-nCoV suggests that they converge to constitute
the receptor binding site. The finding of 4 unique inserts in the 2019-nCoV, all of which have
identity /similarity to amino acid residues in key structural proteins of HIV-1 is unlikely to be
fortuitous in nature. This work provides yet unknown insights on 2019-nCoV and sheds light on
the evolution and pathogenicity of this virus with important implications for diagnosis of this virus.
Introduction
Coronaviruses (CoV) are single-stranded positive-sense RNA viruses that infect animals and
humans. These are classified into 4 genera based on their host specificity: Alphacoronavirus,
Betacoronavirus, Deltacoronavirus and Gammacoronavirus (Snijder et al., 2006). There are seven
known types of CoVs that includes 229E and NL63 (Genus Alphacoronavirus), OC43, HKU1,
MERS and SARS (Genus Betacoronavirus). While 229E, NL63, OC43, and HKU1 commonly
infect humans, the SARS and MERS outbreak in 2002 and 2012 respectively occurred when the
virus crossed-over from animals to humans causing significant mortality (J. Chan et al., n.d.; J. F.
W. Chan et al., 2015). In December 2019, another outbreak of coronavirus was reported from
Wuhan, China that also transmitted from animals to humans. This new virus has been temporarily
termed as 2019-novel Coronavirus (2019-nCoV) by the World Health Organization (WHO) (J. F.-
W. Chan et al., 2020; Zhu et al., 2020). While there are several hypotheses about the origin of
2019-nCoV, the source of this ongoing outbreak remains elusive.
The transmission patterns of 2019-nCoV is similar to patterns of transmission documented in the
previous outbreaks including by bodily or aerosol contact with persons infected with the virus.
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Cases of mild to severe illness, and death from the infection have been reported from Wuhan. This
outbreak has spread rapidly distant nations including France, Australia and USA among others.
The number of cases within and outside China are increasing steeply. Our current understanding
is limited to the virus genome sequences and modest epidemiological and clinical data.
Comprehensive analysis of the available 2019- nCoV sequences may provide important clues that
may help advance our current understanding to manage the ongoing outbreak.
The spike glycoprotein (S) of cornonavirus is cleaved into two subunits (S1 and S2). The S1
subunit helps in receptor binding and the S2 subunit facilitates membrane fusion (Bosch et al.,
2003; Li, 2016). The spike glycoproteins of coronoviruses are important determinants of tissue
tropism and host range. In addition the spike glycoproteins are critical targets for vaccine
development (Du et al., 2013). For this reason, the spike proteins represent the most extensively
studied among coronaviruses. We therefore sought to investigate the spike glycoprotein of the
2019-nCoV to understand its evolution, novel features sequence and structural features using
computational tools.
Methodology
Retrieval and alignment of nucleic acid and protein sequences
We retrieved all the available coronavirus sequences (n=55) from NCBI viral genome database
(https://www.ncbi.nlm.nih.gov/) and we used the GISAID (Elbe & Buckland-Merrett,
2017)[https://www.gisaid.org/] to retrieve all available full-length sequences (n=28) of 2019-
nCoV as on 27 Jan 2020. Multiple sequence alignment of all coronavirus genomes was performed
by using MUSCLE software (Edgar, 2004) based on neighbour joining method. Out of 55
coronavirus genome 32 representative genomes of all category were used for phylogenetic tree
development using MEGAX software (Kumar et al., 2018). The closest relative was found to be
SARS CoV. The glycoprotein region of SARS CoV and 2019-nCoV were aligned and visualized
using Multalin software (Corpet, 1988). The identified amino acid and nucleotide sequence were
aligned with whole viral genome database using BLASTp and BLASTn. The conservation of the
nucleotide and amino acid motifs in 28 clinical variants of 2019-nCoV genome were presented by
performing multiple sequence alignment using MEGAX software. The three dimensional structure
of 2019-nCoV glycoprotein was generated by using SWISS-MODEL online server (Biasini et al.,
2014) and the structure was marked and visualized by using PyMol (DeLano, 2002).
Results
Uncanny similarity of novel inserts in the 2019-nCoV spike protein to HIV-1 gp120 and
Gag
Our phylogentic tree of full-length coronaviruses suggests that 2019-nCoV is closely related to
SARS CoV [Fig1]. In addition, other recent studies have linked the 2019-nCoV to SARS CoV.
We therefore compared the spike glycoprotein sequences of the 2019-nCoV to that of the SARS
CoV (NCBI Accession number: AY390556.1). On careful examination of the sequence
alignment we found that the 2019- nCoV spike glycoprotein contains 4 insertions [Fig.2]. To
further investigate if these inserts are present in any other corona virus, we performed a multiple
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sequence alignment of the spike glycoprotein amino acid sequences of all available
coronaviruses (n=55) [refer Table S.File1] in NCBI refseq (ncbi.nlm.nih.gov) this includes one
sequence of 2019-nCoV[Fig.S1]. We found that these 4 insertions [inserts 1, 2, 3 and 4] are
unique to 2019-nCoV and are not present in other coronaviruses analyzed. Another group from
China had documented three insertions comparing fewer spike glycoprotein sequences of
coronaviruses . Another group from China had documented three insertions comparing fewer
spike glycoprotein sequences of coronaviruses (Zhou et al., 2020).
Figure 1: Maximum likelihood genealogy show the evolution of 2019- nCoV: The evolutionary history
was inferred by using the Maximum Likelihood method and JTT matrix-based model. The tree
with the highest log likelihood (12458.88) is shown. Initial tree(s) for the heuristic search were
obtained automatically by applying Neighbor-Join and BioNJ algorithms to a matrix of pairwise
distances estimated using a JTT model, and then selecting the topology with superior log likelihood
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value. This analysis involved 5 amino acid sequences. There were a total of 1387 positions in the
final dataset. Evolutionary analyses were conducted in MEGA X.
Figure 2: Multiple sequence alignment between spike proteins of 2019-nCoV and SARS. The
sequences of spike proteins of 2019-nCoV (Wuhan-HU-1, Accession NC_045512) and of SARS
CoV (GZ02, Accession AY390556) were aligned using MultiAlin software. The sites of difference
are highlighted in boxes.
We then analyzed all available full-length sequences (n=28) of 2019-nCoV in GISAID (Elbe &
Buckland-Merrett, 2017) as on January 27, 2020 for the presence of these inserts. As most of these
sequences are not annotated, we compared the nucleotide sequences of the spike glycoprotein of
all available 2019-nCoV sequences using BLASTp. Interestingly, all the 4 insertions were
absolutely (100%) conserved in all the available 2019- nCoV sequences analyzed [Fig.S2, Fig.S3].
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We then translated the aligned genome and found that these inserts are present in all Wuhan 2019-
nCoV viruses except the 2019-nCoV virus of Bat as a host [Fig.S4]. Intrigued by the 4 highly
conserved inserts unique to 2019-nCoV we wanted to understand their origin. For this purpose,
we used the 2019-nCoV local alignment with each insert as query against all virus genomes and
considered hits with 100% sequence coverage. Surprisingly, each of the four inserts aligned with
short segments of the Human immunodeficiency Virus-1 (HIV-1) proteins. The amino acid
positions of the inserts in 2019-nCoV and the corresponding residues in HIV-1 gp120 and HIV-1
Gag are shown in Table 1. The first 3 inserts (insert 1,2 and 3) aligned to short segments of amino
acid residues in HIV-1 gp120. The insert 4 aligned to HIV-1 Gag. The insert 1 (6 amino acid
residues) and insert 2 (6 amino acid residues) in the spike glycoprotein of 2019-nCoV are 100%
identical to the residues mapped to HIV-1 gp120. The insert 3 (12 amino acid residues) in 2019-
nCoV maps to HIV-1 gp120 with gaps [see Table 1]. The insert 4 (8 amino acid residues) maps to
HIV-1 Gag with gaps.
Although, the 4 inserts represent discontiguous short stretches of amino acids in spike glycoprotein
of 2019-nCoV, the fact that all three of them share amino acid identity or similarity with HIV-1
gp120 and HIV-1 Gag (among all annotated virus proteins) suggests that this is not a random
fortuitous finding. In other words, one may sporadically expect a fortuitous match for a stretch of
6-12 contiguous amino acid residues in an unrelated protein. However, it is unlikely that all 4
inserts in the 2019-nCoV spike glycoprotein fortuitously match with 2 key structural proteins of
an unrelated virus (HIV-1).
The amino acid residues of inserts 1, 2 and 3 of 2019-nCoV spike glycoprotein that mapped to
HIV-1 were a part of the V4, V5 and V1 domains respectively in gp120 [Table 1]. Since the 2019-
nCoV inserts mapped to variable regions of HIV-1, they were not ubiquitous in HIV-1 gp120, but
were limited to selected sequences of HIV-1 [ refer S.File1] primarily from Asia and Africa.
The HIV-1 Gag protein enables interaction of virus with negatively charged host surface
(Murakami, 2008) and a high positive charge on the Gag protein is a key feature for the host-virus
interaction. On analyzing the pI values for each of the 4 inserts in 2019-nCoV and the
corresponding stretches of amino acid residues from HIV-1 proteins we found that a) the pI values
were very similar for each pair analyzed b) most of these pI values were 10±2 [Refer Table 1] . Of
note, despite the gaps in inserts 3 and 4 the pI values were comparable. This uniformity in the pI
values for all the 4 inserts merits further investigation.
As none of these 4 inserts are present in any other coronavirus, the genomic region encoding these
inserts represent ideal candidates for designing primers that can distinguish 2019-nCoV from other
coronaviruses.
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Motifs
Virus
Glycoprotein
Motif Alignment
HIV
protein
and
Variable
region
HIV
Genome
Source
Country/
subtype
Total
Char
ge
pI
Valu
e
Insert
1
2019- nCoV (GP)
HIV1(GP120)
71 76
TNGTKR
TNGTKR
404 409
gp120-
V4
Thailand
*/
CRF01_
AE
2
2
11
11
Insert
2
2019- nCoV (GP)
HIV1(GP120)
145 150
HKNNKS
HKNNKS
462 467
gp120-
V5
Kenya*/
G
2
2
10
10
Insert
3
2019- nCoV (GP)
HIV1(GP120)
245 256
RSYL- - - -TPGDSSSG
RTYLFNETRGNSSSG
136 150
gp120-
V1
India*/C
2
1
10.84
8.75
Insert
4
2019- nCoV (Poly
P)
HIV1(gag)
676 684
QTNS-----------------------PRRA
QTNSSILMQRSNFKG PRRA
366 384
Gag
India*/C
2
4
12.00
12.30
Table 1: Aligned sequences of 2019-nCoV and gp120 protein of HIV-1 with their positions
in primary sequence of protein. All the inserts have a high density of positively charged
residues. The deleted fragments in insert 3 and 4 increase the positive charge to surface area
ratio. *please see Supp. Table 1 for accession numbers
The novel inserts are part of the receptor binding site of 2019-nCoV
To get structural insights and to understand the role of these insertions in 2019-nCoV glycoprotein,
we modelled its structure based on available structure of SARS spike glycoprotein (PDB:
6ACD.1.A). The comparison of the modelled structure reveals that although inserts 1,2 and 3 are
at non-contiguous locations in the protein primary sequence, they fold to constitute the part of
glycoprotein binding site that recognizes the host receptor (Kirchdoerfer et al., 2016) (Figure 4).
The insert 1 corresponds to the NTD (N-terminal domain) and the inserts 2 and 3 correspond to
the CTD (C-terminal domain) of the S1 subunit in the 2019-nCoV spike glycoprotein. The insert
4 is at the junction of the SD1 (sub domain 1) and SD2 (sub domain 2) of the S1 subunit (Ou et
al., 2017). We speculate, that these insertions provide additional flexibility to the glycoprotein
binding site by forming a hydrophilic loop in the protein structure that may facilitate or enhance
virus-host interactions.
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Figure 3. Modelled homo-trimer spike glycoprotein of 2019-nCoV virus. The inserts from HIV
envelop protein are shown with colored beads, present at the binding site of the protein.
Evolutionary Analysis of 2019-nCoV
It has been speculated that 2019-nCoV is a variant of Coronavirus derived from an animal source
which got transmitted to humans. Considering the change of specificity for host, we decided to
study the sequences of spike glycoprotein (S protein) of the virus. S proteins are surface proteins
that help the virus in host recognition and attachment. Thus, a change in these proteins can be
reflected as a change of host specificity of the virus. To know the alterations in S protein gene of
2019-nCoV and its consequences in structural re-arrangements we performed in-sillico analysis of
2019-nCoV with respect to all other viruses. A multiple sequence alignment between the S protein
amino acid sequences of 2019-nCoV, Bat-SARS-Like, SARS-GZ02 and MERS revealed that S
protein has evolved with closest significant diversity from the SARS-GZ02 (Figure 1).
Insertions in Spike protein region of 2019-nCoV
Since the S protein of 2019-nCoV shares closest ancestry with SARS GZ02, the sequence coding
for spike proteins of these two viruses were compared using MultiAlin software. We found four
new insertions in the protein of 2019-nCoV- “GTNGTKR” (IS1), “HKNNKS” (IS2), “GDSSSG”
(IS3) and “QTNSPRRA” (IS4) (Figure 2). To our surprise, these sequence insertions were not only
absent in S protein of SARS but were also not observed in any other member of the Coronaviridae
family (Supplementary figure). This is startling as it is quite unlikely for a virus to have acquired
such unique insertions naturally in a short duration of time.
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Insertions share similarity to HIV
The insertions were observed to be present in all the genomic sequences of 2019-nCoV virus
available from the recent clinical isolates (Supplementary Figure 1). To know the source of these
insertions in 2019-nCoV a local alignment was done with BLASTp using these insertions as query
with all virus genome. Unexpectedly, all the insertions got aligned with Human immunodeficiency
Virus-1 (HIV-1). Further analysis revealed that aligned sequences of HIV-1 with 2019-nCoV were
derived from surface glycoprotein gp120 (amino acid sequence positions: 404-409, 462-467, 136-
150) and from Gag protein (366-384 amino acid) (Table 1). Gag protein of HIV is involved in host
membrane binding, packaging of the virus and for the formation of virus-like particles. Gp120
plays crucial role in recognizing the host cell by binding to the primary receptor CD4.This binding
induces structural rearrangements in GP120, creating a high affinity binding site for a chemokine
co-receptor like CXCR4 and/or CCR5.
Discussion
The current outbreak of 2019-nCoV warrants a thorough investigation and understanding of its
ability to infect human beings. Keeping in mind that there has been a clear change in the preference
of host from previous coronaviruses to this virus, we studied the change in spike protein between
2019-nCoV and other viruses. We found four new insertions in the S protein of 2019-nCoV when
compared to its nearest relative, SARS CoV. The genome sequence from the recent 28 clinical
isolates showed that the sequence coding for these insertions are conserved amongst all these
isolates. This indicates that these insertions have been preferably acquired by the 2019-nCoV,
providing it with additional survival and infectivity advantage. Delving deeper we found that these
insertions were similar to HIV-1. Our results highlight an astonishing relation between the gp120
and Gag protein of HIV, with 2019-nCoV spike glycoprotein. These proteins are critical for the
viruses to identify and latch on to their host cells and for viral assembly (Beniac et al., 2006).
Since surface proteins are responsible for host tropism, changes in these proteins imply a change
in host specificity of the virus. According to reports from China, there has been a gain of host
specificity in case 2019-nCoV as the virus was originally known to infect animals and not humans
but after the mutations, it has gained tropism to humans as well.
Moving ahead, 3D modelling of the protein structure displayed that these insertions are present at
the binding site of 2019-nCoV. Due to the presence of gp120 motifs in 2019-nCoV spike
glycoprotein at its binding domain, we propose that these motif insertions could have provided an
enhanced affinity towards host cell receptors. Further, this structural change might have also
increased the range of host cells that 2019-nCoV can infect. To the best of our knowledge, the
function of these motifs is still not clear in HIV and need to be explored. The exchange of genetic
material among the viruses is well known and such critical exchange highlights the risk and the
need to investigate the relations between seemingly unrelated virus families.
Conclusions
Our analysis of the spike glycoprotein of 2019-nCoV revealed several interesting findings: First,
we identified 4 unique inserts in the 2019-nCoV spike glycoprotein that are not present in any
other coronavirus reported till date. To our surprise, all the 4 inserts in the 2019-nCoV mapped to
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short segments of amino acids in the HIV-1 gp120 and Gag among all annotated virus proteins in
the NCBI database. This uncanny similarity of novel inserts in the 2019- nCoV spike protein to
HIV-1 gp120 and Gag is unlikely to be fortuitous. Further, 3D modelling suggests that atleast 3 of
the unique inserts which are non-contiguous in the primary protein sequence of the 2019-nCoV
spike glycoprotein converge to constitute the key components of the receptor binding site. Of note,
all the 4 inserts have pI values of around 10 that may facilitate virus-host interactions. Taken
together, our findings suggest unconventional evolution of 2019-nCoV that warrants further
investigation. Our work highlights novel evolutionary aspects of the 2019-nCoV and has
implications on the pathogenesis and diagnosis of this virus.
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Fig.S1 Multiple sequence alignment of glycoprotein of coronaviridae family, representing all the
four inserts.
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Fig.S2: All four inserts are present in the aligned 28 Wuhan 2019-nCoV virus genomes obtained
from GISAID. The gap in the Bat-SARS Like CoV in the last row shows that insert 1 and 4 is very
unique to Wuhan 2019-nCoV.
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Fig.S3 Phylogenetic tree of 28 clinical isolates genome of 2019-nCoV including one from bat as a host.
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Supplementary Fig 4. Genome alingment of Coronaviridae family. Highlighted black sequences are the
inserts represented here.
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... For example, there is no credible evidence that SARS-CoV-2 responsible for the COVID-19 pandemic has a bioengineered origin, but a series of preprints has pushed false narratives along these lines. One such paper, posted to bioRxiv (28), was quickly refuted by bioinformaticians and formally withdrawnbut in the interim, the paper received extensive media attention. If preprint servers try to vet the material, authors find other outlets. ...
... COVID-19 reporting is no exception (33,64). The withdrawn bioRxiv preprint mentioned previously was promoted so broadly that it garnered one of the highest Altmetric scores of all time (28). As another example, a Financial Times headline proclaimed "Coronavirus may have infected half of UK population-Oxford study," even though it was reporting on a preliminary white paper that neither showed nor attempted to show anything of the sort (65,66). ...
Humans learn about the world by collectively acquiring information, filtering it, and sharing what we know. Misinformation undermines this process. The repercussions are extensive. Without reliable and accurate sources of information, we cannot hope to halt climate change, make reasoned democratic decisions, or control a global pandemic. Most analyses of misinformation focus on popular and social media, but the scientific enterprise faces a parallel set of problems-from hype and hyperbole to publication bias and citation misdirection, predatory publishing, and filter bubbles. In this perspective, we highlight these parallels and discuss future research directions and interventions.
... However, the increase in publications usually associated with of quality issues, where proportions of such studies may also be falsified [3,4]. An example of such studies was a paper that suggested a link between coronavirus spike protein and HIV; the paper was among the most commonly discussed papers, despite being withdrawn by its authors [5]. Moreover, a previous study suggested that most studies registered in clinicaltrials.gov ...
Article
Background Meta-analysis of high-quality primary articles represents the top-quality evidence in medical literature. In this project, our aim was to assess the number and quality of COVID-related meta-analysis published since the beginning of the COVID-19 pandemic.Methods The search included the period from January 1, 2020, when the beginning of primary articles on COVID-19, till October 31, 2020. We screened a total of 793 studies. We excluded non-meta-analytic non-COVID-19-related studies. We obtained different characteristics, and we determined the quality of reporting using the AMSTAR tool, an 11-items tool that assesses the content validity and methodological quality of systematic reviews and meta-analysis.ResultsA total of 538 studies were included in our assessment. The first meta-analysis included was published in March, while the last one was on the 31st of October. Upon comparing the mean AMSTAR score for meta-analysis published during each month, we found a significant difference (p < 0.001, F = 4.139), where the mean score almost steadily increased since March.Conclusion The urge to publish during the COVID-19 period or any other surge in publishing should not be at the expense of quality.
... A preprint of the manuscript denoting that the 'COVID-19 as an engineered virus from china', was published in the international journal stated by Indian scientist team, which fed many conspiracy theories in people. The paper entitled 'Uncanny similarity of unique inserts in the 2019-nCoV spike protein to HIV-1 gp 120 and Gag', assented the similarities in the COVID-19 and HIV, unfortunately due to lack of peer-review was not much entertained 5 . However, its human instinct that they adapted in many critical situation, which we have facing from ancient time up to Black Death. ...
Article
A neglected disease originated from Wuhan (China) conquered all worlds with doubt and fear. The current outbreak of viral coronavirus disease (COVID-19) quaked the world with the anxiety of economic and healthcare disturbances. The risk of further spread compelled the World Health Organization (WHO) to declare it as a national emergency and other countries obligated the decision with the provincial lockdown. In the present review, we have discussed the various aspects of pandemic spreads, its historical context and the latest investigations demonstrating the current scenario of COVID-19 in the world. Besides, we have highlighted the various aspects regarding the COVID-19 like preparedness and necessary aspects which will help for risk assessment and crisis management. Rapid sharing of scientific information is an effective way to implement awareness and response. In this perspective, we are providing frontline facets that can be helpful for epidemiologists and research scholars for further assessment and real-time guidance.
... In the absence of reliable information campaigns, young adults may turn to the internet as a primary source of information about COVID-19 where there is little information quality control [41]. Scientific journals, media outlets and other respected sources of information were not immune to baseless claims during this pandemic, including conspiracy theories related to COVID-19 vaccine development and trials [42][43][44][45][46][47][48]. Perceptions of this media landscape and their associations with vaccine uptake are currently unknown among young people living in Switzerland in the context of the COVID-19 pandemic. ...
Article
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Objectives: Young adults are essential to the effective mitigation of the novel coronavirus (SARS-CoV-2/COVID-19) given their tendency toward greater frequency of social interactions. Little is known about vaccine willingness during pandemics in European populations. This study examined young people’s attitudes toward COVID-19 vaccines in Fall 2020. Methods: Data came from an ongoing longitudinal study’s online COVID-19-focused supplement among young adults aged 22 in Zurich, Switzerland ( N = 499) in September 2020. Logistic regressions examined young adults’ likelihood of participating in COVID-19 immunization programs. Results: Approximately half of respondents reported being unlikely to get vaccinated against COVID-19. Compared to males, females were more likely to oppose COVID-19 vaccination ( p < 0.05). In multivariate models, Sri Lankan maternal background and higher socioeconomic status were associated with a greater likelihood of getting vaccinated against COVID-19 ( p < 0.05). Respondents were more likely to report a willingness to get vaccinated against COVID-19 when they perceived 1) an effective government response ( p < 0.05) and 2) their information sources to be objective ( p < 0.05). Conclusion: This study communicates aspects important to the development of targeted information campaigns to promote engagement in COVID-19 immunization efforts.
... 11,12 Nevertheless, in early 2021, this paper was one of the most highly shared and cited articles on social and news media as measured by Altimetric, a data analytics service that tracks the online traffic of academic papers on social media and other websites. 13,14 Thus, despite not being a formal publishing house, pre-print servers have become an important and potentially problematic method of sharing scientific information, especially during a global pandemic in which information is needed rapidly. ...
Article
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The 2020 COVID-19 pandemic has produced an unprecedented amount of scientific research, with over 100,000 articles on the SARS-COV2 virus or the associated pandemic published within the first year. To effectively disseminate such a large volume of research, some academic journal publishers altered their review criteria, and many articles were made available before undergoing a traditional review process. However, with this rapid influx of information, multiple COVID-19 articles have been retracted or withdrawn. Some researchers have expressed concern that these retractions call into question the validity of an expedited review process and the overall quality of the larger body of COVID-19 research. We examined 68 removed articles and determined that many of the articles were removed for unknown reasons (n = 22) or as duplications (n = 12); 24 papers were retracted for more significant reasons (data integrity, plagiarism, reporting or analysis, and IRB or privacy issues). The majority of removed papers were from the USA (n = 23) and China (n = 19).
Preprint
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Releasing preprints is a popular way to hasten the speed of research but may carry hidden risks for public discourse. The COVID-19 pandemic caused by the novel SARS-CoV-2 infection highlighted the risk of rushing the publication of unvalidated findings, leading to damaging scientific miscommunication in the most extreme scenarios. Several high-profile preprints, later found to be deeply flawed, have indeed exacerbated widespread skepticism about the risks of the COVID-19 disease - at great cost to public health. Here, preprint article quality during the pandemic is examined by distinguishing papers related to COVID-19 from other research studies. Importantly, our analysis also investigated possible factors contributing to manuscript quality by assessing the relationship between preprint quality and gender balance in authorship within each research discipline. Using a comprehensive data set of preprint articles from medRxiv and bioRxiv from January to May 2020, we construct both a new index of manuscript quality including length, readability, and spelling correctness and a measure of gender mix among a manuscript's authors. We find that papers related to COVID-19 are less well-written than unrelated papers, but that this gap is significantly mitigated by teams with better gender balance, even when controlling for variation by research discipline. Beyond contributing to a systematic evaluation of scientific publishing and dissemination, our results have broader implications for gender and representation as the pandemic has led female researchers to bear more responsibility for childcare under lockdown, inducing additional stress and causing disproportionate harm to women in science.
Chapter
While technology advances, the applications of those technologies within the scientific publishing ecosystem have lagged. There has never been a greater time to increase the speed and accuracy of scientific reporting. Researchers are under immense pressure to conduct rigorous science, and the publishing industry continues to act as a facilitator. Yet, inefficiencies stall the speed and prohibit the consistency of communicating research. This chapter proposes automating quality checks as a means to scale science. The author also explores the publishing process and potential places to use machine learning and natural language processing to enhance the quality—and thus rigor—of reporting scientific research.
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This is the third part of a series of reports based on our previously unpublished investigations into the origins of SARS-COV-2. We wish to thank all of the independent researchers who have contributed to this investigation, especially members of the DRASTIC Collective, many of whom wish to remain anonymous for reasons of security and privacy (PDF) 3. WUHAN LABORATORIES, BAT RESEARCH AND BIOSAFETY.
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The beginning of the twenty-first century saw an apparent change in language in public discourses characterised by the rise of so-called “essentially oxymoronic concepts”, i.e., mainly oxymora and paradoxes. In earlier times, these rhetorical figures of speech were largely reserved for the domain of literature, the arts or mysticism. Today, however, many new technologies and other innovations are contributing to their rise also in the domains of science and of law. Particularly in law, their inherent contradictory quality of combining apparently antagonistic suppositions challenges the traditional dualistic mode of reasoning and binary logic. As reflected in terms like fake news, alternative facts or conspiracy theories, these concepts are seen as a threat to the rule of law and legal certainty and have been described as harbingers of an age of disinformation or post-truth. The challenge posed by these apparently contradictory concepts requires a closer look at the premises that guide our legal thinking and a more integrated theory of the senses and their role in law, as captured by the terms “legal synaesthesia” and “legal semiotics”. It also calls for an inquiry into the mind’s functioning generally and how it processes information in the creative process of decision making, linking thoughts and actions as well as facts and fictions. Based on the qualification of “fake news” as an oxymoron, this article critically examines the deficiencies in a dichotomous distinction between fact and fiction exemplified by information about the pandemic of coronavirus disease 2019 (Covid-19) in an attempt to clarify the principal issues for a global regulatory debate regarding “fake news”.
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A mysterious outbreak of atypical pneumonia in late 2019 was traced to a seafood wholesale market in Wuhan of China. Within a few weeks, a novel coronavirus tentatively named as 2019 novel coronavirus (2019-nCoV) was announced by the World Health Organization. We performed bioinformatics analysis on a virus genome from a patient with 2019-nCoV infection and compared it with other related coronavirus genomes. Overall, the genome of 2019-nCoV has 89% nucleotide identity with bat SARS-like-CoVZXC21 and 82% with that of human SARS-CoV. The phylogenetic trees of their orf1a/b, Spike, Envelope, Membrane and Nucleoprotein also clustered closely with those of the bat, civet and human SARS coronaviruses. However, the external subdomain of Spike’s receptor binding domain of 2019-nCoV shares only 40% amino acid identity with other SARS-related coronaviruses. Remarkably, its orf3b encodes a completely novel short protein. Furthermore, its new orf8 likely encodes a secreted protein with an alpha-helix, following with a beta-sheet(s) containing six strands. Learning from the roles of civet in SARS and camel in MERS, hunting for the animal source of 2019-nCoV and its more ancestral virus would be important for understanding the origin and evolution of this novel lineage B betacoronavirus. These findings provide the basis for starting further studies on the pathogenesis, and optimizing the design of diagnostic, antiviral and vaccination strategies for this emerging infection.
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In December 2019, a cluster of patients with pneumonia of unknown cause was linked to a seafood wholesale market in Wuhan, China. A previously unknown betacoronavirus was discovered through the use of unbiased sequencing in samples from patients with pneumonia. Human airway epithelial cells were used to isolate a novel coronavirus, named 2019-nCoV, which formed another clade within the subgenus sarbecovirus, Orthocoronavirinae subfamily. Different from both MERS-CoV and SARS-CoV, 2019-nCoV is the seventh member of the family of coronaviruses that infect humans. Enhanced surveillance and further investigation are ongoing. (Funded by the National Key Research and Development Program of China and the National Major Project for Control and Prevention of Infectious Disease in China.).
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Human coronavirus (CoV) HKU1 is a pathogen causing acute respiratory illnesses and so far little is known about its biology. HKU1 virus uses its S1 subunit C-terminal domain (CTD) and not the N-terminal domain like other lineage A b-CoVs to bind to its yet unknown human receptor. Here we present the crystal structure of HKU1 CTD at 1.9Å resolution. The structure consists of three subdomains: core, insertion and subdomain-1 (SD-1). While the structure of the core and SD-1 subdomains of HKU1 are highly similar to those of other b-CoVs, the insertion subdomain adopts a novel fold, which is largely invisible in the cryo-EM structure of the HKU1 S trimer. We identify five residues in the insertion subdomain that are critical for binding of neutralizing antibodies and two residues essential for receptor binding. Our study contributes to a better understanding of entry, immunity and evolution of CoV S proteins.
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The international sharing of virus data is critical for protecting populations against lethal infectious disease outbreaks. Scientists must rapidly share information to assess the nature of the threat and develop new medical countermeasures. Governments need the data to trace the extent of the outbreak, initiate public health responses, and coordinate access to medicines and vaccines. Recent outbreaks suggest, however, that the sharing of such data cannot be taken for granted – making the timely international exchange of virus data a vital global challenge. This article undertakes the first analysis of the Global Initiative on Sharing All Influenza Data as an innovative policy effort to promote the international sharing of genetic and associated influenza virus data. Based on more than 20 semi-structured interviews conducted with key informants in the international community, coupled with analysis of a wide range of primary and secondary sources, the article finds that the Global Initiative on Sharing All Influenza Data contributes to global health in at least five ways: (1) collating the most complete repository of high-quality influenza data in the world; (2) facilitating the rapid sharing of potentially pandemic virus information during recent outbreaks; (3) supporting the World Health Organization's biannual seasonal flu vaccine strain selection process; (4) developing informal mechanisms for conflict resolution around the sharing of virus data; and (5) building greater trust with several countries key to global pandemic preparedness.
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HKU1 is a human betacoronavirus that causes mild yet prevalent respiratory disease, and is related to the zoonotic SARS and MERS betacoronaviruses, which have high fatality rates and pandemic potential. Cell tropism and host range is determined in part by the coronavirus spike (S) protein, which binds cellular receptors and mediates membrane fusion. As the largest known class I fusion protein, its size and extensive glycosylation have hindered structural studies of the full ectodomain, thus preventing a molecular understanding of its function and limiting development of effective interventions. Here we present the 4.0 Å resolution structure of the trimeric HKU1 S protein determined using single-particle cryo-electron microscopy. In the pre-fusion conformation, the receptor-binding subunits, S1, rest above the fusion-mediating subunits, S2, preventing their conformational rearrangement. Surprisingly, the S1 C-terminal domains are interdigitated and form extensive quaternary interactions that occlude surfaces known in other coronaviruses to bind protein receptors. These features, along with the location of the two protease sites known to be important for coronavirus entry, provide a structural basis to support a model of membrane fusion mediated by progressive S protein destabilization through receptor binding and proteolytic cleavage. These studies should also serve as a foundation for the structure-based design of betacoronavirus vaccine immunogens.
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Protein structure homology modelling has become a routine technique to generate 3D models for proteins when experimental structures are not available. Fully automated servers such as SWISS-MODEL with user-friendly web interfaces generate reliable models without the need for complex software packages or downloading large databases. Here, we describe the latest version of the SWISS-MODEL expert system for protein structure modelling. The SWISS-MODEL template library provides annotation of quaternary structure and essential ligands and co-factors to allow for building of complete structural models, including their oligomeric structure. The improved SWISS-MODEL pipeline makes extensive use of model quality estimation for selection of the most suitable templates and provides estimates of the expected accuracy of the resulting models. The accuracy of the models generated by SWISS-MODEL is continuously evaluated by the CAMEO system. The new web site allows users to interactively search for templates, cluster them by sequence similarity, structurally compare alternative templates and select the ones to be used for model building. In cases where multiple alternative template structures are available for a protein of interest, a user-guided template selection step allows building models in different functional states. SWISS-MODEL is available at http://swissmodel.expasy.org/.
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Since the SARS outbreak 18 years ago, a large number of severe acute respiratory syndrome related coronaviruses (SARSr-CoV) have been discovered in their natural reservoir host, bats. Previous studies indicated that some of those bat SARSr-CoVs have the potential to infect humans. Here we report the identification and characterization of a novel coronavirus (nCoV-2019) which caused an epidemic of acute respiratory syndrome in humans, in Wuhan, China. The epidemic, started from December 12th, 2019, has caused 198 laboratory confirmed infections with three fatal cases by January 20th, 2020. Full-length genome sequences were obtained from five patients at the early stage of the outbreak. They are almost identical to each other and share 79.5% sequence identify to SARS-CoV. Furthermore, it was found that nCoV-2019 is 96% identical at the whole genome level to a bat coronavirus. The pairwise protein sequence analysis of seven conserved non-structural proteins show that this virus belongs to the species of SARSr-CoV. The nCoV-2019 virus was then isolated from the bronchoalveolar lavage fluid of a critically ill patient, which can be neutralized by sera from several patients. Importantly, we have confirmed that this novel CoV uses the same cell entry receptor, ACE2, as SARS-CoV.
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The molecular evolutionary genetics analysis (Mega) software implements many analytical methods and tools for phylogenomics and phylomedicine. Here, we report a transformation of Mega to enable cross-platform use on Microsoft Windows and Linux operating systems. Mega X does not require virtualization or emulation software and provides a uniform user experience across platforms. Mega X has additionally been upgraded to use multiple computing cores for many molecular evolutionary analyses. Mega X is available in two interfaces (graphical and command line) and can be downloaded from www.megasoftware.net free of charge.
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The coronavirus spike protein is a multifunctional molecular machine that mediates coronavirus entry into host cells. It first binds to a receptor on the host cell surface through its S1 subunit and then fuses viral and host membranes through its S2 subunit. Two domains in S1 from different coronaviruses recognize a variety of host receptors, leading to viral attachment. The spike protein exists in two structurally distinct conformations, prefusion and postfusion. The transition from prefusion to postfusion conformation of the spike protein must be triggered, leading to membrane fusion. This article reviews current knowledge about the structures and functions of coronavirus spike proteins, illustrating how the two S1 domains recognize different receptors and how the spike proteins are regulated to undergo conformational transitions. I further discuss the evolution of these two critical functions of coronavirus spike proteins, receptor recognition and membrane fusion, in the context of the corresponding functions from other viruses and host cells. Expected final online publication date for the Annual Review of Virology Volume 3 is September 29, 2016. Please see http://www.annualreviews.org/catalog/pubdates.aspx for revised estimates.
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The source of the severe acute respiratory syndrome (SARS) epidemic was traced to wildlife market civets and ultimately to bats. Subsequent hunting for novel coronaviruses (CoVs) led to the discovery of two additional human and over 40 animal CoVs, including the prototype lineage C betacoronaviruses, Tylonycteris bat CoV HKU4 and Pipistrellus bat CoV HKU5; these are phylogenetically closely related to the Middle East respiratory syndrome (MERS) CoV, which has affected more than 1,000 patients with over 35% fatality since its emergence in 2012. All primary cases of MERS are epidemiologically linked to the Middle East. Some of these patients had contacted camels which shed virus and/or had positive serology. Most secondary cases are related to health care-associated clusters. The disease is especially severe in elderly men with comorbidities. Clinical severity may be related to MERS-CoV's ability to infect a broad range of cells with DPP4 expression, evade the host innate immune response, and induce cytokine dysregulation. Reverse transcription-PCR on respiratory and/or extrapulmonary specimens rapidly establishes diagnosis. Supportive treatment with extracorporeal membrane oxygenation and dialysis is often required in patients with organ failure. Antivirals with potent in vitro activities include neutralizing monoclonal antibodies, antiviral peptides, interferons, mycophenolic acid, and lopinavir. They should be evaluated in suitable animal models before clinical trials. Developing an effective camel MERS-CoV vaccine and implementing appropriate infection control measures may control the continuing epidemic.