INTRODUCTION:

SARS-CoV-2, industrial and laboratory

Currently, there are two concepts about origin and source of the novel coronavirus, whether a completely natural virus, or it is a synthetic virus designed as a biological weapon or for other purposes. The two terms are diversified and merged. One hypothesis is that SARS-CoV-2 was originally a virus and then was manipulated. If this hypothesis is right, scientifically and laboratory it is obviously not proved ^{1, 2}.

The synthetic virus and genetic alteration, on the other hand, are not the only ways people can alter the developmental pathway of their viruses. SARS-CoV-2 may be of the wild type and it has undergone spontaneous genetic variation after administration or implantation in laboratory animals or in tissue culture. This may be human intervention or manipulation but it is not a synthesis nor a process of genetic engineering^3,4. This is illustrated by genetic variations in the SARS-CoV outbreak in 2003 and genomic alterations in MERS-CoV in 2018⁵.

Literally, synthetic virus means that it is completely made, but there is variations on the terms such as partially synthesized, mutant, hybrid, or recombinant which are pre-planned and artificial. Furthermore, evolutionary processes leading to similar viruses occur spontaneously in viruses due to human induced through biotechnology assays^6,7.

There are two very important scientific observations in this area. One of them is humans not yet smart enough to produce a complex virus like SARSCoV-2, which means it may have evolved inside a laboratory animal or tissue culture ⁸. The other is that some components and proteins of the virus induced an immune response by the host, which means that it cannot be formed only within the tissue culture. In this reason, implicit in nature or in a laboratory, is that the virus occurs in an animal ^{9, 10}.

One possibility is that the wild type virus first spread repeatedly in human tissue cultures, then the resulting virus was subsequently used to experimentally infect monkeys or rodents, one of which had accidentally infected a person in the laboratory ¹¹. This resulted when rhesus monkeys from the Macaque reproduction base at Suizhou were regularly given for the laboratory ¹².

It is also possible that the wild-type strain has adapted to a human through an entirely natural genetic process that has not yet been determined, and that it infected a person as a result of normal contagion. The possibility of such a completely specific adaptive genetic transformation has been questioned in nature, although various scientific analyzes rely on it.^13,14

There is also another possibility to isolate a wild-type virus but the viral genome sequence has yet to be detected. The point is that the current genomic data related to coronaviruses is insufficient to determine whether comparative analyzes of genetic evolution between a pandemic virus and other related coronavirus family as a result of a natural evolutionary process or a man-made technique ¹⁵.

SARS-CoV-2, politically and intelligence:

In Wuhan, China, last October, the first outbreak emerged. However, the local health committee in the city did not issue an alert of viral pneumonia cases until December 31, 2019, which puts a sign of astonishment. At the time, it was said that the source of the virus was an unidentified infected animal from the wet market of Wuhan after which this claim was abandoned by the government. If whether the virus is natural, modified or synthetic, the alternative possibility here is that the virus may leaked from a laboratory at the Wuhan Institute of Virology (WIV) via an infected worker, a technical malfunction, or an infected laboratory animal ^{16, 17}.

On 2nd February, a US Prof. Francis Boyle claimed that the virus had been stored in the Wuhan laboratory as a biological weapon and had been leaked from the laboratory. On February 17th, Senator Tom Cotton massed the laboratory virus leak theory. This theory was rejected as no concrete evidence was provided ¹⁸.

Subsequently, nine US intelligence and national security officials’ familiar with the ongoing investigation stated that the possibility that the epidemic originated from an accident at a research facility in Wuhan was under scrutiny. Several weeks later, President Trump indicated that the outbreak emanated from WIV and added that he could not reveal details. As for US Secretary of State Mike Pompeo, he stated that there is a great deal of evidence that the virus came from that laboratory in Wuhan. He said that the intelligence community is still figuring out exactly where this virus started. He also noted that he has no reason to suspect that the virus is not synthetic or genetically modified ¹⁹.

One point of view of the US intelligence is that the Virus actually originated in the Wuhan laboratory but not as a biological weapon, but as part of China's attempts to show that it is similar to that in the United States to detect and fight viruses ²⁰.

Then, Assistant to the US President Peter Navarro stated that the virus appeared in the P4 Weapons Laboratory (WIV) by infecting a worker called Ground Zero because he was yards from the laboratory. He was also believed that the Chinese were the ones who generated the virus, not the one who made it, as it was reported that this virus is a product of the Chinese Communist Party. Navarro added that it is China's responsibility to provide evidence that the viral infection is normal and since China has failed to do so, the infection is considered abnormal ²¹.

In fact. The role of the laboratory and the wet market in the initial outbreak has yet to be explained. One possibility is the illicit selling on the market of the contaminated animals from the laboratory. This fits with Navarro's description of the patient (Zero), who was infected before it spread in the market ²².

Colonel Kemp, British researcher, said someone had told him that there was a very high risk of an unintended release of the virus from the Wuhan laboratory. The colonel added that it was also possible that the virus came from an animal that participated in testing at WIV, and ended up in the wet market where it was then believed that an employee sold it in the market for a personal profit without considering that it might be infected. But this story cannot be supported by any evidence. This report was not confirmed and was not rejected ⁴.

On April 30th, Australian Prime Minister Scott Morrison refused to believe the laboratory theory, indicating that he had not noticed anything definitively indicating this and said that The Wuhan wet market virus is more likely to appear ¹⁸.

From a scientific or legal point of view, it is certain that the evidence obtained by intelligence systems may be correct and actually occurs, but in essence, intelligence analysis depends on tracking and the inferential recognition of relevant evidence, even if it is circumstantial. For example, an assessment of intelligence that is always appropriate in any analytical context that relies on deduction may ultimately reach the point where the evidence allows for a solid factual conclusion, even if it is circumstantial. These ratings are valid due to their reasonableness within the available field. This approach is not necessary because of geographical conditions and constraints of the COVID-19 root of the pandemic ²⁴.

Another hypothesis that may be important can be adopted is that the original strain of the virus infected six miners in Mojiang in Yunnan state, in 2012. It is estimated that three of the six infected miners were slain by the virus in the breeding ground of infected bats ².

According to Latham and Wilson's critical genetic hypothesis: An adaptive mutation occurred that underwent the virus while infecting miners. This transformation could have continued during the investigation of the isolated virus in the Wuhan laboratory, before the initial outbreak or during infected patient zero. This situation illustrates the hypothesis of laboratory leakage whether or not SARS-CoV-2 has grown in part of the laboratory. ¹⁵

A sequence of well-planned experiments would better explain animal reservoirs and how people are transmitted. This process is an evolving effort that may lead to more international scientific research and cooperation at the global level ¹⁶.

Two of its experts were initially sent into China by the WHO. The Executive Director of the Health Emergency Service, Mike Ryan, reported it is a matter of research, integrated strategy, a lot of commitment and a lot of hard work to find the true cause of the virus ¹.

The question remains open whether the virus was intentionally introduced in the Chinese laboratory or not. On July 7, the World Health Organization stated that the origin and source of the novel Coronavirus is still an enigma, and it needs to explain. It is hoped that work cooperation will be able to gain access to all private information about the origin and the source of COVID-19 ²⁵.

MATERIALS AND METHODS:

Structural differences between coronavirus family and HIV:

In the current study, we compared 29 complete genomes of different related coronavirus including novel SARS-CoV-2, SARS-CoV, MERS-CoV and HIV taken from NCBI data. Table 1 illustrates description of the different genomes. The complete sequence alignment performed using CLUSTAL-OMEGA and ViPR and MAFFT server tools. The comparison between sequences was presented using BLAST. The phylogenetic tree was extracted using ViPR tool.

Table 1: Complete genomes of different related coronaviruses and HIV extracted from NCBI.

Type	GenBank	Virus name	Release
SARS-CoV-2	MT642416.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/WA-S985/2020, complete genome	19-JUN-2020
	MT642375.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/WA-S990/2020, complete genome	19-JUN-2020
	MT633016.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/WA-S524/2020, complete genome	17-JUN-2020
	MT470142.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/France/10009EE/2020, complete genome	14-MAY-2020
	MT121215.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/CHN/SH01/2020, complete genome	06-APR-2020
	MT019531.1	Severe acute respiratory syndrome coronavirus 2 isolate BetaCoV/Wuhan/IPBCAMS-WH-03/2019, complete genome	11-FEB-2020
	MT371050.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/LKA/COV486/2020, complete genome	23-APR-2020
	MT956917.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/ESP/HUD-79876568/2020, complete genome	03-SEP-2020
	MT385425.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/USA/CA-CZB046/2020, complete genome	21-MAY-2020
	MT365029.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/HKG/HKU-911a/2020, complete genome	05-MAY-2020
	MT835026.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/BRA/RJ-DCVN2/2020, complete genome	04-AUG-2020
	MT731746.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/howo sapiens/MAR/RMPS05/2020, complete genome	08-JUL-2020
	MT358641.1	Severe acute respiratory syndrome coronavirus 2 isolate SARS-CoV-2/human/DEU/FFM5/2020, complete genome	14-MAY-2020
SARS-CoV	JN854286.1	SARS coronavirus HKU-39849 isolate recSARS-CoV HKU-39849, complete genome	23-MAY-2012
	JQ316196.1	SARS coronavirus HKU-39849 isolate UOB, complete genome	20-MAR-2012
	GU553365.1	SARS coronavirus HKU-39849 isolate TCVSP-HARROD-00003, complete genome	08-FEB-2010
	AY313906.1	SARS coronavirus GD69, complete genome	28-FEB-2005
	AY323977.2	SARS coronavirus HSR 1, complete genome	18-MAR-2004
MERS-CoV	MG470650.1	Middle East respiratory syndrome-related coronavirus isolate 2362 genomic sequence	26-SEP-2018
	MT387202.1	Middle East respiratory syndrome-related coronavirus isolate KNIH_002, complete genome	25-MAY-2020
	KX034094.1	Middle East respiratory syndrome coronavirus isolate MERS-CoV/KOR/Seoul/050-1-2015, complete genome	08-MAY-2016
	KT868867.1	Middle East respiratory syndrome coronavirus isolate MERS-CoV/KOR/CNUH_SNU/024_06_2015, partial genome	09-MAR-2016
	KT368871.1	Middle East respiratory syndrome coronavirus isolate camel/Riyadh/Ry162/2015, complete genome	17-DEC-2015
	KT368826.1	Middle East respiratory syndrome coronavirus isolate camel/Riyadh/Ry84N/2014, complete genome	17-DEC-2015
HIV	JX245015.1	Human immunodeficiency virus isolate 11Gab6352, complete genome	26-JUN-2013
	KF859743.1	HIV-1 isolate DEOXXES001 from Spain/complete genome	18-DEC-2013
	KU168295.1	HIV-1 isolate LA52YBF39 from Cameroon, complete genome	15-JAN-2016
	AY169805.1	HIV-1 isolate 97US08692A from USA, complete genome	26-JUL-2016
	FJ424866.1	Simian immunodeficiency virus clone pBR-CP2139.287, complete genome	24-JUL-2016

RESULTS

Complete sequence alignment was performed for 13 SARS-CoV-2 genomes using BLAST –NCBI, CLUSTAL-OMEGA and ViPR server tools. The similar identity shows in fig. 1. The closest similarity between the SARS-CoV-2 genomes approximately (99.98%) according to the sequence alignment analysis. The full alignment genomes are performed in Blast sequence from NCBI, fig. 2. MAFFT server considers similarities sequence in forward strands. Comparison similarity plots between the first sequence (MT642416.1) and related coronaviruses observed in fig. 3.

Figure 1: Partial sequence alignment of 13 complete genomes of SARS-CoV-2. The percentage of similarity between sequences as follows: 100%,100%,100%,99.98%,99.98%,99.98%,99.97%,99.97%,99.98%,99.96%, 99.97%, 99.97%, and 99.98% respectively.

Figure 2: Full similarity genomes of SARS-CoV-2 distributed from Blast sequences in NCBI.

Figure 3: High similarity plots between the (MT642416.1) and (MT642375.1, MT633016.1, MT121215.1, MT470142.1, MT371050.1, MT956917.1, MT385425.1, MT365029.1, MT731746.1, MT358641.1, and MT835026.1).

One complete genome of SARS-CoV-2 compared with 5 genomes of SARS-CoV alignment. The identity results shows in fig. 4. Distribution Blast of 6 subject sequences seems to be closer between them, fig. 5.

Figure 4: Partial sequence alignment between SARS-CoV-2 (MT642416.1) and 5 complete genomes of SARS-CoV. The similarity is: 100%, 79.79%, 79.71%, 79.74%, 79.79%, and 79.78% respectively.

Figure 5: Full genome distributed in 6 Blast sequences. : The region of different nucleotide sequences from the first chain (MT642416.1).

One complete genome of SARS-CoV-2 compared with 6 genomes of MERS-CoV alignment. The identity results shows in fig. 6.

Figure 6: Partial sequence alignment between SARS-CoV-2 (MT642416.1) and 6 complete genomes of MERS-CoV. The similarity is: 100%, 54.78%, 54.81%, 54.80%, 54.83%, 54.79%, and 54.78% respectively.

One complete genome of SARS-CoV-2 compared with 5 genomes of HIV alignment. The identity results shows in fig. 7.

Figure 7: Partial sequence alignment between SARS-CoV-2 (MT642416.1) and 5 complete genomes of HIV. The similarity is: 100%, 44.74%, 54.28%, 44.54%, 43.13%, and 44.98% respectively.

The phylogenetic tree for all genomes under study was extracted using ViPR server, fig. 8.

Figure 8: Phylogenetic tree of 30 complete genomes under study.

DISCUSSION:

The entire 29 complete genomes of the viruses under analysis were randomly selected from the USA, France, China, Spain, Hong Kong, Sri Lanka, Brazil, Morocco, and Germany, Table 1.

By analyzing the whole genome of 13 SARS-CoV-2 complete genomes, it became clear that there is a high percentage match between them, reached up to 99.98%, fig. 1. Through the general distribution of the sequences, by means of a BLAST showing the complete compatibility, fig. 2. It can be Note that also through the comparison graphs between one genome with other related sequences observed continuous red line in all graphs with the same degree, fig. 3. The small difference between genome sequences is considered as weak mutations occur even at the present time. This phenomena confirms that the virus is mutable, in different proportions at undetermined times.

SARS-CoV-2 (MT642416.1) was selected for comparison with 5 SARS-CoV genomes, fig. 4. The average similarity ratio was approximately 79.76%. This difference gives evidence of a continuous mutation of the genome since the emergence of SARS-CoV in 2003. This result is consistent with most of the studies used in this aspect, including our previous study, which found that the similarity rate reaches 80%. Through the genomic distribution, the differences between the chains can be observed through the presence of spaces that represent the change of nitrogen bases in those regions, fig. 5.

A 6 MERS-CoV complete sequences were selected for comparison with the SARS-CoV-2 (MT642416.1). There are significant differences between genomes observed, reaching approximately 54.80%. The findings are not unexpected either and are compatible with previous research, fig. 6.

Shortly after the COVID-19 epidemic, there was a rumor that the novel virus had a structure identical to the HIV virus. We analyzed 5 complete sequences of the HIVs and compared with the MT642416.1. The similarity ratio reached approximately 46.33%, fig. 7. This indicates that there is a great difference between the two species, although the complete genome of HIV reaches (9500bps) ²⁶, while the complete genome of the coronavirus reaches about 30,000bps ^{27, 28}.

The phylogenetic tree analysis for all genomes under study is observed a clear difference between species, fig. 8.

CONCLUSIONS:

By matching the entire genome of the novel virus species related to the same family, it becomes clear that there is a similarity between sequences in different proportions according to the type. It is not possible for the SARS-CoV-2 to be related to HIV through mutation, manipulation, or laboratory artificial. It is certain and without doubt that the new virus was the result of various continuous mutations that occurred for different strains of SARS-CoV, which may have occurred in the host animal, then transmitted to humans. Another possibility that it was a laboratory mutation occurred in the Wuhan laboratory and led to the outbreak of the epidemic, deliberately or accidentally, and this will be determined later.

ACKNOWLEDGMENTS:

The authors thank University of Mosul for documenting this work.

CONFLICT OF INTEREST:

The authors declare no conflict of interest of this article.

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Received on 18.10.2021 Modified on 05.01.2022

Research J. Science and Tech. 2022; 14(1):21-29.

DOI: 10.52711/2349-2988.2022.00003