New Coronavirus 2 (SARS-CoV-2) Detection Method from Human Nucleic Acid Sequences Using Capsule Networks

Das, Bihter; Toraman, Suat

doi:10.1590/1678-4324-2023220316

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Article - Human and Animal Health • Braz. arch. biol. technol. 66 • 2023 • https://doi.org/10.1590/1678-4324-2023220316 copy

New Coronavirus 2 (SARS-CoV-2) Detection Method from Human Nucleic Acid Sequences Using Capsule Networks

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

The new coronavirus SARS-CoV-2 is an infectious virus with a long incubation period, which was first detected in Wuhan, China, spread all over the world, seriously threatening human life. Therefore, accurate and rapid detection of SARS-CoV-2 is very important for controlling the epidemic and preventing its further spread. Currently, nucleic acid detection makes an important contribution to the prevention and control of SARS-CoV-2. In this study, a new and highly sensitive nucleic acid detection method for SARS-CoV-2 has been proposed. The nucleic acid sequences were digitized by Entropy-based mapping technique. Then, the digitized these sequences were divided into 100-unit sections using the sliding window method and given as input to Capsule Networks.10988 segments (5494 SARS-CoV-2, 5494 normal) are classified with capsule nets. With the proposed method, an accuracy performance of 100% was achieved by using capsule networks to identify SARS-CoV-2 from nucleic acid sequences. The results show that the proposed method successfully identifies SARS-CoV-2 from nucleic acid sequences.

Keywords:
SARS-CoV-2; Covid-19; Nucleic acid detection; Capsule networks; Coronavirus

HIGHLIGHTS

• DNA genome sequences of 10 different races are compared.

• Covid-19 nucleic acid sequences are digitized by Entropy based mapping technique.

• The digitized Covid-19 nucleic acid sequences are classified by the capsule networks.

Accession	Race	Accession	Race
SARS-CoV-2 Group		Healthy Group
NC_045512.2	China	NM_001300741.2	China
LC594644.1	Japan	NM_001387088.1	Japan
MW364964.1	Chile	NR_109888.1	Chile
MW482885.1	USA	AJWY01002716.1	USA
MT994989	Egypt	ABCB02000016.1	Egypt
MT994632.1	Iran	AJWY01006830.1	Iran
MT820485.1	Saudi Arabia	BA000015.5	Saudi Arabia
MT233521.1	Spain: Valencia	NG_013248.1	Spain: Valencia
MT253696.1	China: Zhejiang	NC_000002.12	China: Zhejiang
MT240479.1	Pakistan: Gilgit	NR_144759.2	Pakistan: Gilgit

Layers	Filter	Kernel size	Stride	Output
Input	-	-	-	200,1
Conv1D	16	7	1	200,16
Maxpooling1D	-	-	2	100,16
Conv1D	32	5	1	100,32
Maxpooling1D			2	50,32
Conv1D	64	9	1	50,64
Primary capsule	256	9	1	50,256
Label capsule	-	-	-	2,16
Output	-	-	-	2

Routing	Optimizer	lr	Loss weight	Epoch	Batch size	Time (s) (per epoch)
3	Adam	0.001	0.392	10	32	27

Fold	Accuracy (%)	Precision (%)	Sensitivity (%)	Specificity (%)	F1-score (%)
1	94.96	90.92	99.90	90.03	95.20
2	98.40	97.60	99.24	97.56	98.41
3	96.84	98.64	94.98	98.69	96.78
4	96.96	94.90	99.24	94.67	97.02
5	97.88	97.48	98.31	97.45	97.89
Mean ± SD	97.01 ± 1.18	95.91 ± 2.78	98.34 ± 1.75	95.68 ± 3.12	97.06 ± 1.10

Fold	Accuracy (%)	Precision (%)	Sensitivity (%)	Specificity (%)	F1-score (%)
1	100.00	100.00	100.00	100.00	100.00
2	100.00	100.00	100.00	100.00	100.00
3	100.00	100.00	100.00	100.00	100.00
4	99.93	100.00	99.86	100.00	99.93
5	99.83	100.00	99.65	100.00	99.83
Mean ± SD	99.95 ± 0.07	100.00 ± 0.00	99.90 ± 0.14	100.00 ± 0.00	99.95 ± 0.07

Fold	Accuracy (%)	Precision (%)	Sensitivity (%)	Specificity (%)	F1-score (%)
1	100.00	100.00	100.00	100.00	100.00
2	100.00	100.00	100.00	100.00	100.00
3	100.00	100.00	100.00	100.00	100.00
4	100.00	100.00	100.00	100.00	100.00
5	100.00	100.00	100.00	100.00	100.00
Mean ± SD	100.00 ± 0.00	100.00 ± 0.00	100.00 ± 0.00	100.00 ± 0.00	100.00 ± 0.00

Authors	Methods	Dataset	Results (Accuracy)
Uhlenhaut [¹⁰10 Uhlenhaut C, Cohen JI, Pavletic S, Illei G, Banacloche JCG, Asab MA, et al. Use of a Novel Virus Detection Assay to Identify Coronavirus HKU1 in the Lungs of a Hematopoietic Stem Cell Transplant Recipient with Fatal Pneumonia. Transpl. Infect. Dis. 2012 Jul; 14:79-85.]	PCR-based method	Lung cellular DNA	-
Guo et al. [¹⁶16 Guo X, Geng P, Wang Q, Cao B, Liu B. Development of a Single Nucleotide Poly-morphism DNA Microarray for the Detection and Genotyping of the SARS coronavirus. J. Microbiol. Biotechnol. 2014 Oct;24(10):1445-54.]	Microarray-based method	19 cDNAs	100%
Mani et al. [²²22 Mani K, Thirumalmuthu K, Kathiresan D S, Ramalingam S, Sankaran R, Jeyaraj S. In-silico Analysis of Covid-19 Genome Sequences of Indian Origin: Impact of Mutations in Identification of SARS-Co-V2. Molecular and Cellular Probes. 2021 Aug; 58:101748.]	Silico bioinformatics analysis approach	Indian genome sequences	>98.3%
Arslan et al. [²³23 Arslan H, Arslan H. A New COVID-19 Detection Method from Human Genome Sequences Using CpG Island Features and KNN Classifier. Eng. Sci. Technol. Int. J. 2021 Apr; 24(4):839-47.]	A new method based on KNN	CpG island	98.4%
The proposed method	Capsule networks	SARS-CoV-2 DNA sequences	100%

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[1] Editor-in-Chief: Paulo Vitor Farago