Dominance of the ON1 Genotype of RSV-A and BA9 Genotype of RSV-B in Respiratory Cases from Jeddah, Saudi Arabia
Abstract
:1. Introduction
2. Materials and Methods
2.1. Inclusion and Exclusion Criteria
2.2. Sample Collection
2.3. Molecular Detection of Respiratory Viruses
2.4. Virus Isolation
2.5. Whole Genome Sequencing and Typing of RSV
3. Results
3.1. The Characterization and Prevalence of RSV in Respiratory Samples
3.2. Phylogenetic Analysis of RSV
3.3. Amino Acid Sequence Analysis of the G Gene
3.4. N- and O-Glycosylation Site Analysis in Amino Acid Sequence
3.5. Full Genome Sequence
4. Discussions
5. Conclusions
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Frequency N (%) | ||
---|---|---|
Age | <1 year | 60 (71.4) |
1–7 years | 9 (10.7) | |
>7 years | 15 (17.9) | |
Gender | F | 36 (42.9) |
M | 48 (57.1) | |
Month | January 17 | 7 (8.3) |
March 17 | 2 (2.4) | |
September 17 | 2 (2.4) | |
October 17 | 2 (2.4) | |
November 17 | 28 (33.3) | |
December 17 | 43 (51.2) | |
Ward | ER | 57 (67.9) |
ISO | 3 (3.6) | |
MIC | 1 (1.2) | |
PICU | 23 (27.4) |
Sequence Name | Position Site | ON1 Nucleotide | Variant Nucleotide | Amino Acid Change | Codon Change | Protein Effect |
---|---|---|---|---|---|---|
JN257694-Canada-2011 | 910 | U | C | Y to H | UAU to CAU | Substitution |
653 | M | A | X to Q | CMA to CAA | Substitution | |
908 | U | C | V to A | GUC to GCC | Substitution | |
704 | C | T | T to I | ACC to ATC | Substitution | |
958 | A | G | T to A | ACA to GCA | Substitution | |
617 | C | A | P to Q | CCA to CAA | Substitution | |
821 | U | C | L to P | CUA to CCA | Substitution | |
893 | U | C | L to P | CUA to CCA | Substitution | |
929 | U | C | L to P | CUA to CCA | Substitution | |
941 | U | C | L to P | CUA to CCA | Substitution | |
742 | C | A | L to I | CUC to AUC | Substitution | |
401 | A | T | K to I | AAA to ATA | Substitution | |
728 | U | G | I to S | AUC to AGC | Substitution | |
784 | G | A | E to K | GAG to AAG | Substitution | |
69 | G | A | CUG to CUA | None | ||
369 | G | A | GAG to GAA | None | ||
717 | U | C | ACU to ACC | None | ||
840 | U | C | UAU to UAC | None | ||
945 | U | C | UCU to UCC | None |
Sequence Name | Position Site | BA Nucleotide | Variant Nucleotide | Amino Acid Change | Codon Change | Protein Effect |
---|---|---|---|---|---|---|
AY333364-Argentina-1999 | 30 | G | A | AAG to AAA | None | |
177 | C | T | CUC to CUT | None | ||
276 | C | A | AUC to AUA | None | ||
283 | U | C | Y to H | UAC to CAC | Substitution | |
286 | C | T | L to F | CUU to TUU | Substitution | |
329 | U | C | L to P | CUC to CCC | Substitution | |
334 | A | G | T to A | ACC to GCC | Substitution | |
339 | A | G | ACA to ACG | None | ||
349 | U | C | Y to H | UAC to CAC | Substitution | |
375 | U | C | CCU to CCC | None | ||
422 | G | C | R to T | AGA to ACA | Substitution | |
427 | AC | TCT | T to S | ACC to TCT | Substitution | |
490 | CCAAAA | PK to no Amino Acid | CCA, AAA to no codon | Deletion | ||
525 | C | T | UUC to UUT | None | ||
591 | U | C | AAU to AAC | None | ||
612 | C | T | ACC to ACT | None | ||
614 | U | C | I to T | AUA to ACA | Substitution | |
636 | C | T | CCC to CCT | None | ||
663 | A | C | CCA to CCC | None | ||
668 | A | C | K to T | AAA to ACA | Substitution | |
671 | U | C | L to P | CUA to CCA | Substitution | |
683 | U | C | L to P | CUG to CCG | Substitution | |
695 | C | A | T to N | ACC to AAC | Substitution | |
702 | C | T | AUC to AUT | None | ||
732 | C | T | ACC to ACT | None | ||
754 | U | C | S to P | UCA to CCA | Substitution | |
776 | C | T | T to I | ACA to ATA | Substitution | |
824 | C | T | T to I | ACU to ATU | Substitution | |
827 | U | C | V to A | GUG to GCG | Substitution | |
831 | C | T | CUC to CUT | None | ||
857 | U | C | I to T | AUC to ACC | Substitution | |
870 | C | T | UCC to UCT | None | ||
874 | C | T | H to Y | CAC to TAC | Substitution | |
927 | C | T | UCC to UCT | None | ||
948 | C | T | UCC to UCT | None | ||
952 | C | T | Truncation | |||
955 | AAA | CTC | K to L | AAA to CTC | Substitution | |
956 | AA | CT | K to T | AAA to ACT | Substitution | |
959 | UC | AG | L to Q | CUC to CAG | Substitution | |
959 | UC | CA | L to P | CUC to CCA | Substitution | |
961 | UAG | GTC | Extension | |||
962 | AG | CA | Extension | |||
964 | U | A | ||||
965 | C | A | ||||
965 | C | T | ||||
966 | AU | TG | ||||
968 | A | C | ||||
968 | A | G | ||||
969 | U | C | ||||
970 | G | T | ||||
971 | C | A | ||||
971 | C | T | ||||
972 | U | A | ||||
972 | U | G | ||||
973 | U | G | ||||
974 | A | T | ||||
975 | G | A | ||||
975 | G | T | ||||
976 | U | A | ||||
978 | A | T | ||||
979 | UUC | AAA |
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A. Al-Sharif, H.; El-Kafrawy, S.A.; Yousef, J.M.; Kumosani, T.A.; Kamal, M.A.; Khathlan, N.A.; Kaki, R.M.; Alnajjar, A.A.; Azhar, E.I. Dominance of the ON1 Genotype of RSV-A and BA9 Genotype of RSV-B in Respiratory Cases from Jeddah, Saudi Arabia. Genes 2020, 11, 1323. https://doi.org/10.3390/genes11111323
A. Al-Sharif H, El-Kafrawy SA, Yousef JM, Kumosani TA, Kamal MA, Khathlan NA, Kaki RM, Alnajjar AA, Azhar EI. Dominance of the ON1 Genotype of RSV-A and BA9 Genotype of RSV-B in Respiratory Cases from Jeddah, Saudi Arabia. Genes. 2020; 11(11):1323. https://doi.org/10.3390/genes11111323
Chicago/Turabian StyleA. Al-Sharif, Hessa, Sherif A. El-Kafrawy, Jehad M. Yousef, Taha A. Kumosani, Mohammad A. Kamal, Norah A. Khathlan, Reham M. Kaki, Abeer A. Alnajjar, and Esam I. Azhar. 2020. "Dominance of the ON1 Genotype of RSV-A and BA9 Genotype of RSV-B in Respiratory Cases from Jeddah, Saudi Arabia" Genes 11, no. 11: 1323. https://doi.org/10.3390/genes11111323