References
Ahlawat, S., Sharma, R., Maitra, A., Roy, M., & Tantia, M. S. (2014).
Designing, optimization and validation of tetra-primer ARMS PCR protocol
for genotyping mutations in caprine Fec genes. Meta Gene ,2 , 439–449. https://doi.org/10.1016/j.mgene.2014.05.004
Alam, A. S. M. R. U., Islam, M. R., Rahman, M. S., Islam, O. K., &
Hossain, M. A. (2020). Understanding the possible origin and genotyping
of the first Bangladeshi SARS-CoV-2 strain. Journal of Medical
Virology , Epub ahead of print. https://doi.org/10.1002/jmv.26115
Alam, A. S. M. R. U., Islam, O. K., Hasan, M. S., Al‐Emran, H. M.,
Jahid, M. I. K., & Hossain, M. A. (2020). Evolving Infection
Paradox of SARS-CoV-2: Fitness Costs Virulence?https://doi.org/10.31219/OSF.IO/Y36VE (preprint)
Brister, H., Barnum, S. M., Reedy, S., Chambers, T. M., & Pusterla, N.
(2019). Validation of two multiplex real-time PCR assays based on single
nucleotide polymorphisms of the HA1 gene of equine influenza A virus in
order to differentiate between clade 1 and clade 2 Florida sublineage
isolates. Journal of Veterinary Diagnostic Investigation ,31 (1), 137–141. https://doi.org/10.1177/1040638718822693
Brufsky, A. (2020). Distinct viral clades of SARS-CoV-2: Implications
for modeling of viral spread. Journal of Medical Virology , Vol.
92, pp. 1386–1390. https://doi.org/10.1002/jmv.25902
Chellapandi, P., & Saranya, S. (2020). Genomics insights of SARS-CoV-2
(COVID-19) into target-based drug discovery. Medicinal Chemistry
Research , Vol. 29, pp. 1777–1791.
https://doi.org/10.1007/s00044-020-02610-8
Chulakasian, S., Lee, M. S., Wang, C. Y., Chiou, S. S., Lin, K. H., Lin,
F. Y., … Hsu, W. L. (2010). Multiplex Amplification Refractory
Mutation System Polymerase Chain Reaction (ARMS-PCR) for diagnosis of
natural infection with canine distemper virus. Virology Journal ,7 (1), 122. https://doi.org/10.1186/1743-422X-7-122
Dong, E., Du, H., & Gardner, L. (2020). An interactive web-based
dashboard to track COVID-19 in real time. The Lancet Infectious
Diseases , Vol. 20, pp. 533–534.
https://doi.org/10.1016/S1473-3099(20)30120-1
Edwards, M. C., & Gibbs, R. A. (1994). Multiplex PCR: Advantages,
development, and applications. Genome Research , 3 (4).
https://doi.org/10.1101/gr.3.4.S65
El-Metwally, S., Hamza, T., Zakaria, M., & Helmy, M. (2013).
Next-Generation Sequence Assembly: Four Stages of Data Processing and
Computational Challenges. PLoS Computational Biology , Vol. 9.
https://doi.org/10.1371/journal.pcbi.1003345
Islam, M. R., Hoque, M. N., Rahman, M. S., Alam, A. S. M. R. U., Akther,
M., Puspo, J. A., … Hossain, M. A. (2020). Genome-wide analysis
of SARS-CoV-2 virus strains circulating worldwide
implicates heterogeneity. Scientific Reports , 10 (1).
https://doi.org/10.1038/s41598-020-70812-6
Islam, O. K., Al-Emran, H. M., Hasan, M. S., Anwar, A., Jahid, M. I. K.,
& Hossain, M. A. (2020). Emergence of European and North American
mutant variants of SARS-CoV-2 in South-East Asia. Transboundary
and Emerging Diseases , Epub ahead of print.
https://doi.org/10.1111/tbed.13748
Kamitani, W. (2020). Nonstructural proteins of Novel Coronavirus
(SARS-CoV-2)新型コロナウイルス等のウイルス複製に必要な蛋白質.Proceedings for Annual Meeting of The Japanese Pharmacological
Society , 93 (0), 2-ES-2.
https://doi.org/10.1254/jpssuppl.93.0_2-es-2
Korber, B., Fischer, W. M., Gnanakaran, S., Yoon, H., Theiler, J.,
Abfalterer, W., … Montefiori, D. C. (2020). Tracking Changes in
SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the
COVID-19 Virus. Cell , 182 (4), 812-827.e19.
https://doi.org/10.1016/j.cell.2020.06.043
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X:
Molecular evolutionary genetics analysis across computing platforms.Molecular Biology and Evolution , 35 (6), 1547–1549.
https://doi.org/10.1093/molbev/msy096
Lai, C. H., Welter, M. W., & Welter, L. M. (1995). The use of ARMS PCR
and RFLP analysis in identifying genetic profiles of virulent,
attenuated or vaccine strains of TGEV and PRCV. Advances in
Experimental Medicine and Biology , 380 , 243–250.
https://doi.org/10.1007/978-1-4615-1899-0_39
Lee, E. J., Kim, E. J., Shin, Y. K., & Song, J. Y. (2016). Design and
testing of multiplex RT-PCR primers for the rapid detection of influenza
A virus genomic segments: Application to equine influenza virus.Journal of Virological Methods , 228 , 114–122.
https://doi.org/10.1016/j.jviromet.2015.11.012
Li, Y., Ji, D., Cai, W., Hu, Y., Bai, Y., Wu, J., & Xu, J. (2020).
Clinical characteristics, cause analysis and infectivity of COVID‐19
nucleic acid re‐positive patients: A literature review. Journal of
Medical Virology , n/a (n/a). https://doi.org/10.1002/jmv.26491
Liu, D. X., Fung, T. S., Chong, K. K. L., Shukla, A., & Hilgenfeld, R.
(2014). Accessory proteins of SARS-CoV and other coronaviruses.Antiviral Research , Vol. 109, pp. 97–109.
https://doi.org/10.1016/j.antiviral.2014.06.013
Mercatelli, D., & Giorgi, F. M. (2020). Geographic and Genomic
Distribution of SARS-CoV-2 Mutations. Frontiers in Microbiology ,11 . https://doi.org/10.3389/fmicb.2020.01800
Mousavizadeh, L., & Ghasemi, S. (2020). Genotype and phenotype of
COVID-19: Their roles in pathogenesis. Journal of Microbiology,
Immunology and Infection , Epub ahead of print.
https://doi.org/10.1016/j.jmii.2020.03.022
Ou, X., Liu, Y., Lei, X., Li, P., Mi, D., Ren, L., … Qian, Z.
(2020). Characterization of spike glycoprotein of SARS-CoV-2 on virus
entry and its immune cross-reactivity with SARS-CoV. Nature
Communications , 11 (1).
https://doi.org/10.1038/s41467-020-15562-9
Platt, A. R., Woodhall, R. W., & George, A. L. (2007). Improved DNA
sequencing quality and efficiency using an optimized fast cycle
sequencing protocol. BioTechniques , 43 (1), 58–62.
https://doi.org/10.2144/000112499
Rahman, M. S., Islam, M. R., Hoque, M. N., Alam, A. S. M. R. U., Akther,
M., Puspo, J. A., … Hossain, M. A. (2020). Comprehensive
annotations of the mutational spectra of SARS-CoV-2 spike protein: a
fast and accurate pipeline. Transboundary and Emerging Diseases ,
Epub ahead of print. https://doi.org/10.1111/tbed.13834
Shi, X., Zhang, C., Shi, M., Yang, M., Zhang, Y., Wang, J., … Ma,
X. (2013). Development of a single multiplex amplification refractory
mutation system PCR for the detection of rifampin-resistant
Mycobacterium tuberculosis. Gene , 530 (1), 95–99.
https://doi.org/10.1016/j.gene.2013.07.060
Shu, Y., & McCauley, J. (2017). GISAID: Global initiative on sharing
all influenza data – from vision to reality. Eurosurveillance ,
Vol. 22. https://doi.org/10.2807/1560-7917.ES.2017.22.13.30494
Syrmis, M. W., Whiley, D. M., Thomas, M., Mackay, I. M., Williamson, J.,
Siebert, D. J., … Sloots, T. P. (2004). A sensitive, specific,
and cost-effective multiplex reverse transcriptase-PCR assay for the
detection of seven common respiratory viruses in respiratory samples.Journal of Molecular Diagnostics , 6 (2), 125–131.
https://doi.org/10.1016/S1525-1578(10)60500-4
To, K. K.-W., Hung, I. F.-N., Ip, J. D., Chu, A. W.-H., Chan, W.-M.,
Tam, A. R., … Yuen, K.-Y. (2020). COVID-19 re-infection by a
phylogenetically distinct SARS-coronavirus-2 strain confirmed by whole
genome sequencing. Clinical Infectious Diseases, Epub ahead of
print. https://doi.org/10.1093/cid/ciaa1275
Tsuchihashi, Z., & Dracopoli, N. C. (2002). Progress in high throughput
SNP genotyping methods. Pharmacogenomics Journal , Vol. 2, pp.
103–110. https://doi.org/10.1038/sj.tpj.6500094
Untergasser, A., Cutcutache, I., Koressaar, T., Ye, J., Faircloth, B.
C., Remm, M., & Rozen, S. G. (2012). Primer3-new capabilities and
interfaces. Nucleic Acids Research , 40 (15).
https://doi.org/10.1093/nar/gks596
Wang, L., Si, Y., Dedow, L. K., Shao, Y., Liu, P., & Brutnell, T. P.
(2011). A low-cost library construction protocol and data analysis
pipeline for illumina-based strand-specific multiplex RNA-seq.PLoS ONE , 6 (10).
https://doi.org/10.1371/journal.pone.0026426
Wang, Q., Zhang, Y., Wu, L., Niu, S., Song, C., Zhang, Z., … Qi,
J. (2020). Structural and Functional Basis of SARS-CoV-2 Entry by Using
Human ACE2. Cell , 181 (4), 894-904.e9.
https://doi.org/10.1016/j.cell.2020.03.045
Wang, W., Ren, P., Mardi, S., Hou, L., Tsai, C., Chan, K. H., …
Deubel, V. (2009). Design of multiplexed detection assays for
identification of avian influenza a virus subtypes pathogenic to humans
by SmartCycler real-time reverse transcription-PCR. Journal of
Clinical Microbiology , 47 (1), 86–92.
https://doi.org/10.1128/JCM.01090-08
Ye, J., Coulouris, G., Zaretskaya, I., Cutcutache, I., Rozen, S., &
Madden, T. L. (2012). Primer-BLAST: a tool to design target-specific
primers for polymerase chain reaction. BMC Bioinformatics ,13 , 134. https://doi.org/10.1186/1471-2105-13-134
Zhang, C., Liu, Y., Ring, B. Z., Nie, K., Yang, M., Wang, M., …
Ma, X. (2013). A Novel Multiplex Tetra-Primer ARMS-PCR for the
Simultaneous Genotyping of Six Single Nucleotide Polymorphisms
Associated with Female Cancers. PLoS ONE , 8 (4).
https://doi.org/10.1371/journal.pone.0062126
Zhang, J., Yang, J., Zhang, L., Luo, J., Zhao, H., Zhang, J., & Wen, C.
(2020). A new SNP genotyping technology Target SNP-seq and its
application in genetic analysis of cucumber varieties. Scientific
Reports , 10 (1). https://doi.org/10.1038/s41598-020-62518-6
Zuker, M. (2003). Mfold web server for nucleic acid folding and
hybridization prediction. Nucleic Acids Research , 31 (13),
3406–3415. https://doi.org/10.1093/nar/gkg595