1) Coronaviridae Study Group of the International Committee on Taxonomy of Viruses. The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2. Nat Microbiol. 2020; 5(4): 536–544.
2) Zhou P, Yang XL, Wang XG, Hu B, Zhang L, Zhang W et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020; 579(7798): 270-273.
3) Ji W, Wang W, Zhao X, Zai J, Li X. Cross‐species transmission of the newly identified coronavirus 2019‐nCoV. J Med Virol. 2020; 92(4): 433-440.
4) Wang LF, Eaton BT. Bats, civets and the emergence of SARS. In: Childs JE, Mackenzie JS, Richt JA (Eds.) Wildlife and emerging zoonotic diseases: the biology, circumstances and consequences of cross-species transmission. 1st edn. (Springer, Berlin, Heidelberg, 2007) pp 325-344
5) Azhar EI, El-Kafrawy SA, Farraj SA, Hassan AM, Al-Saeed MS, Hashem AM et al. Evidence for camel-to-human transmission of MERS coronavirus. N Engl J Med. 2014; 370(26): 2499-2505.
6) Zhang T, Wu Q, Zhang Z. Probable pangolin origin of SARS-CoV-2 associated with the COVID-19 outbreak. Curr Biol. 2020; 30(8): 1346-1351
7) Andersen KG, Rambaut A, Lipkin WI, Holmes EC, Garry RF. The proximal origin of SARS-CoV-2. Nat Med. 2020; 26(4): 450-452.
8) Handley SA, Virgin HW. Drowning in Viruses. Cell. 2019; 177(5):1084-1085.
9) Sutton TD, Clooney AG, Ryan FJ, Ross RP, Hill C.; Choice of assembly software has a critical impact on virome characterisation. Microbiome. 2019; 7(1):12.
10) Köberl M, Müller H, Ramadan EM, Berg G. Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health. PLoS One. 2011; 6(9): e24452.
11) Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014; 30(15): 2114-2120.
12) Menzel P, Ng KL, Krogh A. Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat Commun. 2016; 7: 11257.
13) Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4): 357-359.
14) World Health Organization. Molecular assays to diagnose COVID-19: Summary table of available protocols [Internet]. Available from: https://www.who.int/who-documents-detail/molecular-assays-to-diagnose-covid-19-summary-table-of-available-protocols [accessed 2020 May 11]
15) Zhang Z, Schwartz S, Wagner L, Miller W. A greedy algorithm for aligning DNA sequences. J Comput Biol. 2000; 7:203-214.
16)Sayers EW, Beck J, Brister JR, Bolton EE, Canese K, Comeau DC et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 2020; 48(D1): D9–D16
17) Shu Y, McCauley J. GISAID: Global initiative on sharing all influenza data–from vision to reality. Eurosurveillance. 2017; 22(13): 30494
18) Elliott JK. Global News. Tanzanian president blames lab after goat, papaya ‘test positive’ for coronavirus [Internet]. Available from: https://globalnews.ca/news/6910821/coronavirus-papaya-goat-tanzania/ [accessed 2020 May 12]
19) Ng K. Independent. Tanzania coronavirus kits raise suspicion after goat and pawpaw test positive [Internet]. Available from: https://www.independent.co.uk/news/world/africa/coronavirus-tanzania-test-kits-suspicion-goat-pawpaw-positive-a9501291.html [accessed 2020 May 12]
20) Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DKW et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. Eurosurveillance 2020. 25(3): 2000045.
21) Vogels CB, Brito AF, Wyllie AL, Fauver JR, Ott IM, Kalinich CC et al. Analytical sensitivity and efficiency comparisons of SARS-COV-2 qRT-PCR assays. medRxiv preprint. doi: https://doi.org/10.1101/2020.03.30.20048108
22) Venugopal A, Ganesan H, Raja SS, Govindasamy V, Arunachalam M, Narayanasamy A, et al. Novel Wastewater Surveillance Strategy for Early Detection of COVID–19 Hotspots. Curr Opin Environ Sci Health. 2020; 17:8-13
23) Ondov BD, Bergman NH, Phillippy AM. Interactive metagenomic visualization in a Web browser. BMC bioinformatics. 2011; 12: 385.