Table 1.

Application of metagenomics in different experimental studies on SARS-CoV-2.

Author and publication year	Objectives of the study	Sequencing platform	Findings
Peddu et al., 2020	Studied on SARS-CoV-2 epidemic, laboratory-confirmed positive and negative samples from Seattle, Washington	Illumina MiSeq	•Betacoronavirus of Bats are the closely related species of SARS-CoV-2 •Colonization with human parainfluenza virus 3 with SARS-CoV-2
Chen et al., 2020	Investigated two pneumonia patients who developed acute respiratory syndromes after independent contact history with Wuhan sea food market	Illumina Miseq	•2019-nCoV was closely related to strains bat-SL-CoVZXC21 and bat-SL-CoVZC45 at ORF1a, S, and N genes •Identified presence of SARS-CoV-2 from pneumonia patients •No other pathogens were identified from the infected sample
Manning et al., 2020	Quick characterization of Cambodia's first case of COVID-2019	iSeq100 Illumina	•All human SARS-CoV-2 genomes are very similar, including the SARS-CoV-2 genome from the Cambodian case •SNP was noted at position 25,654 in ORF3a resulting in a valine-to-leucine substitution
Van Tan et al., 2020	Isolation of other pathogen co-infections in people with COVID-19	Illumina MiSeq	•Several nonsynonymous substitutions in the obtained genomes •SARS-CoV-2 SARS-CoV-2 co-infection with rhinovirus
Tsan-Yuk-Lam et al., 2020	Identification of any intermediate host for SARS-CoV-2 infection transmission to human	Illumina HiSeq	•Malayan pangolin associated coronaviruses belong to sub lineages of SARS-CoV-2 with strong similarity in the receptor binding domain to SARS-CoV-2 •Pangolins should be considered as possible hosts in the emergence of new coronaviruses
Wahba et al., 2020	Examined close matches to the severe acute respiratory syndrome coronavirus 2	NA	•Similar viral sequence found in pangolin lung which hypothesized pangolin as the intermediate host for infection
Zuo et al., 2020	Investigated temporal transcriptional activity of SARS-CoV-2 and its association with longitudinal faecal microbiome alterations in patients with COVID-19	Illumina NextSeq 550	•Faecal samples with signature of high SARS-CoV-2 infectivity had higher abundances of bacterial species Collinsella aerofaciens, Collinsella tanakaei, Streptococcus infantis, Morganella morganii