Identification of consensus hairpin loop structure among the negative sense subgenomic RNAs of SARS-CoV-2

Bulletin of the National Research Centre

Table 1 The description of analyzed negative sense subgenomic RNAs

Sr. No	Type of subgenomic RNA	Location of hairpin structure (from the downstream of initiation codon)	Length of hairpin loop structure with probability	Hairpin structure is distinct or not (merged with different loop carrying initiation codon)	Sequence alignment matches with predicted structure (probability)	Probability of formation of distinct secondary structure
1	S subgenomic	Includes ~ 28 nt of coding region	~ 55 nt	No (merged with initiation codon)	Yes	Less
2	*3a subgenomic	~ 10 nt	~ 58 nt	Yes	Yes	Moderate
3	***E subgenomic	~ 47 nt	~ 52 nt	Yes	Yes	High
4	*M subgenomic	~ 8 nt	Splits in three small hairpin loops	No (first loop merged with initiation codon)	No (three distinct hairpin structures)	Moderate
5	**Orf6 subgenomic	~ 41 nt	~ 47 nt	Yes	Yes	High
6	****Orf7a subgenomic	~ 30 nt	~ 35 nt	Yes	Yes	High
7	Orf7b subgenomic	Includes ~ 6 nt of coding sequence	Splits in two hairpin loop structure	No (first loop merged with initiation codon)	No (two distinct hairpin structures)	Moderate
8	**Orf8 subgenomic	~ 20 nt	~ 57 nt	Yes	Yes	Moderate
9	****N subgenomic	~ 1^st nucleotide of initiation codon	~ 60 nt	Yes	Yes	Moderate

The description is drawn from the combined output of sequence alignment followed by secondary structure prediction results. The number of asterisks (*) denotes to the abundance level for each subgenomic RNA detected by NGS reads mapped to the sequences, and no asterisk is given to particular subgenomic that was detected at very low or near zero level according to previous finding (Alexandersen et al. 2020). Single asterisk denotes low, two and three asterisk denotes moderate and four asterisk denotes high abundance of particular subgenomic RNA (in relative context)