Table 6.

Results from sequencing of samples from RT-qPCR-positive individuals: variant and pangolin lineage analyses.

Household ID	Sample from	Date of Sampling for Sequencing	Material of Sequenced Sample	Breadth of Sequencing Coverage	Depth of Sequencing Coverage	SARS-CoV-2 Variant	Pangolin Lineage
USZ22	Owner 1 Owner 2 Owner 3 Owner 4 Dog 22.1 Cat 22.2	16 November 2021 16 November 2021 16 November 2021 16 November 2021 18 November 2021 16 November 2021	Nasal swab Oral swab Nasal swab Nasal swab Oral swab Oral swab	99.8% 99.8% 99.8% 99.8% 99.8% 99.0%	10,078.325 7357.6606 5991.9077 8399.461 7603.86 8748.53	Delta Delta Delta Delta Delta Delta	AY.129 AY.129 AY.129 AY.129 AY.129 AY.129
USZ29	Owner 1 Dog 29.1 Cat 29.3	24 November 2021 24 November 2021 24 November 2021	Nasal swab Nasal swab Oral swab	99.8% 99.4% 71.3%	7085.115 8431.732 16,659.176	Delta Delta -	AY.4 AY.4 -
USZ39	Owner 1 Owner 2 Owner 3 Owner 4 Cat 39.1 Cat 39.2	9 December 2021 9 December 2021 9 December 2021 9 December 2021 9 December 2021 9 December 2021	Nasal swab Nasal swab Oral swab Oral swab Oral swab Oral swab	99.7% 99.8% 99.7% 99.9% 99.7% 98.8%	21,950.77 20,430.922 303.0392 14,888.675 19,432.705 22,502.582	Delta Delta Delta Delta Delta Delta	B.1.617.2 B.1.617.2 B.1.617.2 B.1.617.2 B.1.617.2 B.1.617.2
USZ38	Owner 1 Owner 2 Cat 38.2	14 December 2021 14 December 2021 14 December 2021	Nasal swab Nasal swab Nasal swab	98.8% 90.3% 98.7%	15,422.453 13,471.375 16,428.799	Delta - Delta	AY.4 - AY.4
USZ36	Owner 1 Owner 2 Cat 36.1	8 December 2021 8 December 2021 8 December 2021	Nasal swab Nasal swab Oral swab	99.8% 99.8% 99.1%	18,054.1 17,920.172 18,757.414	Delta Delta Delta	AY.43 AY.43 AY.43