Phylogenetic landscape of Monkeypox Virus (MPV) during the early outbreak in New York City, 2022

Figures & data

Figure 1. Number of cases MPV reported through time in U.S. The graphic refers 27,632 cases reported of MPV by May to October, 2022 in U.S. The green colour represents the sampling period.

Table 1. Data of the samples subjected to sequencing analysis.

Sample ID	Transport medium	Sample origin	RT-PCR Ct Value	Total # of generated Monkeypox reads	Read length (bp)	Mean depth of coverage	Completeness (%)	Clade	Lineage
PV67599	DRY	CS	15.71	38,542	150	22.5	92.8	IIb	B.1
PV67601	DRY / VTM	CS	16.43 / 18.68	286,104	150	168.9	100.0	IIb	B.1.2
PV67603	DRY / VTM	CS	24.54 / 19.02	262,248	150	157.1	100.0	IIb	B.1
PV67604	DRY / VTM	CS	19.68 / 21.57	736,352	150	438.9	100.0	IIb	B.1.7
PV67606	DRY	CPS	NA	217,164	150	135.8	100.0	IIb	B.1
PV67610	DRY	CPS	NA	50,396	150	30.0	99.3	IIb	B.1.3
PV67611	VTM	CPS	NA	81,522	150	50.4	99.9	IIb	B.1.2
PV67614	DRY	CPS	NA	100,516	150	61.8	100.0	IIb	B.1.2
PV67617-CS	DRY / VTM	CS	16.38 / 18.84	310,120	150	184.0	100.0	IIb	B.1
PV67617-CPS	NA	CPS	NA	138,740	150	86.0	99.9	IIb	B.1
PV67619-CS	DRY / VTM	CS	11.34 / 14.13	102,698	150	59.9	100.0	IIb	B.1.8
PV67619-CPS	NA	CPS	NA	79,212	150	48.7	99.9	IIb	B.1.8
PV67620-CS	VTM	CS	17.38	86,092	150	51.6	99.6	IIb	B.1.1
PV67620-CPS	NA	CPS	NA	193,332	150	121.0	100.0	IIb	B.1.1
PV67621-CS	DRY / VTM	CS	18.59 / 17.89	166,784	150	98.8	100.0	IIb	B.1.3
PV67621-CPS	NA	CPS	NA	190,652	150	118.7	100.0	IIb	B.1.3
PV67622-CS	VTM	CS	20.26	56,304	150	32.9	93.2	IIb	B.1.2
PV67622-CPS	NA	CPS	NA	111,266	150	69.7	99.9	IIb	B.1.2
PV67624	VTM	CS	15.79	101,034	150	60.2	99.9	IIb	B.1.7
PV67625	VTM	CPS	NA	318,518	150	198.5	100.0	IIb	B.1.7
PV67626-CS	DRY	CS	18.87	39,318	150	22.9	97.4	IIb	B.1
PV67626-CPS	NA	CPS	NA	1,283,846	150	813.3	100.0	IIb	B.1
PV67629	DRY	CPS	NA	45,342	150	27.5	97.5	IIb	B.1.7

CS: Clinical sample. CPS: Culture passaged samples.

Figure 2. Phylogenetic relationship of MPV genomes in the global context. (A) Maximum likelihood tree from whole genome SNPs for the 674 genomes sequences analyzed. Each colour represent the three different clusters of MPV described so far (I, IIa and IIb). A magnification of the cluster IIb (to visualize the 23 genomes included in this study) was included. The green dots represent the samples from patients and the red dots the samples from cell culture. The figure shows the identification of each paired sample with their respective connection between direct sample and culture (lines) and highlight in red whose paired sample with differences between them. (B) Maximum likelihood tree highlighting the sub-lineages B.1 identified in this study. Each colour into the tree represents a different sub-lineage; the red lines show the position of the 16 genomes mapped into five different sub-lineages B.1.

Figure 3. SNP characterization between 23 genomes analyzed. Single nucleotide polymorphisms (SNP) found in the 23 MPV isolates (Genome ID) compared with the reference sequence (NC_063383.1). The purple colour represents the non-synonymous substitution (NSS) shared in more than 90% of genomes analyzed, and the grey colour the NSS shared between CS-CPS samples or found in just some genomes.* represents the identification of a N in that position. The colours located in the bottom of the figure represent the function in which have been associated the ORF.

Figure 4. Nucleotide diversity between 23 genomes analyzed. The colours represent the SNPs found throughout MPV genome, to compare the 23 samples included in the study with the reference sequence (NC_063383.1). We observed a major representation in the GA > AA and TC > TT substitutions.

Table 2. SNPs identified with GA > AA and TC > TT nucleotide replacements shared between the different lineages.

Lineage	OPG	Position	Ref	Alt	AA Change ALT	Function
B.1.1	OPG038	22739	C	T	E141K	NFKB Inhibitor
	OPG094	74360	G	A	R194H	Myristylated protein
B.1.2	OPG210	186165	G	A	D1604N	Surface glycoprotein
B.1.3	OPG074	55133	G	A	R665C	Activates of ERK1/2 signaling pathway
	OPG083	64426	C	T	Synonymous variant	Serine protease
	OPG107	85581	G	A	V24I	Entry-fusion complex
	NBT03_gp174	190660	G	A	R84K	Brix domain protein
B.1.7	C3L-like	25644	C	T	R4K	Prevents complement activation