doi:10.1007/s12250-016-3774-9

Figure 4个 Table 3个

Country	Abbreviation	Year	References
Africa
Burkina Faso^*	BF	1981	Faye et al., 2014
Cape Verde	CV	2015	Kindhauser et al., 2016 http://www.cdc.gov/zika/geo/active-countries.html
Central African Republic^*	CF	1968, 1976, 1979, 1980	Saluzzo et al., 1981; Berthet et al., 2014
Cote d'Ivoire^*	CI	1980–1996, 1999	Faye et al., 2014
Egypt	EG	1954	Smithburn et al., 1954
Gabon^*	GA	1975, 2007	Jan et al., 1978; Grard et al., 2014
Nigeria^*	NG	1953, 1964–1970	Macnamara, 1954; Moore et al., 1975; Kindhauser et al., 2016
Senegal^*	SN	1960s–1970s, 1990s–2000s	Faye et al., 2014; Kindhauser et al., 2016
Tanzania	TZ	1952	Smithburn, 1952
Uganda ^*	UG	1947, 1952, 1963	Dick et al., 1952; Smithburn, 1952; Faye et al., 2014
Americas
Barbados	BB	2016	http://www.who.int/csr/don/20-january-2016-zika-guyanabarbados-ecuador/en/
Bolivia	BO	2016	http://www.who.int/csr/don/20-january-2016-zika-bolivia/en/
Brazil^*	BR	2015	Waggoner and Pinsky, 2016 http://www.who.int/csr/don/21-october-2015-zika/en/
Canada^§^*	CA	2014, 2016	Fonseca et al., 2014 http://www.phac-aspc.gc.ca/phn-asp/2016/zika-eng.php
Chile mainland ^§	CL	2016	Kindhauser et al., 2016
Colombia	CO	2015	Enserink, 2015; Kindhauser et al., 2016 http://www.who.int/csr/don/21-october-2015-zika/en/
Commonwealth of Puerto Rico	PR	2015	http://www.who.int/csr/don/8-january-2016-zika-usa/en/
Costa Rica	CR	2016	http://www.who.int/csr/don/8-february-2016-zika-americas-region/en/
Curacao (Netherlands Antilles)^§	Curacao(AN)	2016	http://www.who.int/csr/don/8-february-2016-zika-americas-region/en/
Dominican Republic^§	DO	2016	http://www.who.int/csr/don/27-january-2016-zika-dominican-republic/en/
Easter Island (Chile)^*	Easter Island (CL)	2014	Tognarelli et al., 2015
Ecuador^§	EC	2016	http://www.who.int/csr/don/20-january-2016-zika-guyana-barbados-ecuador/en/
El Salvador	SV	2015	http://www.who.int/csr/don/27-november-2015-zika-el-salvador/en/
French Guiana and Martinique(France)	GF and MQ	2015	http://www.who.int/csr/don/8-january-2016-zika-france/en/
Guatemala	GT	2015	http://www.who.int/csr/don/27-november-2015-zika-guatemala/en/
Guyana	GY	2016	http://www.who.int/csr/don/20-january-2016-zika-guyana-barbados-ecuador/en/
Haiti	HT	2016	http://www.who.int/csr/don/21-january-2016-zika-haiti/en/
Honduras	HN	2015	http://www.who.int/csr/don/21-december-2015-zika-honduras/en/
Jamaica^§	JM	2016	http://www.who.int/csr/don/8-february-2016-zika-americas-region/en/
Mexico^*	MX	2015-2016	http://www.who.int/csr/don/03-december-2015-zika-mexico/en/
Nicaragua	NI	2016	http://www.who.int/csr/don/8-february-2016-zika-americas-region/en/
Panama	PA	2015	http://www.who.int/csr/don/22-december-2015-zika-panama/en/
Paraguay	PY	2015	http://www.who.int/csr/don/03-december-2015-zika-paraguay/en/
Saint Martin and Guadeloupe(France)	Saint Martin and GP	2016	http://www.who.int/csr/don/21-january-2016-zika-france/en/
Suriname^*	SR	2015	Enfissi et al., 2016a http://www.who.int/csr/don/13-november-2015-zika/en/
United States of America^§	US	2007–2016	Duffy et al., 2009; Foy et al., 2011 http://www.who.int/csr/don/12-february-2016-zika-usa/en/; http://www.who.int/csr/don/12-february-2016-microcephaly-usa/en/
United States Virgin Islands	VI(US)	2016	http://www.who.int/csr/don/29-january-2016-zika-usa/en/
Venezuela	VE	2015	http://www.who.int/csr/don/03-december-2015-zika-venezuela/en/
Asia
Cambodia^*	KH	2010	Heang et al., 2012
Guangdong(China)^§	Guangdong(CN)	2016	http://www.nhfpc.gov.cn
India	IN	N/A^†	Kindhauser et al., 2016
Indonesia	ID	1977, 1981, 2012	Olson et al., 1981; Olson et al., 1983; Kindhauser et al., 2016
Israel^§	IL	2016	http://www.haaretz.com/israel-news/.premium-1.698798
Malaysia^*	MY	1966	Pond, 1963; Marchette et al., 1969; Kindhauser et al., 2016
Pakistan	PK	1983	Darwish et al., 1983
Philippines^*	PH	2012	Alera et al., 2015
Taiwan(China)^§	Taiwan(CN)	2016	www.cdc.gov.tw
Thail and ^*	TH	2012-2014	Pond, 1963; Buathong et al., 2015; Kindhauser et al., 2016
Vietnam	VN	N/A^‡	Pond, 1963
Europe
Austria^§	AT	2016	http://www.thelocal.at/20160128/first-confirmed-case-of-zika-virus-in-austria
Denmark^§	DK	2016	http://time.com/4195372/zika-denmark-south-america-europe/
Finl and ^§	FI	2015	http://www.who.int/csr/don/8-february-2016-zika-maldives/en/
Germany^§	DE	2014, 2016	Tappe et al., 2015 http://www.who.int/csr/don/21-january-2016-zika-haiti/en/
Italy^§	IT	2015	Zammarchi et al., 2015
Netherl and s^§	NL	2016	http://www.who.int/csr/don/22-february-2016-zika-netherlands/en/
Norway^{§^*}	NO	2013	Waehre et al., 2014
Portugal^§	PT	1972	Filipe et al., 1973
Spain^§	ES	2016	http://elpais.com/elpais/2016/02/02/inenglish/1454423888_908441.html
Sweden^§	SE	2016	http://sputniknews.com/europe/20160127/1033787120/zika-virus-sweden-case.html
Switzerl and ^§	CH	2016	http://www.thelocal.ch/20160126/two-zika-virus-cases-reported-in-switzerland
United Kingdom^§	UK	2016	http://www.techtimes.com/articles/127390/20160125/uk-confirms-three-new-cases-of-mosquito-borne-zika-virus.htm
Oceania
American Samoa	AS	2015	http://www.nc.cdc.gov/travel/notices/alert/zika-virus-pacific-islands
Australia^§	AU	2015	Leung et al., 2015
Cook Islands^*	CK	2014	Roth et al., 2014
Fiji	FJ	2015	Kindhauser et al., 2016
French Polynesia^*	PF	2013	Baronti et al., 2014; Cao-Lormeau et al., 2014; Hancock et al., 2014
Marshall Islands	MH	2015	http://www.nc.cdc.gov/travel/notices/alert/zika-virus-pacific-islands
New Caledonia^*^§	NC	2013, 2014	Roth et al., 2014; Dupont-Rouzeyrol et al., 2015
Samoa	WS	2015, 2016	Kindhauser et al., 2016 http://www.nc.cdc.gov/travel/notices/alert/zika-virus-pacific-islands
Solomon Islands	SB	2015	Kindhauser et al., 2016
Tonga	TO	2015	http://www.nc.cdc.gov/travel/notices/alert/zika-virus-pacific-islands
Vanuatu	VU	2015	Kindhauser et al., 2016
Yap Island (Micronesia)	Yap Island (FM)	2007	Lanciotti et al., 2008; Duffy et al., 2009
^§Countries and territories where the imported cases were reported. ^*Countries and territories where the complete or partial ZIKV sequences were identified and deposited in GenBank. ^†The year that ZIKV was detected in India is uncertain. It was only mentioned by a WHO research article found online(Kindhauser et al., 2016)that during 1969–1983 the geographic distribution of ZIKV expanded to equatorial Asian countries, including India, Indonesia, Malaysia, and Pakistan. ^‡The year that ZIKV was detected in Vietnam is uncertain. The previous study(Pond, 1963)investigated the serological prevalence of antibodies against ZIKV among the population in Vietnam before 1963.

Table 1. Summary of the countries and territories with a history of ZIKV disease and reported cases

Event No.	Recombinants (location/time/lineage)	Major parents (location/time/lineage)	Minor parents (location/time/lineage)	Methods	RDPRCS	Begin	End
1	ArD157995 Senegal/2001/A1	ArA975 Cote d'Ivoire/1999/A1	ArD132915 Senegal/1998/A2	GENECONV, MaxChi, RDP, SiScan, 3Seq, Chimaera	0.682	9754	10314
2	ArA1456 Cote d'Ivoire/1980/A1	ArD30101 Senegal/1979/A1	ArD132915 Senegal/1998/A2	SiScan, 3Seq, Chimaera	0.594	9672	10315
3	ArD158084 Senegal/2001/A1	ArB15076 Central African Republic/1980/A1	ArD157995 Senegal/2001/A1	3Seq, MaxChi	0.685	9672	10315
Note: A1, African lineage 1; A2, African lineage 2.

Table 2. The recombination events of ZIKV detected by the RDP software package

Strains	Locations	Time	Lineages
Strains	Locations	Time	Full-length	E gene	NS5 gene
ArD157995	Senegal	2001	A1	A1	A1
ArA1465	Cote d'Ivoire	1980	N/A	A2	A1
Notes: A1, African lineage 1; A2, African lineage 2; N/A, not applicable.

Table Table S1. Strains of discrepancies among tree topology by visual comparison