Yellow fever - Angola 14 June 2016 - WHO

[niman]

Yellow fever – Angola

Disease Outbreak News 
14 June 2016

http://www.who.int/csr/don/14-june-2016-yellow-fever-angola/en/

 

Edited June 18, 2016 by niman

[niman]

On 21 January 2016, the Ministry of Health of Angola notified WHO of an outbreak of yellow fever (YF). The first case (with onset date of 5 December 2015) was identified in Viana municipality, Luanda province.

As of 10 June, 3,137 suspected cases, including 345 deaths, had been reported from all the 18 provinces of Angola. A total of 847 cases had been laboratory-confirmed. The confirmed cases are from 78 districts of 16 provinces. Local transmission has been documented in 31 districts of 12 provinces (Benguela, Cuango Cubango, Cuanza Norte, Cuanza Sul, Cunene, Huambo, Huila, Luanda, Lunda Norte, Malanje, Uige, and Zaire).

Luanda and Huambo remain the most affected provinces with 1,778 cases (489 confirmed) and 508 cases (126 confirmed), respectively. The other most affected provinces are Benguela (291 suspected cases), Huila (135 suspected cases), Cuanza Sul (99 suspected cases) and Uige (54 suspected cases). The majority of the cases are aged 15 to 24 years.

Efforts to strengthen surveillance are ongoing, and the number of cases in the country is slowly decreasing, though new clusters of cases are being reported in new districts. The epidemiological trend and pattern show that YF virus circulation continues to extend to other provinces and the risk for exportation to other countries with close linkages to Angola still exists.

The epidemiological situation in Lunda Norte is of particular concern. This province shares borders with the Democratic Republic of the Congo (DRC) and regularly experiences a high flow of people and goods in and out of DRC. To date, three laboratory confirmed cases, imported from Lunda Norte, have been reported by DRC.

[niman]

Public health response

The national task force is leading the response to the outbreak, under the National Director of Public Health (NDPH). WHO set up an Incident Management System (IMS) to coordinate international partners’ support to the NDPH. The IMS integrates and coordinates the work of several organizations, including the Institut Pasteur of Dakar, UNICEF, Centers for Disease Control and Prevention, Medicos del Mundo and Médecins Sans Frontières.

The IMS partner response to the outbreak is articulated around five pillars:

• strengthening surveillance, with a focus on case investigations and laboratory confirmation
• vaccination,
• vector control,
• case management, and
• social mobilization.

As of June 10, almost half of the country had been vaccinated (10,641,209 people) and the country had received 11,635,800 vaccines. Mass vaccination campaigns have taken place in all the districts of Luanda, seven districts of Benguela, five districts of Cuanza Sul, five districts of Huambo, three districts of Huila, and two of Uige. Vaccination is ongoing in two districts of Lunda Norte and one in Zaire, all of which border DRC. Additional mass vaccination campaigns are being planned in these and other provinces, including Cuando Cubango, Cunene and Namibe. Reactive vaccination has taken place in Cafunfu town (Lunda Norte) and the city of Lubango (Huila), among others. Plans are under way to complete vaccination in areas with low vaccination coverage (so called ‘mop up’ campaigns) in Luanda and Benguela.

WHO and partners are providing technical and financial support to the response. The current challenges include the need to strengthen the response to the outbreak at the provincial level and address border health issues.

[niman]

WHO risk assessment

The evolution of the epidemiological situation in Angola is concerning and needs to be closely monitored. Based on experiences from previous similar events, it is expected that additional cases will be reported. The reports of YF imported cases in China, DRC, and Kenya demonstrate the threat that this outbreak constitutes to the entire world. Viraemic patients travelling to areas where competent vectors and susceptible human populations are present pose a risk for the establishment of local cycles of transmission. There is an urgent need to continue strengthening the quality of the response in Angola and to enhance preparedness in neighbouring countries and in countries that have diaspora communities in Angola. WHO continues to monitor the epidemiological situation and conduct risk assessments based on the latest available information.

[niman]

WHO advice

Yellow fever can easily be prevented through immunization provided that vaccination is administered at least 10 days before travel. WHO, therefore, urges Members States especially those where the establishment of a local cycle of transmission is possible (i.e. where the competent vector is present) to strengthen the control of immunisation status of travellers to all potentially endemic areas.

In the context of an ongoing YF outbreak in Angola, special attention should also be placed on travellers returning from Angola and other potentially endemic areas. If there are medical grounds for not getting vaccinated, this must be certified by the appropriate authorities.

WHO does not recommend any restriction of travel and trade to Angola based on the current information available.

[niman]

LOCUS       KX010994               10823 bp    RNA     linear   VRL 08-MAY-2016
DEFINITION  Yellow fever virus isolate CIC1, complete genome.
ACCESSION   KX010994
VERSION     KX010994.1  GI:1024994369
KEYWORDS    .
SOURCE      Yellow fever virus (YFV)
  ORGANISM  Yellow fever virus
            Viruses; ssRNA viruses; ssRNA positive-strand viruses, no DNA
            stage; Flaviviridae; Flavivirus; Yellow fever virus group.
REFERENCE   1  (bases 1 to 10823)
  AUTHORS   Pan,Y., Cui,S., Huo,D., Lyu,Y., Li,J., Chen,L., Wang,Q., Tian,L.,
            Dou,X., Li,X., Sun,Y., Lu,G., Du,Y., Li,S. and Li,X.
  TITLE     Direct Submission
  JOURNAL   Submitted (25-MAR-2016) Department of Infectious Disease and
            Endemic Disease Control, Beijing Center for Disease Prevetion and
            Control, 16 Hepingli Middle Street, Dongcheng District, Beijing
            100013, China
COMMENT     ##Assembly-Data-START##
            Assembly Method       :: samtools v. v1.2
            Sequencing Technology :: IonTorrent
            ##Assembly-Data-END##
FEATURES             Location/Qualifiers
     source          1..10823
                     /organism="Yellow fever virus"
                     /mol_type="genomic RNA"
                     /isolate="CIC1"
                     /isolation_source="blood"
                     /host="Homo sapiens"
                     /db_xref="taxon:11089"
                     /country="China"
                     /collection_date="11-Mar-2016"
                     /note="clinical-imported case 1"

[niman]

Sequences producing significant alignments:

Select:AllNone Selected:0

AlignmentsDownloadGenBankGraphicsDistance tree of resultsShow/hide columns of the table presenting sequences producing significant alignments

Sequences producing significant alignments:

Select for downloading or viewing reports	Description	Max score	Total score	Query cover	E value	Ident	Accession
Select seq gb|KX010994.1|	Yellow fever virus isolate CIC1, complete genome	18465	18465	100%	0.0	100%	KX010994.1
Select seq gb|AY968064.1|	Yellow fever virus strain Angola71, complete genome	18090	18090	100%	0.0	99%	AY968064.1
Select seq gb|KX027336.1|	Yellow fever virus isolate CIC4, complete genome	18006	18006	100%	0.0	99%	KX027336.1
Select seq gb|KX010995.1|	Yellow fever virus isolate CIC2, complete genome	18006	18006	100%	0.0	99%	KX010995.1
Select seq gb|KX010996.1|	Yellow fever virus isolate CIC3, complete genome	17962	17962	100%	0.0	99%	KX010996.1
Select seq gb|DQ235229.1|	Yellow fever virus strain Couma, complete genome	11400	11400	100%	0.0	85%	DQ235229.1
Select seq gb|AY968065.1|	Yellow fever virus strain Uganda48a, complete genome	11376	11376	100%	0.0	85%	AY968065.1
Select seq gb|JN620362.1|	Yellow fever virus strain Uganda 2010, complete genome	11353	11353	100%	0.0	85%	JN620362.1
Select seq gb|JF912179.1|	Yellow fever virus strain BeAR378600, complete genome	8790	8790	100%	0.0	79%	JF912179.1
Select seq gb|AY603338.1|	Yellow fever virus strain Ivory Coast 1999, complete genome	8787	8787	100%	0.0	79%	AY603338.1
Select seq gb|JF912186.1|	Yellow fever virus strain BeH526722, complete genome	8763	8763	100%	0.0	79%	JF912186.1
Select seq gb|JX898868.1|	Yellow fever virus isolate HD117294 from Senegal, complete genome	8758	8758	100%	0.0	79%	JX898868.1
Select seq gb|JF912184.1|	Yellow fever virus strain BeH463676, complete genome	8751	8751	100%	0.0	79%	JF912184.1
Select seq gb|JF912185.1|	Yellow fever virus strain BeAR513008, complete genome	8744	8744	100%	0.0	79%	JF912185.1
Select seq gb|AY572535.1|	Yellow fever virus strain Gambia 2001, complete genome	8742	8742	100%	0.0	79%	AY572535.1
Select seq gb|JF912183.1|	Yellow fever virus strain BeH423602, complete genome	8740	8740	100%	0.0	79%	JF912183.1
Select seq gb|JX898873.1|	Yellow fever virus isolate ArD149214 from Senegal, complete genome	8725	8725	100%	0.0	79%	JX898873.1
Select seq gb|JX898874.1|	Yellow fever virus isolate ArD149194 from Senegal, complete genome	8722	8722	100%	0.0	79%	JX898874.1
Select seq gb|KM388817.1|	Yellow fever virus strain 2A polyprotein gene, complete cds	8720	8720	100%	0.0	79%	KM388817.1
Select seq gb|JX898870.1|	Yellow fever virus isolate ArD121040 from Senegal, complete genome	8720	8720	100%	0.0	79%	JX898870.1
Select seq gb|JX898875.1|	Yellow fever virus isolate ArD149815 from Senegal, complete genome	8716	8716	100%	0.0	79%	JX898875.1
Select seq gb|KM388816.1|	Yellow fever virus strain 10A polyprotein gene, complete cds	8702	8702	100%	0.0	79%	KM388816.1
Select seq gb|JF912187.1|	Yellow fever virus strain BeH622205, complete genome	8702	8702	100%	0.0	79%	JF912187.1
Select seq gb|JF912188.1|	Yellow fever virus strain BeH622493, complete genome	8698	8698	100%	0.0	79%	JF912188.1
Select seq gb|JX898880.1|	Yellow fever virus isolate ArD181564 from Senegal, complete genome	8691	8691	100%	0.0	79%	JX898880.1
Select seq gb|JX898877.1|	Yellow fever virus isolate ArD181464 from Senegal, complete genome	8689	8689	100%	0.0	79%	JX898877.1
Select seq gb|JX898878.1|	Yellow fever virus isolate ArD181250 from Senegal, complete genome	8688	8688	100%	0.0	79%	JX898878.1
Select seq gb|JF912189.1|	Yellow fever virus strain BeAR646536, complete genome	8671	8671	100%	0.0	79%	JF912189.1
Select seq gb|JF912180.1|	Yellow fever virus strain BeH394880, complete genome	8668	8668	100%	0.0	79%	JF912180.1
Select seq gb|JX898876.1|	Yellow fever virus isolate ArD156468 from Senegal, complete genome	8666	8666	100%	0.0	79%	JX898876.1
Select seq gb|HM582851.1|	Yellow fever virus strain TVP11767 polyprotein gene, complete cds	8666	8666	100%	0.0	79%	HM582851.1
Select seq gb|AY640589.1|	Yellow fever virus strain ASIBI, complete genome	8664	8664	100%	0.0	79%	AY640589.1
Select seq gb|KF769016.1|	Yellow fever virus strain Asibi, complete genome	8661	8661	100%	0.0	79%	KF769016.1
Select seq gb|JF912190.1|	Yellow fever virus strain BeH655417, complete genome	8657	8657	100%	0.0	79%	JF912190.1
Select seq gb|KM388815.1|	Yellow fever virus strain 9A polyprotein gene, complete cds	8648	8648	100%	0.0	79%	KM388815.1
Select seq gb|KM388814.1|	Yellow fever virus strain 6A polyprotein gene, complete cds	8648	8648	100%	0.0	79%	KM388814.1
Select seq gb|JX898869.1|	Yellow fever virus isolate DakArAmt7 from Cote d'Ivoire, complete genome	8646	8646	100%	0.0	79%	JX898869.1
Select seq gb|JF912182.1|	Yellow fever virus strain BeH422973, complete genome	8630	8630	100%	0.0	79%	JF912182.1
Select seq gb|KF907504.1|	Yellow fever virus strain 88/1999, complete genome	8608	8608	100%	0.0	79%	KF907504.1
Select seq gb|KM388818.1|	Yellow fever virus strain 8A polyprotein gene, complete cds	8603	8603	100%	0.0	79%	KM388818.1
Select seq gb|U21056.1|YFU21056	Yellow fever virus French viscerotropic strain, complete genome	8601	8601	100%	0.0	79%	U21056.1
Select seq gb|JX898872.1|	Yellow fever virus isolate ArD114972 from Senegal, complete genome	8581	8581	100%	0.0	79%	JX898872.1
Select seq gb|JX898871.1|	Yellow fever virus isolate ArD114896 from Senegal, complete genome	8574	8574	100%	0.0	79%	JX898871.1
Select seq gb|U21055.1|YFU21055	Yellow fever virus French neurotropic strain, complete genome	8561	8561	100%	0.0	79%	U21055.1
Select seq gb|DQ100292.1|	Yellow fever virus strain 17DD-Brazil, complete genome	8552	8552	100%	0.0	79%	DQ100292.1
Select seq gb|U54798.1|YFU54798	Yellow fever virus strain 85-82H Ivory Coast, complete genome	8540	8540	100%	0.0	79%	U54798.1
Select seq gb|U17066.1|YFU17066	Yellow fever virus vaccine strain 17DD, complete genome	8534	8534	100%	0.0	79%	U17066.1
Select seq gb|GQ379162.1|	Yellow fever virus strain case #1, complete genome	8533	8533	100%	0.0	79%	GQ379162.1
Select seq emb|X03700.1|	Yellow fever virus complete genome, 17D vaccine strain	8529	8529	100%	0.0	79%	X03700.1
Select seq gb|KF769015.1|	Yellow fever virus strain 17D-204, complete genome	8525	8525	100%	0.0	78%	KF769015.1
Select seq gb|JN811143.1|	Yellow fever virus 17D YF-VAX Vero adapted Series C P11, complete genome	8525	8525	100%	0.0	78%	JN811143.1
Select seq gb|JX503529.1|	Yellow fever virus strain YF/Vaccine/USA/Sanofi-Pasteur-17D-204/UF795AA/YFVax, complete genome	8525	8525	100%	0.0	78%	JX503529.1
Select seq gb|JN628279.1|	Yellow fever virus strain 17D RKI, complete genome	8525	8525	100%	0.0	78%	JN628279.1
Select seq gb|AF052444.1|AF052444	Yellow fever virus clone HONG8 polyprotein gene, complete cds	8525	8525	100%	0.0	78%	AF052444.1
Select seq gb|JX949181.1|	Yellow fever virus strain 17D polyprotein gene, complete cds	8520	8520	100%	0.0	78%	JX949181.1
Select seq gb|GQ379163.1|	Yellow fever virus strain case #2, complete genome	8520	8520	100%	0.0	78%	GQ379163.1
Select seq gb|FJ654700.1|	Yellow fever virus 17D/Tiantan, complete genome	8520	8520	100%	0.0	78%	FJ654700.1
Select seq gb|DQ118157.1|	Yellow fever virus isolate YF-AVD2791-93F/04 from Spain, complete genome	8520	8520	100%	0.0	78%	DQ118157.1
Select seq emb|X15062.1|	Yellow fever virus genomic RNA	8520	8520	100%	0.0	78%	X15062.1
Select seq gb|AF052446.1|AF052446	Yellow fever virus clone HONG10 polyprotein gene, complete cds	8520	8520	100%	0.0	78%	AF052446.1
Select seq gb|AF052439.1|AF052439	Yellow fever virus clone HONG3 polyprotein gene, complete cds	8520	8520	100%	0.0	78%	AF052439.1
Select seq gb|AF052437.1|AF052437	Yellow fever virus clone HONG1 polyprotein gene, complete cds	8520	8520	100%	0.0	78%	AF052437.1
Select seq gb|U17067.1|YFU17067	Yellow fever virus vaccine strain 17D-213, complete genome	8520	8520	100%	0.0	78%	U17067.1
Select seq gb|JN811141.1|	Yellow fever virus 17D YF-VAX Vero adapted Series A P11, complete genome	8516	8516	100%	0.0	78%	JN811141.1
Select seq gb|AF052445.1|AF052445	Yellow fever virus clone HONG9 polyprotein gene, complete cds	8516	8516	100%	0.0	78%	AF052445.1
Select seq gb|AF052438.1|AF052438	Yellow fever virus clone HONG2 polyprotein gene, complete cds	8516	8516	100%	0.0	78%	AF052438.1
Select seq gb|JN811142.1|	Yellow fever virus 17D YF-VAX Vero adapted Series B P11, complete genome	8511	8511	100%	0.0	78%	JN811142.1
Select seq gb|AF094612.1|AF094612	Yellow fever virus strain Trinidad 79A isolate 788379, complete genome	8477	8477	100%	0.0	78%	AF094612.1
Select seq gb|JF912181.1|	Yellow fever virus strain BeH413820, complete genome	8403	8403	100%	0.0	78%	JF912181.1
Select seq gb|DQ322634.1|	YFV replicon vector FMDV-2A-def, complete sequence	8228	8343	97%	0.0	79%	DQ322634.1
Select seq gb|DQ322633.1|	YFV replicon vector capsid-def, complete sequence	8228	8343	97%	0.0	79%	DQ322633.1
Select seq gb|DQ322635.1|	YFV replicon vector prME-def, complete sequence	6551	6887	81%	0.0	78%	DQ322635.1
Select seq dbj|D14458.1|YFVCMENS	Yellow fever virus prM gene for precursor polyprotein, partial cds	3162	3162	34%	0.0	80%	D14458.1
Select seq gb|AF052443.1|AF052443	Yellow fever virus clone HONG7 polyprotein gene, partial cds	2250	2250	26%	0.0	78%	AF052443.1
Select seq gb|GU951804.1|	Yellow fever virus strain BeAn 131 polyprotein gene, partial cds	2246	2246	26%	0.0	79%	GU951804.1
Select seq gb|AF052441.1|AF052441	Yellow fever virus clone HONG5 polyprotein gene, partial cds	2246	2246	26%	0.0	78%	AF052441.1
Select seq gb|AH005112.2|	Yellow fever virus strain Y5 polyprotein and nonstructural protein NS2A mRNAs, partial cds	2138	2516	27%	0.0	80%	AH005112.2
Select seq gb|DQ322638.1|	VEEV replicon vector YFV-C2, complete sequence	2129	2129	22%	0.0	80%	DQ322638.1
Select seq gb|AF052440.1|AF052440	Yellow fever virus clone HONG4 polyprotein gene, partial cds	2125	2125	22%	0.0	80%	AF052440.1
Select seq gb|L06480.1|YFVCAPSIDM	Yellow fever virus capsid protein, M protein, and envelope protein mRNAs	2125	2125	22%	0.0	80%	L06480.1
Select seq gb|AY960140.1|	Yellow fever virus strain ArB28153 polyprotein gene, partial cds	2098	2098	17%	0.0	86%	AY960140.1
Select seq gb|DQ322642.1|	VEEV replicon vector YFV-C3opt, complete sequence	1929	1929	22%	0.0	78%	DQ322642.1
Select seq gb|DQ322640.1|	VEEV replicon vector YFV-C3opt-NS2mut, complete sequence	1929	1929	22%	0.0	78%	DQ322640.1
Select seq gb|U23578.1|YFU23578	Yellow fever virus isolate SE7445/Uganda/1964/Human envelope protein (E) mRNA, partial cds	1810	1810	14%	0.0	87%	U23578.1
Select seq gb|U23577.1|YFU23577	Yellow fever virus isolate M-112/Sudan/1940/Human envelope protein (E) mRNA, partial cds	1801	1801	14%	0.0	87%	U23577.1
Select seq gb|AY839636.1|	Yellow fever virus strain ETH2777/Ethiopia61 envelope protein gene, partial cds	1786	1786	14%	0.0	87%	AY839636.1
Select seq gb|DQ068260.1|	Yellow fever virus strain SSUD03-01 envelope protein gene, partial cds	1773	1773	14%	0.0	87%	DQ068260.1
Select seq gb|DQ068264.1|	Yellow fever virus strain SSUD03-05 envelope protein gene, partial cds	1768	1768	14%	0.0	87%	DQ068264.1
Select seq gb|DQ068263.1|	Yellow fever virus strain SSUD03-04 envelope protein gene, partial cds	1768	1768	14%	0.0	87%	DQ068263.1
Select seq gb|DQ068262.1|	Yellow fever virus strain SSUD03-03 envelope protein gene, partial cds	1768	1768	14%	0.0	87%	DQ068262.1
Select seq gb|U23569.1|YFU23569	Yellow fever virus isolate 7914/Kenya/1993/Human envelope protein (E) mRNA, partial cds	1764	1764	14%	0.0	86%	U23569.1
Select seq gb|U23575.1|YFU23575	Yellow fever virus isolate KE93-477/Kenya/1993/Mosquito envelope protein (E) mRNA, partial cds	1759	1759	14%	0.0	86%	U23575.1
Select seq gb|U23573.1|YFU23573	Yellow fever virus isolate DaHB1504/C. African Republic/1985/Human envelope protein (E) mRNA, partial cds	1755	1755	14%	0.0	86%	U23573.1
Select seq gb|AY839634.1|	Yellow fever virus strain HB1782/CAR86 envelope protein gene, partial cds	1750	1750	14%	0.0	86%	AY839634.1
Select seq gb|U23576.1|YFU23576	Yellow fever virus isolate Kouma/Ethiopia/1961/Human envelope protein (E) mRNA, partial cds	1745	1745	14%	0.0	86%	U23576.1
Select seq gb|AY960138.1|	Yellow fever virus strain ArA 20628 polyprotein gene, partial cds	1743	1743	17%	0.0	81%	AY960138.1
Select seq gb|U23571.1|YFU23571	Yellow fever virus isolate ArB8883/C. African Republic/1977/Human envelope protein (E) mRNA, partial cds	1732	1732	14%	0.0	86%	U23571.1
Select seq gb|AY960137.1|	Yellow fever virus strain Ara29436 polyprotein gene, partial cds	1710	1710	17%	0.0	81%	AY960137.1
Select seq gb|AY960139.1|	Yellow fever virus strain Ara6734 polyprotein gene, partial cds	1680	1680	17%	0.0	81%	AY960139.1