Households as hotspots of Lassa fever? Assessing the spatial distribution of Lassa virus-infected rodents in rural villages of Guinea

Figures & data

Figure 1. Map of Guinea showing the location of Faranah district and the six villages included for the cluster analyses [Brissa (10°13.010′ N; 10°41.326′ W), Dalafilani (10°08.590′ N; 10°36.303′ W), Damania (09°48.410′ N; 10°51.796′ W), Sokourala (10°03.407′ N; 10°39.950′ W) and Sonkonia (09°54.763′ N; 10°47.888′ W)], and Bantou from which the LASV strain was used as reference for the IFA slides and the phylogenetic analysis.

Table 1. Monte Carlo p-values (based on 1000 simulations) to infer if LASV infected M. natalensis (antibody and PCR positive) are significantly clustered in the rodent populations of the villages based on the Cuzick-Edwards test.

Village	Date	Positives^a	Total^b	N^c = 2	N = 4	N = 6	N = 8	N = 10
Brissa	14/12/2013	18	51	<0.01	<0.01	<0.01	<0.01	<0.01
Brissa	26/03/2015	9	25	0.03	0.20	0.07	0.19	NA^d
Brissa	9/11/2015	22	56	0.10	0.35	0.46	0.31	0.10
Brissa	12/11/2016	13	35	0.44	0.07	0.11	0.07	0.27
Dalafilani	28/11/2013	10	39	0.25	0.02	0.25	0.15	0.13
Dalafilani	17/04/2014	5	11	0.88	0.55	NA	NA	NA
Dalafilani	15/01/2016	13	30	<0.01	<0.01	0.02	<0.01	<0.01
Dalafilani	16/01/2017	11	23	0.02	0.01	0.01	0.16	0.17
Damania	15/11/2013	30	50	0.64	0.63	0.53	0.36	0.15
Damania	25/03/2014	25	59	0.13	0.77	0.60	0.62	0.37
Damania	13/11/2015	17	28	0.12	<0.01	<0.01	<0.01	<0.01
Damania	16/11/2016	14	45	<0.01	<0.01	<0.01	0.02	0.03
Sokourala	3/04/2013	25	46	0.15	<0.01	<0.01	<0.01	<0.01
Sokourala	31/01/2017	24	46	0.02	0.02	0.03	0.09	0.29
Sonkonia	12/11/2013	13	46	0.10	0.04	0.09	0.26	0.52
Sonkonia	7/04/2014	11	58	0.52	0.35	0.68	0.62	0.42
Sonkonia	19/11/2015	12	53	0.41	0.33	0.76	0.64	0.62
Sonkonia	24/11/2016	18	41	0.85	0.55	0.67	0.65	0.65
Yarawalia	20/11/2013	16	44	<0.01	0.06	0.07	0.02	0.27
Yarawalia	13/04/2014	7	17	0.15	0.05	<0.01	NA	NA
Yarawalia	21/03/2015	8	36	0.23	0.21	0.27	0.38	NA
Yarawalia	20/11/2016	14	25	0.05	<0.01	<0.01	<0.01	<0.01
All		335	864

^aTotal number of LASV antibody or PCR positive M. natalensis.

^bTotal number of M. natalensis captured per trapping session in the villages.

^cNumber of nearest neighbours (q).

^dNot applicable; bold numbers were considered to be significant.

Figure 2. Position of houses (rooms) in the village of Damania where traps were placed. Empty circles represent houses (rooms) where no M. natalensis were captured and circles with dots represent houses where M. natalensis were captured. Red dots represent LASV-infected individuals (antibody or PCR-positive) and black dots uninfected ones. Red circles represent significant clusters of cases based on the spatial statistic scan. Coordinates of houses without rodents were only taken in 2016.

Table 2. List with significant local clusters based on the Kulldorff’s spatial scan statistic for M. natalensis that were infected (antibody or PCR-positive) with LASV.

Village	Date	P-values	Pos/neg^a
Brissa^b	14/12/2013	.05	5/0
Brissa^c	14/12/2013	.05	7/2
Dalafilani	15/01/2016	.03	5/0
Damania	13/11/2015	.04	7/0
Damania^b	16/11/2016	.03	5/0
Damania^c	16/11/2016	.03	5/0
Sokourala	3/04/2013	.01	10/0
Sokourala	31/01/2017	.03	6/1
Yarawalia	13/04/2014	.02	5/1
Yarawalia	20/11/2016	<.01	10/0

^aNumber of positive versus negative animals that are located within the cluster (e.g. the first cluster in Brissa contained 5 positive and zero negative animals).

^b,cIndicates that two clusters were found during the same trapping session.

Figure 3. Probability that 0–6 M. natalensis were captured in a house (room) based on field observations (red) and random permutations (black) in rural villages in Guinea. Black bars represent 95% confidence intervals of probability density estimations.

Figure 4. Principal component analysis on the genetic distance matrix of LASV sequences derived from captured M. natalensis in Guinea. X-axis represents principal component 1 and Y-axis represents principal component 2. Different symbols represent different years and colours different villages.

Figure 5. Boxplots representing the difference in mean genetic distance of LASV-sequences (100% = completely similar) obtained from M. natalensis captured in the same house or in different houses from the same village and year.