Dataset accompanying the article: West Nile virus surveillance using sentinel birds: results of eleven years of West Nile virus testing in corvids in a region of Northern Italy

In this dataset are resumed the results of West Nile virus surveillance in sentinel corvids in the Emilia-Romagna region, Northern Italy. Overall, 15,632 European magpies (Pica pica), 4670 Hooded crows (Corvus cornix), and 2012 Eurasian jays (Garrulus glandarius) were collected between May and October 2013-2023. In the nine provinces of the region, birds were shot or captured using Larsen traps and killed by trained hunters by cervical dislocation in accordance with the provisions of the national legislation on animal welfare (Council Regulation (EC) 1099/2009). Sampling was carried out on a voluntary basis under the supervision of the official veterinary services, which ensured rapid delivery of the birds to the laboratory in charge of testing.

From each sampled bird, heart, brain, kidney, and spleen were pooled, mechanically homogenized and tested by real-time PCRs to detect WNV RNA (Del Amo et al., 2013; Eiden et al., 2010; Tang et al., 2006). All tests were performed in the same laboratory (Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna; IZSLER, Reggio Emilia site).

The following data are available for statistical analysis: bird species, sampling date, sampling province, date of delivery to the laboratory, testing start date, test result, date of notification of positive result.

In the same dataset are reported some data about incidence of human cases of disease due to West Nile virus infection (neurological disease or fever), per year, week, and province.

The record trace is described in Table 1.

References

1.      Del Amo, J., Sotelo, E., Fernández-Pinero, J., Gallardo, C., Llorente, F., Agüero, M., Jiménez-Clavero, M.A., 2013. A novel quantitative multiplex real-time RT-PCR for the simultaneous detection and differentiation of West Nile virus lineages 1 and 2, and of Usutu virus. J Virol Methods 189, 321–327. https://doi.org/10.1016/j.jviromet.2013.02.019

2.      Eiden, M., Vina-Rodriguez, A., Hoffmann, B., Ziegler, U., Groschup, M.H., 2010. Two new real-time quantitative reverse transcription polymerase chain reaction assays with unique target sites for the specific and sensitive detection of lineages 1 and 2 West Nile virus strains. J Vet Diagn Invest 22, 748–753. https://doi.org/10.1177/104063871002200515 

3.      Tang, Y., Anne Hapip, C., Liu, B., Fang, C.T., 2006. Highly sensitive TaqMan RT-PCR assay for detection and quantification of both lineages of West Nile virus RNA. J Clin Virol 36, 177–182. https://doi.org/10.1016/j.jcv.2006.02.008

Table 1. Dataset record trace

Field_name

Description

Year

Year of sampling

province_CODE

Italian code of the province of sampling

BIRD_species

Bird species collected: magpie (Pica pica), hooded crow (Corvus cornix);    jay (Garrulus glandarius)

N_birds_collected

Number of birds collected

Sampling_ID

Sampling code

dt_sampling

Sampling date of birds

dt_delivery

Date of delivery to the lab (birds)

dt_registration

Date of registration of the lab (birds)

dt_analysis

Date of analysis (birds)

dt_notification

Date of result notification (birds)

WNV_PCR_Positive

Number of birds with WNV Positive result (PCR)

WNV_PCR_tested

Number of birds tested (PCR)

WNV_PCR_not_tested

Number of birds not tested

WNV_PCR_Negative

Number of birds with WNV Negative result (PCR)

sampling_week_corvids

Number of week of sampling (birds)

notification_week_corvids

Number of week of result notification (birds)

num_WNhuman_cases

Number of WN disease human cases

first_human_notification_dt

Date of notification of the first human disease case

province_pop

Province population

human_inc

Incidence of human cases (x100,000)

flag_season_human_cases

Occurrence of WN human cases (1=Yes; 0=No)

week_first human_case

Number of week of notification of the first human disease case

early_detection_code

Early detection code (1=first detection in birds; 0=first detection in human beings; 9=No case detection in human beings)

province_sup_km2

Province surface (km2)

delta_sampling_lab

Days from sampling to delivery to the lab (birds)

delta_lab_testing

Days from lab registration to test (birds)

delta_testing_notification

Days from testing to result notification (birds)

delta_sampling_notification

Days from sampling to result notification (birds)