Incubation period and serial interval of Covid-19 in a chain of infections in Bahia Blanca (Argentina)

Viego, Valentina; Geri, Milva; Castiglia, Juan; Jouglard, Ezequiel

doi:10.1590/1413-81232020259.20852020

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ARTICLE • Ciênc. saúde coletiva 25 (9) • Sept 2020 • https://doi.org/10.1590/1413-81232020259.20852020 copy

Incubation period and serial interval of Covid-19 in a chain of infections in Bahia Blanca (Argentina)

Authorship SCIMAGO INSTITUTIONS RANKINGS

Abstract

The objective of this work was to estimate the incubation period and the serial interval of Covid-19 from a sample of symptomatic patients in Bahia Blanca city during the period March-May 2020. We collected dates of illness onset for primary cases and secondary cases for the first 18 secondary patients infected with SARS-Cov-2. Estimations of incubation period are based on a log-normal distribution while we assume a Gamma distribution for the serial interval. In both cases maximum likelihood estimator was applied to estimate main parameters. Of the total of 18 cases of local transmission analyzed, 17% occurred in the presymptomatic and asymptomatic phase. The mean incubation period for symptomatic patients is 7.9 days (95%CI: 4.6, 11.1) considering the full sample and 7.5 days (95%CI: 4.1, 10.9) if the sample is restricted to the most certain cases. The median is 6.1 and 5.8 days respectively. The point estimation for the mean serial interval is 6.8 days (95%CI: 4.0-9.6). or 5.5 days (95%CI: 2.8, 8.1) for most certain pairs. The estimated median serial intervals were 5.2 and 4.1 days respectively. Comparisons with foreign estimates show that incubation period and serial interval could be longer in Bahia Blanca city than in other regions. Transmission from pre-symptomatic and asymptomatic is not negligible.

Key words
Covid-19; Serial interval; Epidemiology; Bahia Blanca

Study	Region	Number of pairs	Median	Mean
(4)	Wuhan	6	not reported	7.5
(4)	Wuhan	6	not reported	[5.3-19.0]
(5)	S. Korea	12	4.0	6.6
(5)	S. Korea	12	4.0	[3.0-9.0]
(6)	China excl Hubei	468	not reported	3.96
(6)	China excl Hubei	468	not reported	[3.53-4.39]
(7)	China excl Hubei	35	not reported	5.1
(7)	China excl Hubei	35	not reported	[1.3-11.6]
(8)	China excl Hubei	71	4.0	4.27
(8)	China excl Hubei	71	4.0	(3.44)
(9) ^U U unpublished, during peer review process.	Hong Kong	21	not reported	4.4
(9) ^U U unpublished, during peer review process.	Hong Kong	21	not reported	[2.9-6.7]
(10)	Principalmente regiones	28^* * The authors also provide estimations for 18 pairs with certainty about onset dates;	4.0	4.7
(10)	Mainly Asian regions and cases reported in Germany		4.0	[3.7-6.0]
(11) ^U U unpublished, during peer review process.	Lombardy (Italy)	90	not reported	6.6
(11) ^U U unpublished, during peer review process.	Lombardy (Italy)	90	not reported	[0.7-19]

Study	Region	N	Mean -days-	SD -days-
(12)	travelers from and to Wuhan (China)	88	6.4	2.3
(12)	travelers from and to Wuhan (China)	88	[5.6-7.7]	[1.7-3.7]
(4)	China	10	5.2	no report
(4)	China	10	[4.1-7.0]	no report
(13)	China excl Hubei	181	5.1 M	no report
(13)	China excl Hubei	181	[4.5-5.8]	no report
(14)	China excl Wuhan	52	5.0	3 [2.1-4.5]
(14)	China excl Wuhan	52	[4.2-6.0]^* * The mean is around 5.6 with SD of 2.8 when the inhabitants of Wuhan were included.	3 [2.1-4.5]
(7)	China excl Hubei	49	5.2	no report
(7)	China excl Hubei	49	[1.8-12.4]	no report
(8)	China excl Hubei	65	5.33	3.3
(8)	China excl Hubei	65	5.0 M	3.3

	Incubation period param bootstrapping	Incubation period param bootstrapping reduced sample	Incubation period non param bootstrapping	Incubation period non param bootstrapping reduced sample	Serial interval param bootstrapping	Serial interval param bootstrapping reduced sample	Serial interval non param bootstrapping	Serial interval non param bootstrapping reduced sample
Distribution	Log normal	Log normal	Log normal	Log normal	Gamma	Gamma	Gamma	Gamma
Mean (1)	6.08	7.30	6.21	7.36	6.6	5.24	6.68	5.46
Standard deviation (2)	5.76	5.63	6.06	5.86	5.47	4.36	5.61	4.63
CV (2)/(1)	0.95	0.77	0.98	0.80	0.83	0.83	0.84	0.85
n	15	12	15	12	17	13	17	13

	Incubation period	Incubation period for most certain cases	Serial interval Parametric approach	Serial interval for most certain pairs Parametric approach	Serial interval full sample Bayesian approach	Serial interval for most certain pairs Bayesian approach
Assumed distribution	Log normal	Log normal	Gamma	Gamma	Gamma^ It is the prior distribution, not the posterior. 95% CI and 95% CrI in brackets, depending on parametric or Bayesian estimation.	Gamma^ It is the prior distribution, not the posterior. 95% CI and 95% CrI in brackets, depending on parametric or Bayesian estimation.
Mean (1)	7.86	7.50	6.82	5.46	6.88	6.12
Mean (1)	[4.63-11.09]	[4.11-10.89]	[4.04-9.61]	[2.84-8.08]	[2.0-32.14]	[1.31-31.73]
Standard deviation (2)	6.38	6.23	5.86	4.81	5.89	4.55
Standard deviation (2)	[3.42-15.87]	[3.21-16.99]	[1.80-3.69]	[2.48-13.12]	[2.09-17.76]	[1.47-16.77]
Median ^* * CI for the median computed based on quantile matching estimator. Parameters differ only in the standard deviation estimation;	6.1	5.76	5.24	4.13	6.4	5.15
	[4.06-9.18^* * CI for the median computed based on quantile matching estimator. Parameters differ only in the standard deviation estimation; ]	[3.56-9.33^* * CI for the median computed based on quantile matching estimator. Parameters differ only in the standard deviation estimation; ]	[2.96-8.11]^* * CI for the median computed based on quantile matching estimator. Parameters differ only in the standard deviation estimation;	[2.04-6.93^* * CI for the median computed based on quantile matching estimator. Parameters differ only in the standard deviation estimation; ]	[4.6-9.2]	[2.95-7.50]
CV (2)/(1)	0.81	0.83	0.86	0.88	0.86	0.74
n	15	12	17	13	17	13
lnL	-43.31	-34.19	-49.21	-34.83	-52.52	-37.96

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[1] Collaborations

Data collection was carried out by J Castiglia and E Jouglard. V Viego and M Geri made the estimates and the final report.