Table 1.
Summary of transmission lineages identified in Ecuador.
| Transmission lineage | Number of sequences (% of total sequences) | Earliest sample collection date | Latest sample collection date | Median TMRCA (95% HPD) | Detection lag (days)c | Provinces where it has been sampled |
|---|---|---|---|---|---|---|
| A | 3 (1.875) | 16/3/2020 | 23/3/2020 | 3/3/2020 (25/2/2020–9/3/2020) | 13 | Guayas |
| B | 5 (3.125) | 30/3/2020 | 30/6/2020 | 16/3/2020 (2/3/2020–30/3/2020) | 14 | Imbabura, Los Rios, Pichincha |
| C | 2 (1.25) | 30/3/2020 | 30/3/20 | 29/3/2020 (26/3/2020–30/3/2020) | 1 | Pichincha |
| Da | 21 (13.125) | 7/4/2020 | 1/10/2020 | 2/3/2020b (19/2/2020–14/3/2020) | 36b | Bolivar, Cañar, Carchi, Esmeraldas, Guayas, Imbabura, Loja, Los Rios, Morona Santiago, Pichincha, Tungurahua |
| E | 3 (1.875) | 7/4/2020 | 30/6/2020 | 2/4/2020 (10/3/2020–7/4/2020) | 5 | Guayas, Manabi |
| F | 6 (3.75) | 13/4/2020 | 10/10/2020 | 12/7/2020 (2/6/2020–28/7/2020) | 23 | Azuay, Bolivar, El Oro, Guayas, Loja |
| G | 8 (5) | 17/4/2020 | 7/1/2020 | 1/4/2020 (25/2/2020–9/4/2020) | 16 | Chimborazo, Imbabura, Los Rios |
| Ha | 18 (11.25) | 17/4/2020 | 30/11/2020 | 21/2/2020b (11/2/2020–28/2/2020) | 56b | Azuay, Cotopaxi, El Oro, Esmeraldas, Imbabura, Loja, Orellana, Pastaza, Santa Elena, Sucumbios, Zamora Chinchipe |
| I | 3 (1.875) | 29/4/2020 | 7/8/2020 | 22/3/2020 (24/2/2020–8/4/2020) | 38 | Guayas |
| J | 2 (1.25) | 26/5/2020 | 15/6/2020 | 22/5/2020 (3/5/2020–26/5/2020) | 4 | Napo |
| K | 2 (1.25) | 29/5/2020 | 20/7/2020 | 25/5/2020 (13/5/2020–29/5/2020) | 4 | Guayas |
| L | 5 (3.125) | 3/7/2020 | 19/8/2020 | 16/6/2020 (8/6/2020–2/7/2020) | 17 | Azuay, Loja, Napo, Orellana |
| M | 3 (1.875) | 14/7/2020 | 13/8/2020 | 30/4/2020 (26/3/2020–18/6/2020) | 75 | Los Rios, Zamora Chinchipe |
| N | 7 (4.375) | 14/7/2020 | 20/8/2020 | 20/6/2020 (19/5/2020–12/7/2020) | 24 | Azuay, Esmeraldas, Imbabura, Los Rios, Orellana, Pichincha, Zamora Chinchipe |
| O | 3 (1.875) | 22/7/2020 | 7/9/2020 | 15/7/2020 (2/7/2020–22/7/2020) | 7 | Imbabura |
| P | 3 (1.875) | 27/7/2020 | 11/4/2020 | 9/3/2020 (24/2/2020–8/4/2020) | 140 | Guayas |
| Q | 2 (1.25) | 11/8/2020 | 26/11/2020 | 6/7/2020 (22/5/2020–24/7/2020) | 36 | Guayas, Pichincha |
| R | 2 (1.25) | 12/8/2020 | 12/8/2020 | 9/8/2020 (20/7/2020–12/8/2020) | 3 | Imbabura |
| S | 2 (1.25) | 1/10/2020 | 5/10/2020 | 13/9/2020 (16/8/2020–1/10/2020) | 18 | Cotopaxi, Tungurahua |
| T | 2 (1.25) | 5/11/2020 | 9/11/2020 | 27/10/2020 (5/10/2020–4/11/2020) | 9 | Guayas |
| U | 2 (1.25) | 9/11/2020 | 9/11/2020 | 13/9/2020 (16/8/2020–1/10/2020) | 57 | Guayas |
| V | 3 (1.875) | 28/11/2020 | 9/12/2020 | 21/11/2020 (1/11/2020−27/11/2020) | 7 | Santo Domingo de los Tsachilas, Sucumbios |
a
Transmission complex, composed of two or more potential introductions of very genetically similar viruses.
b
TMRCA of various transmission lineages and sequences outside of Ecuador; node not inferred in Ecuador.
c
Number of days between the inferred TMRCA and the earliest collection date in the transmission lineage.