Evolutionary and spatiotemporal analyses reveal multiple introductions and cryptic transmission of SARS-CoV-2 VOC/VOI in Malta

Abstract

Our study provides insights into the evolution of the coronavirus disease 2019 (COVID-19) pandemic in Malta, a highly connected and understudied country. We combined epidemiological and phylodynamic analyses to analyze trends in the number of new cases, deaths, tests, positivity rates, and evolutionary and dispersal patterns from August 2020 to January 2022. Our reconstructions inferred 173 independent severe acute respiratory syndrome coronavirus 2 introductions into Malta from various global regions. Our study demonstrates that characterizing epidemiological trends coupled with phylodynamic modeling can inform the implementation of public health interventions to help control COVID-19 transmission in the community.

Keywords: SARS-CoV-2; epidemiology; next-generation sequencing; phylodynamics.

FIG 1

Maltese government response to the ongoing pandemic in 2020 and 2021. Line plots for four different indices observed over the period between 2020 and 2021 in Malta are drawn above a timeline of important policy changes enacted by the Maltese government. Adapted from a Policy Note by Kurt Sant (21).

FIG 2

SARS-CoV-2 new cases and deaths in Malta. Frequency of new positive samples (black) and newly recorded deaths (red). Counts were aggregated by collection week for better visualization. Shaded rectangles represent the periods of the universal travel ban (March 2020-July 2020) and non-essential workplace closures (March 2021-May 2021). Green dashed line indicates the date of the most recent sequence in the genomic data set.

FIG 3

SARS-CoV-2 new tests in Malta. Counts of newly collected samples (black) and the positivity rate for these new samples (blue). Sample counts were aggregated by collection week for better visualization. Shaded rectangles represent the periods of the universal travel ban (March 2020-July 2020) and non-essential workplace closures (March 2021-May 2021). The green dashed line indicates the date of the most recent sequence in the genomic data set. The number of new tests collected and the positivity rate are not available after June 2022. Total counts of newly collected samples and positivity rates are not available after 22 June 2022.

FIG 4

Frequency of PANGO lineages circulating in Malta between August 2020 and January 2022. The stacked area chart reflects the proportion of collected sequences and their respective PANGO lineages, clustered by week. VOI/VOC lineages are identified, and all other lineages are grouped. No sequences were collected during the months of October 2020 to February 2021 and August to September 2021. Fig. S1 depicts the counts of lineages circulating in Malta over time.

FIG 5

The flow of SARS-CoV-2 lineages into Malta. Left: time-resolved maximum-likelihood tree containing high-quality near-complete genome sequences from Malta obtained in this study (n = 659; red dots) analyzed against a background of global sequences. Right: Sankey plot depicts the reconstructed origin location and PANGO lineage of the Maltese sequences. The number between square brackets depicts the number of sequences attributed to the specific reconstructed origin location (left side) or PANGO lineage (right side).

FIG 6

Timeline of introductions of VOC/VOI and other lineages into Malta. Bubbles represent the lineage-specific viral introductions over time of the most recent common ancestor inferred from Malta-specific clades in the phylogenetic tree (Fig. 5, left). The circle size depicts the number of Maltese sequences in each clade.

FIG 7

Cryptic transmission of SARS-CoV-2 in Malta revealed by genomic epidemiology. Top: violin plots represent the date of sample collection of the earliest genome in a Maltese clade (blue) and the TMRCA (green) of an introduction. Middle: violin and box plots depict the time lag between the introduction and the first surveilled genome. Bottom: box plots depict the time lag between introduction and the first surveilled genome for each PANGO lineage.