New Zealand, an island country in the southwestern Pacific Ocean, is marked by its early and fierce resolve to entirely arrest the spread of critical acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the viral disease that is triggering the recent COVID-19 pandemic.
The SARS-CoV-2 virus aroused great panic the earth more than simply because of its significant case fatality price in contrast to other viruses, as very well as its speedy amount of unfold and the higher proportion of asymptomatic infections.
Genomics has played a critical job in tracing the distribute and prevalence clusters of the ailment, as very well as the numerous mutations it has undergone.
Now a new examine revealed on the preprint server medRxiv* in August 2020 stories the utility of genomics in finding out the epidemiology of the virus, from analysis in New Zealand.
The New Zealand Outbreak – Genomic Detectives
The initially SARS-CoV-2 scenario was noted at the close of February 2020, and New Zealand responded with a countrywide lockdown of all products and services deemed non-critical. The existing analysis focuses on 56 complete-genome sequences retrieved from as a lot of situations in this region, combining them with epidemiologic data to get there at an comprehension of in which the virus arrived from, about what time scale, and how it entered the place.
In between the 1st situation and July 1, 2020, abround 1,200 instances were being verified, 55% feminine, 45% male. Most instances ended up aged 20-29 many years, and about 37% experienced a history of overseas vacation.
The most major number of new conditions was in the Southern District Overall health Board, which much less densely populated than several NZ metropolitan areas. The highest level of lockdown was declared on March 25, just right before the working day on which the greatest variety of confirmed instances was described. The claimed incidence attained zero on Might 23 and remained at that stage until finally June 16.
On this day, new circumstances were being uncovered, associated to overseas vacation, yet again. Having said that, each and every circumstance from then on has been identified in quarantine centers. All scenarios in the existing review ended up taken from the period of time amongst the first scenario and the very last situation outside these amenities, from about 650 genomes. This represents ~56% of all confirmed circumstances in this period.
(a) Frequency of transmission lineage dimensions. (b) The selection of samples in each individual transmission lineage as a perform of the day at which the transmission lineage was sampled, colored by the probable origin of each individual lineage (inferred from epidemiological info). Importation occasions that led to only a single additional circumstance (singletons) are shown in gray above time. (c) Frequency of TMRCA (the time of the most recent widespread ancestor) of importation situations in excess of time. (d) The difference among the TMRCA and the date as which a transmission lineage was detected (i.e. detection lag) as a operate of TMRCA. Spearman’s ρ signifies a significant unfavorable marriage (p<0.01).
Viruses in NZ Represent Globally Present Strains
The viral genomes from NZ were found to represent almost every strain sequenced so far globally. The genomes had 24% aspartic acid, SD614, and 73% glycine SG614 at the 614 positions of the spike protein. This mutation has been linked to higher infectivity in cell cultures.
This increase in the frequency of glycine indicates that this variant was imported several times into NZ, and not that this strain was selected for. Moreover, the temporal signal shows that the virus mutation rate is low, as expected.
Among the 649 cases, the researchers found that the virus was introduced 277 times, and in a quarter of these, only one more case was secondarily infected before the chain was broken. A fifth of introduced cases caused an ongoing chain of spread called a transmission lineage. However, 57% of the cases did not cause even one more case.
The study also shows that most of the transmission lineages in NZ were from viral strains brought in from North America, which is probably a reflection of the high prevalence of the virus in that continent during the period when these cases occurred. However, the researchers did not find any sign of the virus in NZ before February 26.
The study also shows that case detection is most efficient in the second half of the epidemic than in the earlier part, because the detection lag dipped as the age of transmission lineages went down. In other words, fewer cases went undetected as the time from the first inferred transmission event in each cluster to the first detected case dropped.
Drivers of Transmission
The most significant clusters of transmission occurred after social gatherings. The biggest one is thought to have come from the US, and spread via a superspreading event (a wedding) in NZ before the lockdown, in the jurisdiction of the Southern District Health Board.
The subsequent lockdown-related change in transmission of this cluster shows how effective the intervention is. The researchers saw that the effective reproduction number Re went down from 7 at the outset to 0.2 by the end of March. Most of the cases in this cluster were sequenced in the current study, and genomic analysis threw up five hitherto unrelated cases that had escaped the first epidemiological tracing study.
The findings from this study show how important this tool can be in tracing case transmission. For one, it can help to trace unknown cases using genomic similarity. Secondly, as the researchers comment, “This cluster, seeded by a single-superspreading event that resulted in New Zealand’s largest chain of transmission, illustrates the link between micro-scale transmission to nation-wide spread.”
And thirdly, the effectiveness of the lockdown is reflected in the dramatic drop in Re in this cluster as well as the very low number of continuing infections resulting from virus importations into NZ.
At present, community transmission is absent in NZ, but border quarantine facilities continue to throw up confirmed cases because of the high case number in other places. The lesson? “Ongoing genomic surveillance is an integral part of the national response to monitor any re-emergence of the virus, particularly when border restrictions might eventually be eased.”
medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.