This morning, I read
that paper more carefully. If you open that link, click on the PDF icon and you'll open the full text of this paper. It's too large to attach here. Here are the take home messages:
- The paper refers to the SARS-Cov-2 virus. It's the same as what the World Health Organization now calls COVID-19. Don't be confused by the different names.
- The authors' major point is that SARS-Cov-2 is really two different strains of related viruses. They named them L and S. As a result, all prior analyses of this epidemic must be re-evaluated because of the differences between L and S types. This could explain some of the confused reports about virulence and mortality during January and February.
- The S type has been around longer and is less aggressive. It's less contagious, or replicates slower, than the L type. However, the L type has not been the predominant virus strain since January 2020. To answer why, the authors suggest this possible explanation:
"… since January 2020, the Chinese central and local governments have taken rapid and comprehensive prevention and control measures. These human intervention efforts might have caused severe selective pressure against the L type, which might be more aggressive and spread more quickly. The S type, on the other hand, might have experienced weaker selective pressure by human intervention, leading to an increase in its relative abundance among the SARS-CoV-2 viruses."
- As a result, we now face the less aggressive S type Covid-19 virus. That's a good thing, not a reason for panic.
To support my bullet points, I've directly quoted these passages from the paper:
"Population genetic analyses of 103 SARS-CoV-2 genomes indicated that these viruses evolved into two major types (designated L and S), that are well defined by two different SNPs that show nearly complete linkage across the viral strains sequenced to date. Although the L type (~70%) is more prevalent than the S type (~30%), the S type was found to be the ancestral version. Whereas the L type was more prevalent in the early stages of the outbreak in Wuhan, the frequency of the L type decreased after early January 2020. Human intervention may have placed more severe selective pressure on the L type, which might be more aggressive and spread more quickly. On the other hand, the S type, which is evolutionarily older and less aggressive, might have increased in relative frequency due to relatively weaker selective pressure."
"Thus far, we found that, although the L type is derived from the S type, L (~70%) is more prevalent than S (~30%) among the sequenced SARS-CoV-2 genomes we examined. This pattern suggests that L has a higher transmission rate than the S type. Furthermore, our mutational load analysis indicated that the L type had accumulated a significantly higher number of derived mutations than S type (P < 0.0001, Wilcoxon rank-sum test; Fig. S5). We propose that, although the L type newly evolved from the ancient S type, it transmits faster or replicates faster in human populations, causing it to accumulate more mutations than the S type. Thus, our results suggest the L might be more aggressive than the S type due to the potentially higher transmission and/or replication rates."
"To test whether the two types of SARS-CoV-2 had differences in temporal and spatial distributions, we stratified the viruses based on the locations and dates they were isolated (Table S1). Among the 27 viruses isolated from Wuhan, 26 (96.3%) were L type, and only 1 (3.7%) was S type. However, among the other 73 viruses isolated outside Wuhan, 45 (61.6%) were L type, and 28 (38.4%) were S type. This comparison suggests that the L type is significantly more prevalent in Wuhan than in other places (P = 0.0004, Fisher’s exact test, Fig. 6 and Table S3). All of the 26 samples isolated before January 7, 2020, were from Wuhan, and among the 74 samples collected from January 7, 2020, only one was from Wuhan, 33 were from other places in China, and 40 were from patients outside China. Thus, it is not surprising that the L type was significantly more prevalent before January 7, 2020 (96.2%, 25 L and 1 S) than after January 7, 2020 (62.2%, 46 L and 28 S) (P = 0.0008, Fisher’s exact test, Fig. 6 and Table S3)."
"If the L type is more aggressive than the S type, why did the relative frequency of the L type decrease compared to the S type in other places after the initial breakout in Wuhan? One possible explanation is that, since January 2020, the Chinese central and local governments have taken rapid and comprehensive prevention and control measures. These human intervention efforts might have caused severe selective pressure against the L type, which might be more aggressive and spread more quickly. The S type, on the other hand, might have experienced weaker selective pressure by human intervention, leading to an increase in its relative abundance among the SARS-CoV-2 viruses. Thus, we hypothesized that the two types of SARS-CoV-2 viruses might have experienced different selective pressures due to different epidemiological features. Of note, the above analyses were based on very patchy SARS-CoV-2 genomes that were collected from different locations and time points. More comprehensive genomic data is required for further testing of our hypothesis."
