If you need more [counter]evidence, there's a newer paper "The proximal origin of SARS-CoV-2" by Andersen et al. (March, 17) that touches on the same topic.
The paper brings up two reasons why SARS-CoV-2 is not "made in a lab". The first is the (relative) [in]efficiency of its spike protein; the second is somewhat more complex to explain and is related to cleavage site in said protein that is usually an indicator of rapid (but natural) evolution; this cleavage site is actually not found in the most related relatives of SARS-CoV-2 (the B-lineage of the betacoronaviruses), but only in the more distant A-lineage. Features related to this cleavage site also suggest that it was probably shaped by an immune system, something unlikely to happen in mere cell cultures.
Our comparison of alpha- and betacoronaviruses identifies two notable genomic features of SARS-CoV-2: (i) on the basis of structural studies and biochemical experiments, SARS-CoV-2 appears to be optimized for binding to the human receptor ACE2; and (ii) the spike protein of SARS-CoV-2 has a functional polybasic (furin) cleavage site at the S1–S2 boundary through the insertion of 12 nucleotides, which additionally led to the predicted acquisition of three O-linked glycans around the site.
The receptor-binding domain (RBD) in the spike protein is the most variable part of the coronavirus genome. Six RBD amino acids have been shown to be critical for binding to ACE2 receptors and for determining the host range of SARS-CoV-like viruses. [...] Five of these six residues differ between SARS-CoV-2 and SARS-CoV. On the basis of structural studies and biochemical experiments, SARS-CoV-2 seems to have an RBD that binds with high affinity to ACE2 from humans, ferrets, cats and other species with high receptor homology. [cites 6 references in support]
While the analyses above suggest that SARS-CoV-2 may bind human ACE2 with high affinity, computational analyses predict that the interaction is not ideal [citing: Wan et al.] and that the RBD sequence is different from those shown in SARS-CoV to be optimal for receptor binding. Thus, the high-affinity binding of the SARS-CoV-2 spike protein to human ACE2 is most likely the result of natural selection on a human or human-like ACE2 that permits another optimal binding solution to arise. This is strong evidence that SARS-CoV-2 is not the product of purposeful manipulation.
Wan et al. indeed mention that
several other critical residues in 2019-nCoV RBM (particularly Asn501) are compatible with, but not ideal for, binding human ACE2, suggesting that 2019-nCoV has acquired some capacity for human-to-human transmission.
Basically what Andersen et al. say is that if someone made SARS-CoV-2 in the lab, they could have made it better in terms of human transmission by using what we knew from previously studied SARS-like viruses, instead of coming up with a completely new and somewhat inefficient solution.
Another argument of Andersen et al. (somewhat similar to Chris' #4), which they only mention briefly is that
if genetic manipulation had been performed, one of the several reverse-genetic systems available for betacoronaviruses would probably have been used. However, the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone.
As I mentioned in my first paragraph, Andersen also discuss that SARS-CoV-2 "borrows" a fairly distant feature, namely a polybasic cleavage site, which is only found in more remote "cousins" of the A-lineage of betacoronavirues:
The second notable feature of SARS-CoV-2 is a polybasic cleavage site (RRAR) at the junction of S1 and S2, the two subunits of the spike [...]. This allows effective cleavage by furin and other proteases and has a role in determining viral infectivity and host range. [...] Polybasic cleavage sites have not been observed in related ‘lineage B’ betacoronaviruses, although other human betacoronaviruses, including HKU1 (lineage A), have those sites.
And if you think this was an international manipulation, the trouble is that we still have no precise idea what that cleavage site does in SARS-CoV-2, although cleavage sites observed in other coronaviruses are thought responsible for cross-species infectivity and also are thought to be related to rapid evolution in highly dense populations.
Neither the bat betacoronaviruses nor the pangolin betacoronaviruses sampled thus far have polybasic cleavage sites. Although no animal coronavirus has been identified that is sufficiently similar to have served as the direct progenitor of SARS-CoV-2, the diversity of coronaviruses in bats and other species is massively undersampled. Mutations, insertions and deletions can occur near the S1–S2 junction of coronaviruses, which shows that the polybasic cleavage site can arise by a natural evolutionary process. For a precursor virus to acquire both the polybasic cleavage site and mutations in the spike protein suitable for binding to human ACE2, an animal host would probably have to have a high population density (to allow natural selection to proceed efficiently) and an ACE2-encoding gene that is similar to the human ortholog.
The acquisition of both the polybasic cleavage site and predicted O-linked glycans also argues against culture-based scenarios. New polybasic cleavage sites have been observed only after prolonged passage of low-pathogenicity avian influenza virus in vitro or in vivo. Furthermore, a hypothetical generation of SARS-CoV-2 by cell culture or animal passage would have required prior isolation of a progenitor virus with very high genetic similarity, which has not been described. Subsequent generation of a polybasic cleavage site would have then required repeated passage in cell culture or animals with ACE2 receptors similar to those of humans, but such work has also not previously been described. Finally, the generation of the predicted O-linked glycans is also unlikely to have occurred due to cell-culture passage, as such features suggest the involvement of an immune system.